BLAST nucleotide (BLASTN) searches nucleotide subjects using a nucleotide query. Registration not required.
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Tfsitescan is intended for promoter sequence analysis and works best with sequences of ~500 nt Registration not required.
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TFBIND for online searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)). This tool uses weight matrix in transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, and the cut-offs originally estimated by our research. Registration not required.
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TRAP (from Max Planck Isntitute of Molecular genetics) is a web tool to predict which transcription factors are susceptible to bind a DNA sequence (e.g. promotor of a gene of interest) Registration not required.
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PROMO (from Universitat Politècnica de Catalunya) from is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files. PROMO is using version 8.3 of TRANSFAC. Registration not required.
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analysis of transcription factor binding sites
Category: Transcription factors analysis
DiRE (Distant Regulatory Elements of co-regulated genes) uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the use... Registration not required.
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a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics
Category: Literature search
Pubmed allows: to search in the literature
PubMed is a free database accessing the MEDLINE database of citations, abstracts and some full text articles on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health (NIH) maintains PubMed as part of the Entrez information retrieval system. Listing an article or journal in PubMed is not endorsement. Registration not required.
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online PCR primer design
Category: PCR primers design
Primer Blast allows: to design PCR primers
Primer Blast is a web application that uses Primer3 to design PCR primers and then submits them to BLAST search against user-selected database. The blast results are then automatically analyzed to avoid primer pairs that can cause amplification of targets other than the input template. Registration not required.
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Category: Calculators and converters
GraphPad Molarity Calculators allows: Calculate how to dilute a stock solution, calculate molarity from mass and volume, calculate mass from volume and concentration, calculate volume from mass and concentration
Molarity Calculators (QuickCalcs) is a web application (no installation required) that helps to dilute a stock solution or to calculate molarity from mass and volume, mass from volume and concentration, volume from mass and concentration. Registration not required.
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high-throughput discovery of functional regulatory elements
Category: Transcription factors analysis
Finding potential regulatory elements in noncoding regions of the human genome is a challenging problem. Analyzing novel sequences for the presence of known transcription factor binding sites or their weight matrices produces a huge number of false positive predictions that are randomly and uniformily distributed. rVista combines database searches with comparative sequence analysis, reducing the number of false positive predictions by ~95% while maintaining a high sensitivity of the search.
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Multiple Sequence Alignment is the arrangement of several protein or nucleic acid sequences with postulated gaps so that similar residues (in one-letter code) are juxtaposed. Registration not required.
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PASTAA is a web app to evaluate if there is a regulatory association between transcription factors and groups of genes. Input: List of gene IDs. Registration not required.
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free online tool free plagiarism detection
Category: Plagiarism Detection
Dupli Checker allows: check for plagiarism
Dupli Checker is one of the most effective free plagiarism detection tools on the Internet. While it doesn’t have a fancy interface, it certainly gets the job done well. You don’t have to pay anything. Whether you are a one-time user or plan to make the most of this free plagiarism detection tool on a daily basis, you are not required to pay for subscription. You are presented with a very basic, functional layout that does not require for any previous experience with plagiarism detection too... Registration not required.
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ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. The online version is hosted by EMBL. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Registration not required.
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Primer3 Plus is the new improved web interface to the popular Primer3 primer design program. Registration not required.
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This page computes various statistics from a 2-by-2 table. It will calculate the Yates-corrected chi-square, the Mantel-Haenszel chi-square, the Fisher Exact Test, and other indices relevant to various special kinds of 2-by-2 tables. Registration not required.
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Naturejobs is in association with Nature magazine. It is a worldwide career resource for scientists, providing a wide range of career advice and information. Registration not required.
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Online conversions (e.g. metric conversions) for many measurement systems. Conversion tables are provided for both common (U.S., metric, etc.) and quite exotic units like Ancient Greek and Roman. You can also ask your questions and discuss how to convert units on our Units Conversion Forum. Registration not required.
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sTRAP (Transcription factor Affinity Prediction) is a web application to calculate how the binding of different TFs is affected by the sequence differences (e.g. by single-nucleotide polymorphism) Registration not required.
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Category: Calculators and converters
Mole/Gram Converters allows: convert between moles and grams, GraphPad
Mole/Gram Converters (QuickCalcs) converts between moles and grams Registration not required.
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Use this calculator to compute a P value from a Z, t, F, r, or chi-square value. Registration not required.
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TRAP (multiple sequences) is a web tool to evaluate which TFs are over represented in a data set (Chip-seq or Chip-chip data). Registration not required.
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It's a simple and well constructed Excel spreadsheet from Jon Wittwer of Vertex42 for graphing a Normal distribution curve by inputing either a mean & SD or single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.
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Buffer solutions for pH control Registration not required.
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PepNovo is a high throughput de novo peptide sequencing tool for tandem mass spectrometry data. PepNovo typically runs in less than 0.2 seconds per spectrum. PepNovo uses a probabilistic network to model the peptide fragmentation events in a mass spectrometer. Registration not required.
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The Gene Expression Omnibus (GEO - NCBI) is a public repository archiving and freely distributing microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the experiments and gene expression patterns stored in GEO. Registration not required.
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Ensembl, a genome browser project, produces genome databases for vertebrates, and makes this information freely available online. Registration not required.
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The mission of UniProt is to provide the scientific community with a comprehensive, high quality and freely accessible resource of protein sequence and functional information. The site provides UniProtKB (protein knowledgebase) consisting of Swiss-Prot and TrEMBL sections; UniRef that speeds up sequence similarities search; and UniParc a squence archive. Registration not required.
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QuantPrime is very user-friendly tool for primer pair design in small- to large-scale real-time reverse transcription qPCR analyses. It offers design and specificity checking with highly customizable parameters and is ready to use with most publicly available eukaryotic transcriptomes, including all higher eukaryote model organisms and important plant crops, while benefiting from exon-intron border and splice variant information in available genome annotations. Registration not required.
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A very intuitive tool to design primer. The request need the entering of gene sequence or sequence of interest (multiple sequences in FASTA format with exons in uppercase letters and introns in lowercase letters, positive orientation). A complete tutorial is available. Registration not required.
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GeneFisher2 is a very good site allowing great control over primer design Registration not required.
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Compare two sequences aligns two sequences using the indicated algorithm, and calculates the statistical significance using shuffled sequences. Registration not required.
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This web tool allows you to assemble a set of contiguous sequences (contigs) Registration not required.
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SDS (siRNA Design Software) is a software tool that helps to design siRNAs for silencing gene expression. The tool takes an mRNA sequence and makes use of existing design tools to output a set of candidates. These candidates are then filtered based on the secondary structure. With the following features: It provides a unified platform for using existing software. It compares the output of existing software. It enhances the existing software by filtering ineffective siRNAs based on secondary stru... Registration not required.
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Category: Calculators and converters
Expasy Translate allows: translate a nucleotide (DNA/RNA) sequence to a protein sequence
Expasy Translate is a web application (no installation required) which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence. Registration not required.
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Plagiarism destroys your career life. Plagiarisma is the plagiarism checker considered as an important tool for students, teachers, scholars and professional writers. It works on Windows, Android, BlackBerry and Web. It detects copyright infringement in your essay, research paper, coursework or dissertation. It supports Google, Yahoo, Scholar and Books. It helps avoid plagerism. It will only take a few minutes to check your document. Are you searching for plagarism detector that is accurate enou... Registration not required.
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Gene ID Conversion Tool is a comprehensive and fast accession mapping system in DAVID 2.1. With it any given gene accession can be quickly mapped to another based on the user's choice. The tool also automatically suggests possible choices for the ambiguous gene accessions in the list. Registration not required.
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dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations. Registration not required.
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KEGG Pathway is a collection of manually drawn pathway maps (see new maps, change history, and last updates) representing our knowledge on the molecular interaction and reaction networks. Pathway entries are text representation of pathway maps, containing descriptions (for a limited number of entries, at the moment). KEGG PATHWAY mapping is the process to map molecular datasets, especially large-scale datasets in genomics, transcriptomics, proteomics, and metabolomics, to the KEGG pathway maps... Registration not required.
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Cancer Genome Project has embarked on a systematic characterisation of the genetics and genomics of large numbers of cancer cell lines. Prior knowledge of their genetic abnormalities may allow more informed choice of cancer cell lines in biological experiments and drug testing and more informed interpretation of results. Registration not required.
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KEGG DRUG is a unified drug information resource that contains chemical structures and/or chemical components of all prescription and OTC drugs in Japan, most prescription drugs in the USA, and many prescription drugs in Europe. Thus, all the marketed drugs in Japan are fully represented in KEGG DRUG and linked to the package insert information (labels information). These include crude drugs and TCM (Tradictional Chinese Medicine) drugs, which are very popular in Japan and some of which are spec... Registration not required.
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JANE, the Journal/Author Name Estimator, is built on a database of millions of Medline records. Given an article title or abstract, JANE suggests related journals, authors or articles. It is useful to pinpoint journals closely aligned with our research. It is useful also to editors to find potential peer reviewers. Registration not required.
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a comprehensive collection of experimental protocols
Category: Biomedical protocols
The www.bio-protocol.org (originally from Stanford Univerisity) aims to provide life science researchers with a comprehensive collection of experimental protocols free of charge. Each protocol published on the website bears high standards in quality and provides accurate and detailed guidance which allows even rookie researchers to easily repeat experiments. Contribution to www.bio-protocol.org is by invitation only to maintain the quality of the protocols. The invitations are issued by their ed... Registration not required.
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The site is organized around key concepts, explained by: animation, image gallery, video interviews, problems, biographies, and links. There are three main sections: Classical Genetics, Molecular Genetics, Genetic Organization & Control. Registration not required.
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free online library of abbreviations and acronyms
Category: Dictionaries and writing aids
Free online library of full forms, abbreviations, acronyms, initialisms, references and much more. Registration not required.
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ExPASy is the Swiss Institute of Bioinformatics (SIB)Bioinformatics Resource Portal which provides access to scientific databases and software tools (i.e., resources) in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc. (see Categories in the left menu). On this portal you find resources from many different SIB groups as well as external institutions. Registration not required.
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COBALT computes a multiple protein sequence alignment using conserved domain and local sequence similarity information. Registration not required.
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design siRNA sequences
Category: SiRNA design
Scitools RNAi design allows: Design siRNA sequences
Scitools RNAi design is a web application to design siRNA sequences. Registration not required.
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Category: Calculators and converters
Chemical and radiochemical calculators allows: Dilute molar solutions, convert between moles and grams, calculate EC(anything) from EC50
Chemical and radiochemical calculators (QuickCalcs) offers radioactivity calculators. Moreover it create and dilute molar solutions, convert between moles and grams and calculate EC(anything) from EC50. Registration not required.
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RxC table concerns a basic two dimensional crosstable procedure. The statistical tests include Chi-squares, Gamma, Tau, Lambda, Kappa/Bowker. Formatting table and graphs are allowed. Registration not required.
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Home Recent Results Saved Strategies Needleman-Wunsch Global Align Nucleotide Sequences
Category: Protein sequences alignment
The Needleman-Wunsch global alignment (now hosted by BLAST/NLM) performs a global alignment on two sequences. It is commonly used in bioinformatics to align protein or nucleotide sequences. Registration not required.
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The web pages listed here comprise a powerful, conveniently-accessible, multi-platform statistical software package. There are also links to online statistics books, tutorials, downloadable software, and related resources. Registration required.
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Various categorica & proportion
Category: Categorical data
QuickCalc allows: GraphPad
Confidence interval of a proportion or count.; Chi-square test; 2x2 contingency table; McNemar's test to analyze a matched case-control & paired comparison; binomial and sign test for two possible outcome; NNT (Number Needed to Treat); predictive values from sensitivity, specificity, and prevalence; Kappa test. Registration not required.
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Which sequence is more susceptible to be bound to your transcription factor represented by your matrix? Input data: Multiple DNA sequences, personal matrix. Registration not required.
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OligoAnalyzer is a web application from IDT that provides the opportunity to analyze hairpin and self-dimer of existing primers this site. Moreover this site allows you to BLAST the sequence against NCBI's database and measure the impact of incorporating 5'-modifications into the sequence. The oligos can then be ordered directly. Registration not required.
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"How people in science see each other" is an absolutely brilliant and hilarious chart created by @biomatushiq about how people in science see each other. Registration not required.
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expression and localization of proteins in human tissues
Category: Protein informations
The human protein atlas shows expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images (Marx V., Nature 509:645, 2014). Registration not required.
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LALIGN/PLALIGN find internal duplications by calculating non-intersecting local alignments of protein or DNA sequences. LALIGN shows the alignments and similarity scores, while PLALIGN presents a "dot-plot" like graph. Registration not required.
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technical definitions and synonyms for drugs/agents used to treat patients with cancer or conditions related to cancer
Category: Drugs search
NCI Drug Dictionary allows: search drugs used to treat patients with cancer
The NCI Drug Dictionary contains technical definitions and synonyms for drugs/agents used to treat patients with cancer or conditions related to cancer. Each drug entry includes links to check for clinical trials listed in NCI's PDQ® Cancer Clinical Trials Registry. Registration required.
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Job Seeker is a job search engine in association with Science magazine. Options include keywords, discipline, period and location Registration not required.
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The Khanacademy web site, in statistical section, provides very well done video tutorials modeling a class on several statistical topics from descriptive stat to regression and inferential stat. Khan Academy is a non-profit educational website created in 2006 by educator Salman Khan to provide a free, world-class education for anyone, anywhere. The website features thousands of educational resources, including a personalized learning dashboard, over 100,000 exercise problems, and over 4000 micro... Registration not required.
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Gene (NCBI) is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer Registration not required.
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Normal, Student's T, Chi-Square and F Statistical Tables from SOCR (UCLA) Registration not required.
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open access biomedical image search engine
Category: Biomedical images search
OPENi allows: search biomedical images
Description not available. Registration not required.
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Lab Security and Basic Lab Techniques Registration not required.
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COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. Registration not required.
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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. Registration required.
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The National Toxicology Program (NTP) was established in 1978 as a cooperative effort to: Coordinate toxicology testing programs within the federal government; strengthen the science base in toxicology; develop and validate improved testing methods; provide information about potentially toxic chemicals. Registration not required.
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Description not available. Registration not required.
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Wolfram Alpha offers a variety of calculators and converters for many topics: mathematics, statistics, medicine, chemistry, weather, dates, geography, life sciences, etc. Registration not required.
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connect with researchers, make your work visible and stay current
Category: Biomedical communities
Researchgate allows: connect with researchers, make your scientific work visible
ResearchGate is a network dedicated to science and research. Connect, collaborate and discover scientific publications, jobs and conferences. All for free. Registration required.
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The non-profit ATCC (American Type Culture Collection) Cell Products is the most comprehensive and diverse of its kind in the world, consisting of over 3,600 cell lines from over 150 different species. It holds over 950 cancer cell lines, 1,000 hybridomas and several special collections including stem cells. Registration not required.
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With New Scientist Jobs you can search our database for hundreds of science jobs. Registration is free and you can upload your CV, set up email job alerts, subscribe to RSS feeds and apply for science jobs online Registration required.
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Category: Continuous data
Simple statistics on one or two samples allows: GraphPad
Descriptive statistics and confidence interval of a mean; Grubbs' test to detect an outlier; t test; One sample t test; post test following two-way (or higher) ANOVA; confidence interval of a sum, difference, quotient or product of two means; Confidence interval of a standard deviation. Registration not required.
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BMI calculator calculates your Body Mass Index (BMI), from NHLBI Registration not required.
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a collection of disease entries capturing knowledge on genetic and environmental perturbations
Category: Diseases search
The KEGG DISEASE database is a collection of disease entries capturing knowledge on genetic and environmental perturbations. Diseases are viewed as perturbed states of the molecular system. Different types of diseases, including single-gene (monogenic) diseases, multifactorial diseases, and infectious diseases, are all treated in a unified manner as follows: Genetic perturbations, Environmental perturbations --> Perturbed molecular network --> Disease. Registration not required.
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designs primers around exons in genomic sequence. All you need is a GenBank file containing your gene. Registration not required.
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The aim of the GLOBOCAN project (developed by IARC) is to provide contemporary estimates of the incidence of, mortality, prevalence and disability-adjusted life years (DALYs) from major type of cancers, at national level, for 184 countries of the world. The GLOBOCAN estimates are presented separately for each sex and, for incidence and mortality data, for ten age groups. 1-, 3- and 5-year prevalence data are available for the adult population only (ages 15 and over). DALYs, life years lost lost ... Registration not required.
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SISA allows to do quite complete statistical analysis directly on the Internet. Registration not required.
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Jpred3 is a web applicaion that predicts secondary structure from a protein sequence. Registration not required.
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The Genome Data Viewer, NCBI genome browser, allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. Registration not required.
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Google Scholar allows users to search for digital or physical copies of articles, whether online or in libraries Google Scholar is relatively quick and easy to use. “Scholarly” searches will appear using the references from “’full-text journal articles, technical reports, preprints, theses, books, and other documents, including selected Web pages that are deemed to be “scholarly.’” Because most of Google Scholar's search results link directly to commercial journal articles, a major... Registration not required.
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A major goal of the Encyclopedia of DNA Elements (ENCODE) is to annotate all functional elements of the human genome including protein-coding genes, pseudogenes, and non-coding transcribed loci and to catalog the products of transcription including splice isoforms and regulatory elements that control the cells and circumstances in which a gene is active. Registration not required.
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AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation. Registration not required.
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The EDA allows scientists to create a visual representation of an animal experiment by laying out its key elements — hypothesis, experimental method and planned analysis — in logically connected, coloured boxes. The software then uses a built-in set of rules to spot potential prob¬lems, and suggests refinements. These may be simple — the researcher hasn’t specified how to randomize animals to the control or treatment arm — or more complex: there are potential confounding variables in ... Registration required.
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This is a simple but fairly general numeric expression evaluator, with a large number of built-in transcendental functions. Registration not required.
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Search protein databases with a protein query sequence to either identify the query sequence or find protein sequences similar to the query.Searches can be refined using algorythms available in the page: PSI-Blast, PHI-BLAST & DELTA-BLAST. Registration not required.
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Report on Carcinogens, U.S. Department of Health and Human Services, Public Health Service, National Toxicology Program . Registration not required.
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The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. Registration not required.
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WikiDoc was created to freely share medical knowledge and to foster collaboration among healthcare providers. Launched by Dr. C. Michael Gibson of Harvard Medical School in late 2005, WikiDoc is the first and largest wiki dedicated to medicine on the Internet. WikiDoc is kept up to date by over 5,000 collaborators around the world. The content has now been updated nearly half a million times. There is no pharmaceutical or device industry support for the site. WikiDoc is intended to be a free sh... Registration not required.
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browse restriction enzymes by name, sequence, overhang, or type
Category: Biomedical products search
Enzyme Finder by New England Biolabs allows you to select restriction enzymes by name, sequence, overhang, or type. Sequences should be entered using single letter code nomenclature. In search results, enzymes supplied by NEB are listed first and displayed as links. Registration not required.
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Chemical Probes Objective Assessment Resource
Category: Chemicals search, Biomedical products search
The Probe Miner: Objective Assessment of Chemical Probes is a community resource for the evaluation of chemical probes based on large-scale, publicly available, medicinal chemistry data. It is intended to empower researchers to select the best probes based on objective, data driven criteria. This resource provides evaluation of > 1.8m small molecules against for >2,200 human targets and is regularly updated in response to updates in the publicly available medicinal chemistry data. Our continuing... Registration not required.
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PRALINE is a multiple sequence alignment program with many options to optimise the information for each of the input sequences; e.g. homology-extended alignment, predicted secondary structure and/or transmembrane structure information and iteration capabilities. Registration not required.
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YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Registration not required.
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BASE is a comprehensive free web-based database solution for the massive amounts of data generated by microarray analysis. Registration not required.
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Description not available. Registration not required.
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OMIM (Online Mendelian Inheritance in Man) is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. Registration not required.
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PipeAlign2 is a protein family analysis tool integrating a multi-step process ranging from the search for sequence homologues in protein and 3D structure databases to the structural / functional annotation of the family. The complete, automatic pipeline takes a single sequence or a set of sequences as input and constructs a high-quality, validated multiple sequence alignment (MSA) in which sequences are clustered into potential functional subgroups. Registration not required.
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SCAN2 is a we app for aligning two multimegabyte-size genome sequences Registration not required.
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Java Dot Plot Alignments (JDotter) is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. JDotter runs as a client-server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter also interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly s... Registration not required.
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PS is an interactive Windows program from Vanderbilt University for performing power and sample size calculations. It can be used for studies with dichotomous, continuous, or survival response measures. Registration not required.
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Category: Biomedical images search, Imaging software
Broad Bioimage Benchmark Collection allows: Image database, Broad
The Broad Bioimage Benchmark Collection (BBBC) is a collection of freely downloadable microscopy image sets intended as a resource for testing and validating automated image-analysis algorithms. In addition to the images themselves, each set includes a description of the biological application and some type of ground truth. Registration not required.
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Established in 2000, International Cancer Research Partnership (ICRP) is a unique alliance of cancer organizations working together to enhance global collaboration and strategic coordination of research. Registration not required.
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This online program helps to evaluate the quantity of primers and nucleotides for optimal PCR reaction and the necessary number of cycles. Registration not required.
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known and predicted protein interactions
Category: Protein interactions
STRING allows: database of known protein interactions, predict protein interactions
STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations. They are derived from Genomic Context, High-throughput Experiments (Conserved), Coexpression, Previous Knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 2,590,259 proteins from 630 organ... Registration not required.
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zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites. Registration not required.
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TReverse Translate accepts a protein sequence as input and uses a codon usage table to generate a DNA sequence representing the most likely non-degenerate coding sequence. A consensus sequence derived from all the possible codons for each amino acid is also returned. Use Reverse Translate when designing PCR primers to anneal to an unsequenced coding sequence from a related species Registration not required.
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Multiuse converter for units on: Angle, Area, Bits, Density, Electric, Energy, Focrce, Fuel, Length, Mass, Power, Pressure, Speed, Temperature, Time, Volume Registration not required.
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AHRQ, a web site of the US Dept Of Human Services, provides several funding opportunities in healthcare for US. Registration not required.
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ScienceJobs is a job site for recruiting the top scientists in associations with the Journal of American Science. Registration not required.
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Overlapping Primers interacts with the Whitehead's Primer3 progra to create multiple overlapping PCR products in one sequence. Registration not required.
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While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Registration not required.
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ESPript, 'Easy Sequencing in PostScript', is a program which renders sequence similarities and secondary structure information from aligned sequences for analysis and publication purpose. Registration not required.
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Compare gene order between two small bacterial genomes Registration not required.
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Browse the Web's Largest Acronyms & Abbreviations Resource Registration not required.
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H-BloX is a web-based JavaScript application that allows one to calculate and visualize the Shannon information or the relative entropy (Kullback-Leibler distance) of sequence alignment blocks. Various residue alphabets may be defined and useful modifications of the alignment block and the alphabet can be applied before calculation. Registration not required.
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PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results. Registration not required.
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VISualization Tools for Alignments: VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. Registration not required.
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designs primers around every SNP in a GenBank file. Registration not required.
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A 'module map' showing conditional activity of microarray expression modules in cancer Registration not required.
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DNA or genome alignment and visualization tool based on blastz alignment program. Alignments can be automatically submitted to rVista 2.0 to identify evolutionary conserved transcription factor binding sites. Registration not required.
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The HUGO Gene Nomenclature Committee (HGNC) has assigned unique gene symbols and names to over 33,000 human loci, of which around 19,000 are protein coding. http://genenames.org is a curated online repository of HGNC-approved gene nomenclature and associated resources including links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages. Registration not required.
Click here for more informationsCompute post test probability, Multiple comparisons correction Registration not required.
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FOLDALIGN is an algorithm for local or global simultaneous folding and aligning two or more RNA sequences and is based on the Sankoffs algorithm (SIAM J. Appl. Math., 45:810-825, 1985). Foldalign can make pairwise local or global alignments and structure predictions. FoldalignM makes a multiple global alignment and structure prediction. Registration not required.
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With more than 900,000 human-edited definitions, Acronym Finder is a largest dictionary of acronyms, abbreviations, and initialisms. Combined with the Acronym Attic, Acronym Finder contains more than 4 million acronyms and abbreviations. Registration not required.
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I-TASSER server is a web application for protein structure and function predictions. Models are built based on multiple-threading alignments by LOMETS and iterative TASSER simulations. I-TASSER (as 'Zhang-Server') was ranked as the No 1 server in recent CASP7 and CASP8 experiments. The server is in active development with the goal to provide accurate structural and function predictions using state-of-the-art algorithms. References: Ambrish Roy, Alper Kucukural, Yang Zhang. I-TASSER: a unified pl... Registration not required.
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Category: Gene information search, Gene expression
WashU Human Epigenome Browser allows: Epigenome
The browser currently hosts Human (and other species) Epigenome Atlas data produced by the Roadmap Epigenomics project,but lets users diverge from the strict genome-centric view of the UCSC browser to, for instance, view all genes (or promoters, or 3’ UTRs) in a given pathway side by side. “You can do lots of Google Maps-style operations, and you can look at your data in the context of their metadata.
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Category: Biomedical protocols
Protocol Exchange allows: to discover protocols, to share protocols, to comment on protocols, to organize your favorites protocols
Protocol Exchange from Nature Protocols is an open resource where the community of scientists pool their experimental know-how to help accelerate research. Discover the protocols, share a protocol, join a lab group, comment on protocols, organize your favorites and personalize your experience. Registration not required.
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Calculate volumes and dilutions using both % and molar Registration not required.
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R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS Registration not required.
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EMBO Fellowships fund and support young scientists in their pursuit of both pre- and post-doctoral research. Registration not required.
Click here for more informationsOverlapping Primers creates multiple overlapping PCR products in one sequence. Registration not required.
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Click here for more informationsDistributions: Binomial, Normal, Student's T, Chi Square, Fisher's F Registration not required.
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This page allows you to generate random integers in a given interval.
Click here for more informationsdesigns primers around exons in genomic sequence. All you need is a GenBank file containing your gene. Registration not required.
Click here for more informationsdesigns primers around every SNP in a GenBank file. Registration not required.
Click here for more informationsdesigns primers around open reading frames. Simply upload a GenBank file containing your genes. Registration not required.
Click here for more informationsmulti-objective multiplex PCR assay design - designed for large-scale multiplex PCR assay design in an automated high-throughput environment, where high coverage is required. Registration not required.
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GeneCards maintained by Weizmann Institute of Science is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes. Registration not required.
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Mascot is a powerful and widely used search engine that uses mass spectrometry data to identify proteins from primary sequence databases.
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The UCSC Genome Browser is an on-line genome browser hosted by the University of California, Santa Cruz (UCSC).[2] [3] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. Registration not required.
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expression, homology and other information on groups of genes
Category: Gene expression
Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways. Registration not required.
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an online tool that allows to calculate the molar mass of a chemical compound
Category: Calculators and converters
MOLAR MASS CALCULATOR allows: calculate the molar mass of a chemical compounds
MOLAR MASS CALCULATOR is an online tool that allows to calculate the molar mass of chemical compounds.
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This converter calculates the measured value in units of [ppm] into units of [mg/m3] and visa versa. Registration not required.
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The Giovanni Armenise Harvard Foundation grant and fellowship programs supports individual scientists at Harvard Medical School and in Italy Registration not required.
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Randomly assign subjects to groups; Simulate data by generating random numbers; Randomly select a subset of subjects. Registration not required.
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a video journal for biological, medical, chemical and physical research
Category: Biomedical communities, Biomedical protocols
JoVE (Journal of Visualized Experiments) is a peer-reviewed journal that publishes written protocols accompanied by video for biological, medical, chemical and physical research. Currently, JoVe charges a $1200 publication fee for self-produced videos and $2400 if JoVE does the filming. There's an added fee of $1800 to provide open access. Registration not required.
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Web-based Calculator for ROC Curves Registration not required.
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This screen computes several statistics from a table whose row and column categories form logically ordered sequences. It can accommodate a table with up to five rows and/or five columns Registration not required.
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Morpheus (from Broad Institute) is a web-based versatile matrix visualization and analysis software. View your dataset as a heat map, and then explore the interactive tools in Morpheus. Cluster, create new annotations, search, filter, sort, display charts, and more. Registration not required.
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Distributed trough GitHub
Category: Imaging software
CISMM allows: Image tools listing
CISMM is one of several groups providing visualization and analysis tools freely usable by the biomedical microscopy community. There are a number of freely-available tools from other National Research Resources and elsewhere. We list some of them here for easy reference, along with brief descriptions Registration not required.
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Loop is an open, cross-platform network for researchers and academics, allowing for the discoverability of researchers and their work across multiple domains. Loop is committed to enhancing the academic reputation and impact of researchers within an international community, enabling them to stay up-to-date with new research and connecting them to their peers. Registration required.
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Postdoctoral Fellowships of Human Frontier Science Program HFSP are available for scientists who wish to work in foreign laboratories, with emphasis on individuals early in their careers who wish to obtain training in a different field of research. Fellows who return to their home countries are eligible to apply for a Career Development Award. Cross-disciplinary fellowships are intended for postdoctoral fellows with a Ph.D. degree in the physical sciences, chemistry, mathematics, engineering and... Registration not required.
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The web site calculates the body shape index (ABSI). A body shape index that, by quantifying abdominal adiposity relative to BMI and height, is thought to be a better predictor of mortality than BMI (see Krakauer & Krakauer, PLoS ONE 7, e39504, 2012; Ahima & Lazar, Science 341:856, 2013). Registration not required.
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The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. Registration not required.
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The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. Registration not required.
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RANDOM.ORG offers true random numbers to anyone on the Internet. The randomness comes from atmospheric noise, which for many purposes is better than the pseudo-random number algorithms typically used in computer programs. Registration not required.
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This website provides a variety of online calculators, such as math and physics, financial, statistics, engineering and conversion calculators Registration not required.
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ImageJ from NIH is the most diffused public domain Java image processing program suitable for several scientific applications. Registration not required.
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Galaxy is an open source, web-based platform for data intensive biomedical research whose purpose is to make complex analysis more accessible. It is a useful tool for bioinformaticians and DNA sequencers. Galaxy provides a point-and-click web interface alternative to the bioinformatics command line, thus allowing researchers to easily create, run, and troubleshoot analytical pipelines (see Perkel JM, The Scientist 08/2016, p 57). Registration required.
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This website provide several protocols and methods for histotechnology. Registration not required.
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The Nucleotide database (NCBI) is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery. Registration not required.
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Description not available. Registration not required.
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Addgene is a non-profit plasmid repository dedicated to helping academic scientists around the world share high-quality plasmids. Registration not required.
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The A.D.A.M. Medical Encyclopedia includes over 4,000 articles about diseases, tests, symptoms, injuries, and surgeries. It also contains an extensive library of medical photographs and illustrations. Registration not required.
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Online Statistics, an interactive multimedia course of study ideated by David Lnae of Rice University, is a resource for learning and teaching introductory statistics. It contains material presented in textbook format and as video presentations. This resource features interactive demonstrations and simulations, case studies, and an analysis lab. Registration not required.
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ResearcherID provides a solution to the author ambiguity problem within the scholarly research community. Each member is assigned a unique identifier to enable researchers to manage their publication lists, track their times cited counts and h-index, identify potential collaborators and avoid author misidentification. In addition, your ResearcherID information integrates with the Web of Science and is ORCID compliant, allowing you to claim and showcase your publications from a single one account... Registration required.
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The Mouse Tumor Biology (MTB) Database supports the use of the mouse as a model system of hereditary cancer providing online access to a variety of information on tumor models, genetic factors, tumor pathology, etc. Registration not required.
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The site lists positions offered at Universities, Academies, Colleges, Faculties, Schools, Academic Departments, Institutes and Research Centers. It is possible to post a job request. The list of offered positions is free, posting a job and premium adverts require payment. Registration not required.
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The ProteomeTools project is a joint effort of the Technical University of Munich (TUM), JPT Peptide Technologies, SAP SE and Thermo Fisher Scientific. It is dedicated to translating the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. Over the course of the project, ~1.4 million synthetic peptides covering essentially all human gene products including important post translational modifications will be synthesized and analyzed u... Registration not required.
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Description not available. Registration not required.
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As researchers and scholars, you face the ongoing challenge of distinguishing your research activities from those of others with similar names. You need to be able to easily and uniquely attach your identity to research objects such as datasets, equipment, articles, media stories, citations, experiments, patents, and notebooks. As you collaborate across disciplines, institutions and borders, you must interact with an increasing number and diversity of research information systems. Entering data ... Registration required.
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This web site offers free resources for students and researchers working with statistics. All the calculators and tools featured here have been designed with ease of use and clarity of presentation in mind. The web site has three main sections: statistical calculators, which deals mainly with hypothesis testing; p-value calculators, which allow you to derive p-values from Z, t, chi-square and Pearson (r); and descriptive statistics - averages, variance, and easy histogram and bar chart makers.... Registration not required.
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free, online, open-source curated knowledgebase of biological pathways
Category: Pathways
Reactome allows: to analyse pathways, to visualize pathways
Reactome is a free, online, open-source curated knowledgebase of biological pathways for several species, encompassing many areas of human biology (D Croft et al., Nucleic Acid Res 39, D691, 2011). Registration not required.
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Tissue dissociation and primary cell isolation and harvesting
Category: Biomedical protocols
This guide summarizes our knowledge of how using enzymes to accomplish the routine operations of tissue dissociation and cell harvesting. It describes standard lab procedures, offers a logical experimental approach for establishing a cell isolation protocol, and lists many tissue specific references. Registration not required.
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Histology/Immunohistochemistry
Category: Biomedical protocols
IHCWORLD protocols allows: to search protocols
This protocol database is a collection of histology/immunohistochemstry protocols compiled based on published literatures, laboratory submissions, as well as individual experimental data. Registration not required.
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Codeacademy is an online interactive platform for those who want to learn programming on their own. It offers free classes on 12 different programming languages including Python, Java, PHP, JavaScript (jQuery, AngularJS, React.js), Ruby, SQL, and Sass, as well as markup languages HTML and CSSIt. Codeacademy is a tutorial that mainly teaches you the syntax of a programming language. Registration required.
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Description not available. Registration not required.
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ESF is a strong international network of 75 research funding, performing organisations and academics. ESF offers a number of opportunities, scientific and non-scientific, and provides career opportunities that could progress in management and administrative science activities. Registration required.
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match your article to Elsevier journals
Category: Biomedical journals
Elsevier Journal Finder allows: find journals for publishing your scientific article, to match your article to Elsevier journals
Elsevier Journal Finder helps you find journals that could be best suited for publishing your scientific article. It uses smart search technology and field-of-research specific vocabularies to match your article to Elsevier journals. Simply insert your title and abstract and select the appropriate field-of-research for the best results. Registration not required.
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QCancer is an algorithm, which can be used to calculate the absolute risk of a patient having an undiagnosed cancer based on a number of factors.The QCancer algorithm and the cancer risk score take into account patient symptoms, risk factors, such as age and sex, smoking status, family history, postcode and certain comorbidities. Registration not required.
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ChemSpider is a free-to-access collection of compound data from across the web, that offers text and structure searching to find compounds of interest and provides unique services to improve this data by curation and annotation and to integrate it with users’ applications. Registration not required.
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Resource Identification Portal
Category: Biomedical products search, Biomedical journals
This is the Resource Identification Portal, supporting NIH's new guidelines for Rigor and Transparency in biomedical publications. Authors are instructed to authenticate key biological resources: Antibodies, Model Organisms, and Tools (software, databases, services), by finding or generating stable unique identifier named Research Resource Identifiers or RRIDs (Bandrowski et al., F1000Research 4:134, 2015). See also The Resource Identification Initiative Force 11 at: https://www.force11.org/grou... Registration not required.
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WormBase is the repository of mapping, sequencing and phenotypic information for C. elegans (and some other nematodes). The worm informatics group at the Sanger Institute play a key role in assembling the whole database (a new release occurs every three weeks). Registration not required.
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The web site presents a collection of normal and pathological digitalized histological sections that can be easily navigated and observed at various magnifications Registration not required.
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The Sergio Lombroso Foundation offers fellowships for Italian graduate students, post-docs, and visiting scientists, in the area of Cancer Research at the Weizmann Institute of Science in Israel. Registration not required.
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Find A PhD is a guide to current postgraduate research and PhD studentships. We list details of graduate research programmes from universities throughout the UK, Europe and further afield. New PhDs are added every day, and our listings include PhD Research Projects, PhD Research Programmes, Four Year PhD Programmes, International PhD Programmes and Clinical PhD Programmes. Registration not required.
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ERC Starting Independent Researcher Grants (ERC Starting Grants) aim to support up-and-coming research leaders who are about to establish or consolidate a proper research team and to start conducting independent research in Europe. Registration not required.
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A complete tutorial on lentiviral vectors. Registration not required.
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The Structured International Post Doc program od the European School of Molecular Medicine,located in Milan, is designed to boost the career of postdocs and to encourage them to become successful and independent research scientists. Positions are intended for outstanding and highly-motivated applicants of any nationality. Registration not required.
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Perform currency and foreign exchange calculations using live, mid-market rates. Registration not required.
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The European Association for the Study of the Liver (EASL) Post-Doctorat Fellowship, Entry Level Fellowship and Short-Term Fellowship programmes are open to all registered EASL members and aim to enhance the mobility of investigators within different European institutions, to actively promote scientific exchange among research units in hepatology. Registration not required.
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The Gene Expression Omnibus (GEO - NCBI) is a public repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomic data submitted by the scientific community. In addition to data storage, a collection of web-based interfaces and applications are available to help users query and download the experiments and gene expression patterns stored in GEO. Registration not required.
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The main sources of TheFreeDictionary's Medical dictionary are The American Heritage® Stedman's Medical Dictionary, Second Edition and Dorland's Medical Dictionary for Health Care Consumers, which provide authoritative descriptions of medical conditions, medications, anatomical terms, noted medical personalities and much more. The American Heritage® Stedman's Medical Dictionary is ideal for both medical professionals and anyone who wants to keep up with the burgeoning array of terminology foun... Registration not required.
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Reference for all scientist working on p53 or in cancer research in general. Registration not required.
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BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. Registration not required.
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BioMed Central is a publisher of 206 peer-reviewed open access journals. All original research articles published by BioMed Central are made freely and permanently accessible online immediately upon publication. BioMed Central views open access to research as essential in order to ensure the rapid and efficient communication of research findings. BioMed Central's portfolio of 206 journals includes general titles BMC Biology and BMC Medicine alongside specialist journals (e.g. BMC Bioinformatics... Registration not required.
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Elvira is a set of tools and procedures designed for high throughput assembly of small genomes such as viruses. The name Elvira stands for Executive for Large-scale VIRal Assembly. Elvira is particularly suitable in situations where any of the following occur: 1. Sequences must be individually trimmed against specific primers. 2. Sequences must be trimmed against degenerate primers. 3. Assemblies need to be explicitly partitioned based on sequence origin. The Elvira package includes s... Registration not required.
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This screen computes the sample size required to detect a difference between two proportions. Registration not required.
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Updated maps and charts of COVID-19 infection in Italy updated 2023(website in Italian) Registration not required.
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The Cell: An Image Library™ is a freely accessible, easy-to-search, public repository of reviewed and annotated images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. The purpose of this database is to advance research, education, and training, with the ultimate goal of improving human health. Registration not required.
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PSIPRED is a highly accurate method for protein secondary structure prediction, including MEMSAT - a transmembrane topology prediction method and GenTHREADER - a sequence profile based fold recognition method. Registration not required.
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BioImageXD,written in Python and C++, is a free open source software project for analyzing, processing and visualizing of multi dimensional microscopy images.BioImageXD is a multi-purpose post-processing tool for bioimaging. The software can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once. Registration not required.
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Various proteomic software Registration not required.
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Description not available. Registration not required.
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miRDB is an online database for miRNA target prediction and functional annotations in animals. All the targets were predicted by a new bioinformatics tool, which was developed by analyzing thousands of genes impacted by miRNAs with an SVM learning machine. Common features associated with miRNA target binding have been identified and used to predict miRNA targets. miRDB hosts predicted miRNA targets in five species: human, mouse, rat, dog and chicken. Registration not required.
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The International Agency for Research on Cancer (IARC) is the specialized cancer agency of the World Health Organization. The objective of IARC is to promote international collaboration in cancer research. The Agency is interdisciplinary, bringing together skills in epidemiology, laboratory sciences, and biostatistics to identify the causes of cancer so that preventive measures may be adopted and the burden of disease and associated suffering reduced. A significant feature of the Agency is its e... Registration not required.
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PubChem (NCBI) provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative. PubChem includes substance information, compound structures, and BioActivity data in three primary databases, Pcsubstance, Pccompound, and PCBioAssay, respectively. The Substance/Compound database, where possible, provides links to BioAssay description, literature, references, and assay data points. The BioAssay database also includes links back... Registration not required.
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QUARK is a computer algorithm for ab initio protein folding and protein structure prediction, which aims to construct the correct protein 3D model from amino acid sequence only. QUARK models are built from a small fragments (1-20 residues long) by replica-exchange Monte Carlo simulation under the guide of an atomic-level knowledge-based force field. QUARK was ranked as the No 1 server in Free-modeling (FM) in CASP9. Since no global template information is used in QUARK simulation, the server is ... Registration not required.
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Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases (EG Cerami et al., Nucleic Acid Res 39, D685, 2011) Registration not required.
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I2D (Interologous Interaction Database) is a web application designed to explore known and predicted protein-protein interactions and to facilitate bioinformatics initiatives exploring protein interaction networks. Registration not required.
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SimuCell is an open-source framework for specifying and rendering realistic microscopy images containing diverse cell phenotypes, heterogeneous populations, microenvironmental dependencies and imaging artifacts. SimuCell can generate heterogeneous cellular populations composed of diverse cell types and allows users to specify interdependencies among population, biomarker and cell phenotypes (S. Rajaram et al., Nature Methods 9, 634, 2012). Registration not required.
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Biocompare is a resource for up-to-date product information, product reviews, and new technologies for life scientists. Biocompare combines an in-depth knowledge of life science products and new technologies with the power of the Internet to offer scientists the most dynamic, relevant, and innovative media-based marketplace for life science information. Produced by scientists, Biocompare's mission is to provide free, time saving services to life science researchers, allowing scientists to find a... Registration not required.
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The EMBL International PhD Programme, originally established in 1983, represents the flagship of EMBL's commitment to first class training and education. Registration not required.
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WikiPathways is an open, public platform dedicated to the curation of biological pathways by and for the scientific community Registration not required.
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PMP gives access to various models computed by comparative modeling methods provided by different partner sites, and provides access to various interactive services for model building, and quality assessment.Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase Registration not required.
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Gene SNP is part of the Environmental Genome Project (from NIESH) web resource that integrates gene, sequence and polymorphism data into individually annotated gene models. The human genes included are related to DNA repair, cell cycle control, cell signaling, cell division, homeostasis and metabolism, and are thought to play a role in susceptibility to environmental exposure. Registration not required.
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Compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of Swiss-Prot entries or for a user entered sequence of aminoacids. The resulting theoretical values check the consistency of the position on a 2D PAGE gel of the identified and unmodified proteins. Registration not required.
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Oligo Analysis Tool calculates molecular weight (MW), extinction coefficient (E260), pmoles/µg, pmoles/OD and µg/OD. Also displayed for your convenience are the % GC Content, melting temp (TM),the reverse complement of the oligo sequence you enter, and show primer-dimer sets Registration not required.
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Online calculation for sample size, power or the minimal detectable difference for parallel studies, crossover studies, or studies to find associations between variables, where the dependent variable is Success or Failure, a Quantitative Measurement, or a time to an event such as a survival time. Registration not required.
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We offer three programs aimed at encouraging and advancing the work of early career cancer researchers with high promise: Damon Runyon Fellowship Award, Damon Runyon Clinical Investigator Award, Damon Runyon-Rachleff Innovation Award. Registration not required.
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The Atlas of histological images is part of the Anatomy Atlases, a digital library of anatomy information curated by Ronald A Bergman. Registration not required.
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This online textbook evolved from notes of John H. McDonald Biological Data Analysis class at the University of Delaware. The main goal is to teach how to choose the appropriate statistical test for a particular experiment, then apply that test and interpret the results. Registration not required.
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CellProfiler is a free open-source software for high-throughput image-based cell profiling using fluorescence microscopy. It is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes. Registration not required.
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GenePattern is a powerful genomic analysis platform that provides access to more than 150 tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. Registration not required.
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DSMZ is the German Resource Center for Human, Animal Cell and microorganisms Culture Collection. The DSMZ currently hosts more than 79,000 bioresources, most of them are available from online catalogues. Registration required.
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ArrayMining is a web-server for online automating microarray statistical analysis of gene and protein expression microarray data, designed as a supporting tool for investigation of the genetic components of diseases. By providing feature selection, clustering and prediction analysis, it performs five common gene expression analysis tasks:cross-study normalisation, feature selection, sample clustering, sample classification, network analysis, gene set analysis. Registration not required.
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collection, archiving and distribution of relevant mutant strains
Category: Laboratory animals
The European Mouse Mutant Archive (EMMA) is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research.The laboratory mouse is the most important mammalian model for studying genetic and multi-factorial diseases in man. Thus the work of EMMA will play a crucial role in exploiting the tremendous potential benefits to human health presented by the current research in mammalian genetics. Registration not required.
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The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation da... Registration not required.
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The Whitehead Institute for Biomedical Research in Boston offers the Whitehead Fellows and Postdoctoral Programs. Fellows are given the space, resources and support needed to run their own labs and pursue an independent research agenda. Fellows are appointed for a three-year term with the expectation that it will be extended to five years. Postdocs are appointed directly by Whitehead labs. Registration not required.
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Frequent math for the lab.DNA & Protein conversions. Dilution, molarity & temperature calculators Registration not required.
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Description not available. Registration required.
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It's a simple Excel spreadsheet from Jon Wittwer of Vertex42 for constructin box-plots by inputing single subject values. In addition the spreadsheet includes examples for generating a random number from a Normal distribution, for calculating cumulative probabilities and for shading a portion of the distribution. Registration not required.
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The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Registration not required.
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BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data.The array tools package utilizes an Excel front end. Registration not required.
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Flash animation to demonstrate how DNA microarray experiments are performed Registration not required.
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ProSight Lite is a free Windows application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Registration required.
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Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions. Although originally designed for visualizing genomic data, it can create figures from data in any field. It requires PERL software language. Registration not required.
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Information & treatment con various cancer types Registration not required.
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Sage Bionetworks is an open-access online resource that helps researchers of all stripes access network biology. The Sage Bionetworks Commons will be used to integrate diverse molecular mega-datasets, to build predictive bionetworks and to offer advanced tools proven to provide unique new insights into human disease biology. Registration required.
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The Cochrane Collaboration is an international, non-profit, independent organisation, established to ensure that up-to-date, accurate information about the effects of healthcare interventions is readily available worldwide. It produces and disseminates systematic reviews of healthcare interventions, and promotes the search for evidence in the form of clinical trials and other studies of the effects of interventions. Registration not required.
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Category: Imaging software, Biomedical images search
OME | The Open Microscopy Environment allows: Image database
OME (Open Microscopy Environment) is a consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data. It is an open-source client-server software platform that enables access to and use of a wide range of biological data. You can access your data in OME from any platform. By combining facilities for large-scale data management and a flexible, model-based architecture, OMERO provides a foundation for many different data-... Registration not required.
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Statistics101 is a giftware computer program that interprets and executes the simple but powerful “Resampling Stats” programming language. Although it was originally developed to aid students, the Statistics101 program is suitable for all levels of statistical sophistication. It is especially useful for Monte Carlo, resampling, and bootstrap applications.Statistics101 is written in Java and will run on Windows, Mac, Unix, Linux, or any other platform that supports Java 1.4 or better. Registration not required.
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All that you need to know about retroviral infection, packaging cells and T-helper plasmid. Registration not required.
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The Allen Mouse Brain Atlas is a comprehensive genome-wide map of the adult mouse brain revealing where each gene is expressed, or “turned on. A combination of RNA in situ hybridization data, detailed Reference Atlases and informatics analysis tools are integrated to provide a searchable digital atlas of gene expression. Together, these resources present a comprehensive online platform for exploration of the brain at the cellular and molecular level. Registration not required.
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CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. CellDesigner is implemented in Java and thus supports various operating systems. Registration not required.
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protein-protein interactions mined from the scientific literature
Category: Protein interactions
The Molecular INTeraction database (MINT) focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The full MINT dataset can be freely downloaded. Registration not required.
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MGI (Mouse Genome Informatics) is an international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data for researching human health and disease. Registration not required.
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The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans Registration not required.
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VnD (Variations and Drugs)is a consolidated database containing information on diseases, disease and drug related genes, genetic variations, protein structures, and drug information, to understand the trilateral relationship among genomic variations, diseases, and drugs. Registration not required.
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The Broad-Novartis Cancer Cell Line Encyclopedia (CCLE) is an ongoing project from collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative ... Registration required.
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ProteinProphetTM automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST Registration not required.
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Pathorama provides you with high quality images and virtual slides for teaching and self-instruction covering a wide range of topics in all subspecialities of surgical pathology and cytology. Various courses, slide seminars, quizzes, and learning games for both students, surgical pathologists, and cytopathologists are available. Registration not required.
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Empowering the Development of Genomics Expertise
Category: DNA sequencing, Sequencing and assembly software
EDGE bioinformatics is intended to help truly democratize the use of Next Generation Sequencing for exploring genomes and metagenomes. Given that bioinformatic analysis is now the rate limiting factor in genomics, we developed EDGE bioinformatics with a user-friendly interface that allows scientists to perform a number of tailored analyses using many cutting-edge tools. Users can explore those and other data sets using a free demo hosted on the LANL server. Researchers who wish to analyse their ... Registration required.
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ELM(Eukariotic Linear Motif)is a resource for predicting functional sites in eukaryotic proteins. Registration not required.
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Bad Project is a funny Lady Gaga parody realized by scientists at the Hui Zheng lab at Baylor College of Medicine. Registration not required.
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HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. It brings together data from chromatin-mapping and comparative-genomics studies. Researchers can enter common variants and see whether they fall in a highly conserved region, disrupt a regulatory motif or are associated with a regulatory element in a particular cell type. It provides the same information for common variants that tend ... Registration not required.
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A wide collection of Proteomic tools hosted by the Swiss Proteomics Society
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Category: Proteomics data analysis, Gene expression
GenPattern Proteomics allows: Broad
GenePatern allowr various data analyses for proteomics: MRM-MS; peptide signature prediction; PEPPeR algorhitms; detection and alignment features across runs in LC-MS; support for SELDI/MALDI data. Registration not required.
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QMinim is an online free minimisation service for minimising subjects to different arms of a clinical trial. Registration required.
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PhenoRipper is an open-source software tool designed for rapid exploration of high-content microscopy images that permits rapid and intuitive comparison of images obtained under different experimental conditions based on image phenotype similarity.PhenoRipper is designed to serve as an unsupervised exploratory tool for analysis of fluorescence microscopy images for both novices and experts. Registration not required.
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3D Visualization-Assisted Analysis (Vaa3D) is an open source cross-platform (Mac, Linux, and Windows) tool based on ITK libraries for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Registration required.
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CClustal Omega is the latest addition to the Clustal family of general purpose multiple sequence alignment programs for DNA, RNA or proteins. The online version is hosted by EMBL. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular b... Registration not required.
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Category: Other topics, Gene expression
Roadmap Epigenomics Project allows: Epigenome
The NIH Roadmap Epigenomics Mapping Consortium was launched with the goal of producing a public resource of human epigenomic data to catalyze basic biology and disease-oriented research. The Consortium leverages experimental pipelines built around next-generation sequencing technologies to map DNA methylation, histone modifications, chromatin accessibility and small RNA transcripts in stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ system... Registration not required.
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The Integrated Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. Registration required.
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Research Randomizer is a closed-source, clinical randomization web service, It can be used for random sampling, random assignment to treatment groups, and block randomization. This randomization service has an excellent tutorial with five sample randomization scenarios for random sampling, random assignment, random block assignment, generating random numbers in a specified range, and random ordering of a set of items, Registration not required.
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The Vienna Biocenter PhD programme in Molecular Life Sciences is a programme for talented and highly motivated students of any nationality that covers a range of topics in modern biological sciences, including gene regulation, cell division, neural circuits, and evolutionary genomics. Registration required.
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This web site presents a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray–based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Registration not required.
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MAPU is the Max-Planck Unified Proteome DB. Mass spectrometry (MS)-based proteomics on body fluids, cell lines, red blood cells, liver. MAPU datasets can serve as reference proteomes in biomarker discovery. Registration not required.
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The Human Gene Mutation Database (HGMD) represents an attempt to collate known (published) gene lesions responsible for human inherited disease. Registration not required.
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The NCBO aims to be “the place to be” for biomedical ontologists across the globe. Registration not required.
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LOMETS (Local Meta-Threading-Server) is a locally installed meta-server for protein structure prediction. It generates 3D models by collecting consensus target-to-template alignments from 9 locally-installed threading programs (FUGUE, HHsearch, PAINT, PPA-I, PPA-II, PROSPECT2, SAM-T02, SPARKS, SP3). References: S. Wu, Y. Zhang. LOMETS: A local meta-threading-server for protein structure prediction. Nucleic Acids Research 2007; 35: 3375-3382 Registration not required.
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TM-align is a computer algorithm for quick and accurate protein structure alignment using dynamic programming and TM-score rotation matrix. An optimal alignment between two proteins, as well as the TM-score, will be reported for each comparison. References:Y. Zhang, J. Skolnick, TM-align: A protein structure alignment algorithm based on TM-score. Nucleic Acids Research, 2005 33: 2302-2309 Registration not required.
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The Connectivity Map uses computer algorithms and genome-wide expression data to explore the connection between diseases, genes, and drugs. Cmap is a collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms that together enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes. The aim of theConnectivity ... Registration required.
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SAMtools provide various utilities for manipulating alignments in the Sequence Alignment/Map (SAM) format, including sorting, merging, indexing and generating alignments in a per-position format. Registration not required.
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EMBL European Bioinformatic Istitute
Category: Gene information search, Protein informations
EBI (EMBL European Bioinformatic Istitute) home page provides a central access point to search several databases for information on genes, proteins, enzymes etc. Registration not required.
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a free, full-length, and occasionally interactive statistics textbook
Category: Other tutorials
Concepts and Applications of Inferential Statistics is a free, full-length, and occasionally interactive statistics textbook. Registration not required.
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a public archive and repository where nucleotide sequences generated by next-generation sequencing methodologies can be submitted
Category: Gene information search
ENA (European Nucleotide Archive) operates as a public archive and repository where nucleotide sequences generated by next-generation sequencing methodologies can be submitted. Data can be searched interactively and programmatically using free text and sequence similiary search based queries. It is a useful utility also for patent data search.ENA Registration not required.
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msInspect is an open source application written in Java that allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration. Registration not required.
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TargetScan (Whitehead Institute) predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA Registration not required.
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μManager is a open source microscopy software package for control of automated microscopes. It mainly targets camera-based imaging, although it is also used with scanning systems. It includes an easy-to-use interface that runs as an ImageJ plug-in and enables researchers to design and execute common microscopy functions as well as customized image-acquisition routines.The program can be used to collect multichannel data over space and time, such as tracking fluorescently tagged cell fusion even... Registration not required.
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Protégé is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. It is a tool that acts like the “word processor” of an ontology and uses a language like OWL as a convenient standard. At its core, Protégé implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats.... Registration required.
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Data input in a table format Registration not required.
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The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function. Registration not required.
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Babelomics is an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. This new version of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using f... Registration not required.
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This site is dedicated to explain concepts and technology behind the Comet Assay to detect DNA damage.
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Stem Book is an open access collection of invited, original, peer-reviewed chapters covering a range of topics related to stem cell biology written by top researchers in the field at the Harvard Stem Cell Institute and worldwide. Stem Book is aimed at stem cell and non-specialist researchers. Registration not required.
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A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function (see Wu et al., Genome Biol 10, R130, 2009.) Registration not required.
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eMolecules is a chemical structure search engine that links also to suppliers. The standard search allows querying for names, substructures, and suppliers. Registration not required.
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Commercial Company. The Charles River Animal Model Evaluation Program allows you to assess the quality and compatibility of available animal models before making a commitment. Whether you have a new research protocol, are conducting or fine-tuning a pilot study, or simply exploring the opportunity to switch to a new animal model, this program can help you make the right choice. Registration not required.
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This page from RV Lenth provides graphical interfaces for studying the power of one or more tests. They include sliders (convertible to number-entry fields) for varying parameters, and a simple provision for graphing one variable against another. Registration not required.
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BoxplotR is an interactive web application written in R for generation of customized box plots. Box Plots can be downloaded (Spitzer et al., Nat Meth 11:121, 2014). Registration not required.
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The Boehringer Ingelheim Fonds awards PhD fellowships to outstanding junior scientists (max. age: 27 years) who wish to pursue an ambitious PhD project of approximately 3 years in basic biomedical research in an internationally leading laboratory. Registration not required.
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The Cell Line Integrated Molecular Authentication (CLIMA) database is the result of an integration effort aimed at including all certified STR profiles of human cell lines in a unique database. Its main feature is cell line identification according to the standard ANSI/ATCC ASN-0002-2011, but it also provides features for searching profiles by cell line name and by locus. Registration not required.
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The ProMAT (Protein Microarray Analysis Tool) is a data analysis application for protein microarray data. The software was developed for use with ELISA microarray experimental data by the Statistics Group and the Cell Biology and Biochemistry Group at Pacific Northwest National Laboratory. Registration required.
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Access to high quality, well characterized, affordable affinity reagents has been deemed a major hurdle in cancer research by representatives of the scientific community. The reagents program within CPTC provides tools, reagents, technologies, and reference materials to allow for peptide and protein analysis for a variety of platforms and applications. The reagents generated within the CPTC program include cancer-related monoclonal antibodies and hybridomas, reference materials, standards kits a... Registration not required.
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geWorkbench (for genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications Registration not required.
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The International Genome Sample Resource (IGSR) maintains and shares the human genetic variation resources built by the 1000 Genomes Project. We also update the resources to the current reference assembly, add new data sets generated from the 1000 Genomes Project samples and add data from projects working with other openly consented samples. Registration not required.
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FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, and it helps them better visualize the fluorescent-stained confocal samples. Registration not required.
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DOAJ is a directory of Open Access Journals, maintained by Lund University, that covers free, full text, quality controlled scientific and scholarly journals. The aim of the Directory of Open Access Journals is to increase the visibility and ease of use of open access scientific and scholarly journals thereby promoting their increased usage and impact. The Directory aims to be comprehensive and cover all open access scientific and scholarly journals that use a quality control system to guarantee... Registration not required.
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LabX has evolved as a highly specialized business-to-business marketplace where scientific equipment and supplies can be bought and sold. It provide a means for buyers and sellers to connect. Professionals from all industries visit LabX to buy and sell equipment and supplies. While 85% of customers are from North America, LabX enjoys a worldwide user base that includes Europe, Asia, Central and South America, and Australia. Registration not required.
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Daily Med (from NIH) provides high quality information about marketed drugs. Registration not required.
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Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration and visualization. Registration not required.
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NNetwork Analysis, Visualization, & Graphing TORonto is a software system for scalable visualizing and analyzing networks. NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics e... Registration not required.
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Since it has been an obligation to submit microarray experiment data to public repositories for publishing the experimental results, collecting and storing the data is an essential step in microarray study. Implemented with H2 DBMS as the backend storage, Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which is MIAME compliant (Minimal Informa... Registration not required.
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MUSTER (MUlti-Sources ThreadER) is a new protein threading algorithm to identify the template structures from the PDB library. It generate sequence-template alignments by combining sequence profile-profile alignment with multiple structural information. References: S. Wu, Y. Zhang. MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins: Structure, Function, and Bioinformatics 2008; 72: 547-556. Registration not required.
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This web site allows you to generate random numbers from a Gaussian distribution under a given mean and standard deviation. Registration not required.
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The CRG International PhD programme in Barcelona aims to provide graduate students from all over the world with the possibility for training and doing research in the attractive scientific environment of the CRG, which is part of the Barcelona Biomedical Research Park (PRBB). Our resources, facilities, and staff provide the necessary technical support for the research projects and promote high quality training for graduate students. Registration not required.
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The European Collection of Authenticated Cell Cultures (ECACC) is one of four Culture Collections of the UK Health Security Agency. We supply authenticated and quality controlled cell lines, nucleic acids and induced Pluripotent Stem Cells (iPSCs). Registration not required.
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The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes. It's a free and open source standalone Java 1.4 application. Registration not required.
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JaMBW, the Java based Molecular Biologist's Workbench, is an online platform that had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use. Registration not required.
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The genome-wide association study (GWAS) publications listed in this catalog establish genetic associations between hundreds of genomic loci and complex (multigenic)traits, many of them diseases. Only those attempting to assay at least 100,000 single nucleotide polymorphisms (SNPs) in the initial stage, are included here. Registration not required.
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SEGMER is a segmental threading algorithm designed to recoginzing substructure motifs from the Protein Data Bank (PDB) library. It first splits target sequences into segments which consists of 2-4 consecutive or non-consecutive secondary structure elements (alpha-helix, beta-strand). The sequence segments are then threaded through the PDB to identify conserved substructures. It often identifies better conserved structure motifs than the whole-chain threading methods, especially when there is no ... Registration not required.
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MM-align is designed to structurally align multimeric protein complexes using heuristic iteration of dynamic programming based on TM-score rotation matrix. The multple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignment prevented. The alignment on interface structures can be enhenced by MM-align by an interface-specific weighting factor. A TM-score is reported for assessing the structural similarity of two complexes. Refere... Registration not required.
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PolyPhen-2 (Polymorphism Phenotyping v2) is a tool which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. Registration not required.
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The Atlas present and interactive view of histologial images of human body. In each topic, you will find a laboratory exercise, and brief description of the histological material. Click on the highlighted terms to display the histological images. Registration not required.
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The Integrated Risk Information System (IRIS) is a human health assessment program that evaluates quantitative and qualitative risk information on effects that may result from exposure to environmental contaminants. The information in IRIS is intended for those without extensive training in toxicology, but with some knowledge of health sciences. Registration not required.
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Confocal Microscopy tutorial (University of Helsinki) does not copy all the theoretical and technical details of confocal microscopy, instead, it delineate the outline about how confocal microscope works, and some basic concepts that are important for a user to understand or decide which button to press, which knob to turn, etc.. Registration not required.
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Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is previously known as mapass2. Registration not required.
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"Time Estimation for Bacteria Growth" web application is important for the preparation of chemical- or electro-competent cells and protein expression. The program may be used also for other organisms in the logarithmic stage of growth. It is possible to evaluate the precision of prognosis Registration not required.
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The Common Fund's Genotype-Tissue Expression (GTEx) program aims to map all sites in the human genome where sequence variation quantitatively affects gene expression and regulation in multiple tissues, providing valuable insights into the mechanisms of gene regulation and its disease-related perturbations. Registration not required.
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Icy is a collaborative bioimage informatics platform that combines a community website for contributing and sharing tools and material, and software with a high-end visual programming framework for seamless development of sophisticated imaging workflows.It offers unique features for behavioral analysis, cell segmentation and cell tracking, Registration not required.
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Category: Gene expression, Biomedical communities
International Human Epigenome Consortium (IHEC) allows: Epigenome
The International Human Epigenome Consortium (IHEC) is a global consortium with the primary goal of providing free access to high-resolution reference human epigenome maps for normal and disease cell types to the research community. Registration required.
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FANTOM is a large international consortium led by Japanese RIKEN that releases the first comprehensive map of gene activity across the human body. FANTOM5 has been mapping which genes are active in virtually all cell types across the human body, and the regions which determine where the genes are read from the genome. An associated data processing and visualization web system, Zenbu, enables researchers to quickly and easily integrate, visualize and compare large amounts of genomic information r... Registration not required.
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Although addressed to pet rats, this web site is filled up with behavioural, physiological and health issues that can be of help to researchers working with laboratory rats. Registration not required.
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The Goodness-of-fit test is calculated for a table 2 x C (max 14 column). The sum of values should be the same for observed and expected row. Therefore, expected values should be calculated using the sum of observed values. Registration not required.
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The Genome database (NCBI) provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. The database is organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids and includes complete chromosomes, organelles and plasmids as well as draft genome assemblies. Registration not required.
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The aim of MIQE,is to provide specifications for the minimum information that must be reported for a qPCR experiment in order to ensure its relevance, accuracy, correct interpretation and repeatability. Registration not required.
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The ArrayExpress Archive (EMBL-EBI) is a database of functional genomics experiments including gene expression where you can query and download data collected to MIAME and MINSEQE standards. Registration not required.
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The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research. Its goal is the establishment of a Rat Genome Database, to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other p... Registration not required.
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Description not available. Registration not required.
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A database that collects, encodes and makes accessible current data on human genetic variation effect on drug response, gene–drug–disease relationships (literature curation), key genes and drug pathways. The database also contains drugs with annotations related to some pharmacokinetic properties. Registration not required.
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OpenMS is an open-source software C++ library for LC/MS data management and analyses, developed by researchers at three German Universities in Tübingen, Berlin and Saarbrücken. It offers an infrastructure for the development of mass spectrometry related software. OpenMS is free software available under the LGPL. Registration not required.
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SVMSEQ is a new algorithm for protein residue-residue contact prediction using Support Vector Machines. References: S. Wu, Y. Zhang. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics, vol 24, 924-931 (2008). Registration not required.
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An Online Catalog of Human Genes and Genetic Disorders. OMIM is supported by a grant from NHGRI. Registration not required.
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GATK (Broad Institute) is a structured programming framework designed to enable rapid development of efficient and robust analysis tools for next-generation DNA sequencers and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. The GATK s a Java-based tool intended for use on Linux (and other POSIX compatible) platforms. Registration not required.
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Engine for Protein Similarity Search. SSearch is optimal for short peptides, GGsearch is optimal to find sequences similar (>80%) in length to the guery sequence, GLsearch is fine to match a short sequence or domain to the full protein. Registration not required.
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Ilastik (Interactive Learning and Segmentation Toolkit) is an open-source tool that enables researchers to train a machine-learning Random Forest classifier algorithm to identify which pixels of an image belong to which class of interest, based on the researcher providing example regions of each. Using it requires no experience in image processing. Registration not required.
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protocols for 2D and 3D quantification in microscopic images
Category: Imaging software, Imaging tutorials
Microscopy-based imaging is booming and the need for tools to retrieve quantitative data from images is urgent. This book provides simple but reliable tools to generate valid quantitative gene expression data, at the mRNA, protein and activity level, from microscopic images in relation to structures in cells, tissues and organs in 2D and 3D. Volumes, areas, lengths and numbers of cells and tissues can be calculated and related to these gene expression data while preserving the 2D and 3D morpholo... Registration not required.
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Rapid access to internationally peer reviewed information on chemicals commonly used throughout the world, which may also occur as contaminants in the environment and food. It consolidates information from a number of intergovernmental organizations whose goal it is to assist in the sound management of chemicals. Registration not required.
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List of sites with large collections of Material Safety Data sheets (MSDS). Registration not required.
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A brief methodological description of the main technologies used in biomedical labs Registration not required.
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HERVd (Human Endogenous Retrovirus DB) is a database compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. It is a relatively simple and fast environment for screening human genome for endogenous retrovirus. Registration not required.
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Gypsy Database (GyDB) is an open editable database devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (Llorens et al., Nucleic Acids Res 39:D70, 2011). Registration not required.
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The DrugBank database contains extensive data on the nomenclature, ontology, chemistry, structure, function, action, pharmacology, pharmacokinetics, metabolism and pharmaceutical properties of both small molecule and large molecule (biotech) drugs. It also contains comprehensive information on the target diseases, proteins, genes and organisms on which these drugs act. Registration not required.
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GeneTests Web site is a publicly funded medical genetics information resource developed for physicians, other healthcare providers, and researchers, available at no cost to all interested persons. Registration not required.
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TM-score is an algorithm to calculate the topological similarity of two protein structures. It can be used to quantitatively access the quality of protein structure predictions relative to the native. Because TM-score weights the close matches stronger than the distant matches, TM-score is more sensitive to the global topology of structures than the often-used root-mean-square deviation (RMSD). References: Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure temp... Registration not required.
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In this site it is possible to calculate online Cohen's d and effect size correlation r Registration not required.
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VAAST (the Variant Annotation, Analysis and Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. Registration required.
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The cBio Cancer Genomics Portal provides visualization and analysis for working with data from TCGA and other data sets and provides download of large-scale cancer genomics data sets. You can query this user-friendly portals maintained by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center by entering the name of one or more genes. The output is a list of cancer studies of different tumor types; click on a study, and then on View Cancer Study Details, to call up a graphic... Registration not required.
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A collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools. The Allen Brain Atlas website contains a downloadable 3-D interactive Brain explorer for locations of gene expression. Users can delineate networks and pathways using this application by connecting regions that co-express a certain gene. Registration not required.
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Bisque (Bio-Image Semantic Query User Environment) is web-based open-source client-server project developed for the exchange and exploration of biological images. The Bisque system supports several areas useful for imaging researchers from image capture to image analsysis and querying. Registration required.
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The site proviedes an input form for creating primers around the Open Reading Frame of cDNAs. For primer design, the Primer3 program is used. The input file is a list of GenBank sequences. Registration not required.
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AltAnalyze is an easy-to-use application for microarry and RNA-Seq analysis. For splicing sensitive platforms, AltAnalyze will assess alternative exon expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, AltAnalyze provides comprehensive methods for conventional arrays (RMA summarization, QC, statistics, annotation, clustering, lineage characterization and gene-set enrichement). Registration not required.
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MassBank is the first public repository of mass spectral data for sharing them among scientific research community. MassBank data are useful for the chemical identification and structure elucidation of chemical comounds detected by mass spectrometry. MassBank system is originally designed for public sharing of reference mass spectra for metabolite identification. It is also useful for their in-house or local sharing. Recently it finds another application; sharing mass spectra of unknown metabo... Registration not required.
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This tool calculates a set of confidence intervals for the entered binomial trial result - the number of trials and the number of successes. Registration not required.
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International PhD program in Basic and Applied Molecular Life Sciences: Biochemistry, Cell Biology, Molecular Biology, Genetics and Evolution Plant Biology
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DoCM is database of curated mutations in cancer, an open-source, openly licensed resource to enable the cancer research community to aggregate, store, and track biologically important cancer variants with provenance supported by the literature (see Ainscough BY et al., Nat Meth 13:806, 2016) Registration not required.
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The platform SourceData, an initiative by EMBO, is based on annotation of the figures in papers in a way thatbis machine readable and therefore searchable. SourceData is an openly accessible and easily applicable data discovery tool allowing biomedical scientists to share figures and the underlying source data in a way that is machine-readable. SourceData provides a novel platform for researchers who wish to make their publications discoverable based on their data content, to find specific data,... Registration not required.
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DeepL is a freely available translation service based on neural machine learning capable of translating to and from seven major European languages. It provides a natural translation that comes closer to that of a trained translatoe and it does particularly well with technical text. Registration not required.
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Free Statistics Calculators from Daniel Soper is a comprehensive, easy to navigate, well organized and well presented site to perform several statistical calculi Registration not required.
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JBrowse is a fast and full-featured scalable genome browser built completely with JavaScript and HTML5. It can run on your desktop, or be embedded in your website (see Bues et al., Genome Biol 17, 66 (2016) doi:10.1186/s13059-016-0924-1). Registration not required.
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This utility calculates confidence limits for a population proportion for a specified level of confidence using various methods (Wilson, Copper-Pearson exact, Jeffreys, etc.). Registration not required.
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VIPERdb is a database for icosahedral virus capsid structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. Registration not required.
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searchable collection of complete and incomplete large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms
Category: Gene information search
The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organism-specific overviews that function as portals from which all projects in the database pertaining to that organism can be browsed and retrieved (see Figure 1). For example, you will find all information regarding the human genome project on this pro... Registration not required.
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Guidelines for the care and use of laboratory animals, from the Office of Animal Care and Use (OACU) program of the National Institutes of Health (NIH. Registration not required.
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The NIOSH Pocket Guide to Chemical Hazards (NPG) presents key information and data in abbreviated or tabular form for chemicals or substance groupings (e.g. cyanides, fluorides, manganese compounds) that are found in the work environment. Registration not required.
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SNPedia is a wiki investigating human genetics. SNPedia shares information about the effects of variations in DNA, citing peer-reviewed scientific publications. It is used by Promethease to analyze and help explain your DNA Registration not required.
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Virtual Laboratories in Probability and Statistics provide free, high quality, interactive, web-based resources for students and teachers of probability and statistics. Registration not required.
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Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). Registration not required.
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MSight, created by the Proteome Informatics Group, was specifically developed for the 2-D representation of mass spectra along with data from the separation step. The software allows graphical exploration inside huge dataset and gives the scientist access to information that previously was hidden. Registration required.
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dbCRID is a curated database of human chromosome rearrangements and associated diseases Registration not required.
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This page performs logistic regression, in which a dichotomous outcome is predicted by one or more variables. The program generates the coefficients of a prediction formula, and odds ratios. Data can be copied and pasted from files. Registration not required.
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This page analyzes survival-time data by the method of Proportional Hazards regression (Cox). Given survival times, final status (alive or dead), and one or more covariates, it produces a baseline survival curve and covariate coefficient estimates with their standard errors, confidence intervals, and significance levels. Registration not required.
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PostdocJobs.com (or Postdoc.com) is the first niche recruiting channel to bring together recent Ph.D.s, professors, research institutions and other employers to find a good match. Over 1,000 universities, companies, research institutions and government agencies worldwide use our service for recruiting talented postdocs and scientists. Each month, over 100,000 Ph.D.s visit our website and seek postdoctoral opportunities. Jobs posted on our website are normally viewed 2,000 to over 5,000 times. Po... Registration required.
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The standard MS/MS experiment starts by digesting the proteins into peptides with an enzyme such as trypsin. USe Protein Digestor to see what peptides will result from digesting a protein. Registration not required.
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BSpred is a neural network based algorithm for predicting binding site of proteins from amino acid sequences. The algorithm was extensively trained on the sequence-based features including protein sequence profile, secondary structure prediction, and hydrophobicity scales of amino acids. References: S Mukherjee, Y Zhang Protein-protein complex structure prediction by multimeric threading and template recombination. Structure, in press (2011). Registration not required.
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TopHat is a Linux or OS X program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is designed to work with reads produced by the Illumina Genome Analyzer, although it was successful used with reads from other technologies. TopHat aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. It requires Bowtie, SAMtools an Python ... Registration not required.
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SIFT (Sorting Intolerant From Tolerant) predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. Registration not required.
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This web site provides short and effective free statistical lectures and videos. Registration not required.
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BrowserGenome is a web-based deep-sequencing data-analysis platform offering barcode deconvolution, read mapping, real-time data visualization, transcript-count analysis and data normalization. BrowserGenome is specifically focused on the evaluation of mRNA-seq data, but it can easily be extended to other applications (Schmid-Burgk JL, Hornung V, Nature Meth 12:1001, 2015).
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The Antibody Resource Page is a guide designed by scientists for scientists to find companies that sell custom monoclonal, polyclonal, and catalogue antibodies. Registration not required.
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PDBsum provides an at-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.
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It allows to examine pathological sections at different magnifications as under a microscope Registration required.
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Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments. Registration not required.
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Lucy was designed and written at The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute), and it has been used here for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence da... Registration not required.
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Infernal (inference of RNA alignments) is a software package for searching DNA sequence databases for RNA structure and sequence similarities. It allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments. Registration not required.
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Rfam is a collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format. In conjunction with the Infernal software package, Rfam covariance models (CMs) can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families. Registration not required.
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SRA stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, Helicos Heliscope®, Complete Genomics®, and others Registration not required.
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COXPRESdb (coexpressed gene database) represents the coexpression relationship for human, mouse, rat, chicken, zebrafish, fly and nematoda. COXPRESdb can help researchers to clarify the functional and regulatory networks of genes in a broad array of animal species. Registration not required.
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Category: Calculators and converters
Speed of Rotation to Relative Centrifuge Force allows: convert the speed of centrifugation in relative centrifuge force
This program helps to convert the speed of centrifugation in relative centrifuge force. The radius of rotor should be known for the calculation. Registration not required.
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PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs). In addition to providing an extensive, manually curated phosphorylation site database, other commonly studied PTMs are included in PSP. Registration not required.
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X!Tandem is a very fast seach engine which searches for matches of MS/MS spectra to a protein database. X!Tandem is free to use on the web or to download. X!Tandem works in conjunction with thegpm.org and can take advantage of the information gleaned from previous searches. It has an option, PPP, which searches first only the peptides that have been found most frequently for each protein Registration not required.
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ANGLOR is a machine-learning based algorithm for ab initio prediction of protein backbone torsion angles. For a given amino acid sequence, the real-value backbone torsion angles (phi and psi) for each residue are predicted by the combination of the neural network training and the support vector machine. References: S. Wu, Y. Zhang. ANGLOR: A Composite Machine-Learning Algorithm for Protein Backbone Torsion Angle Prediction. PLoS ONE 2008; 3: e3400. Registration not required.
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Genomic Evolutionary Rate Profiling (GERP) identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Registration not required.
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Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC)facilitates access to a growing number of neuroimaging tools and resources. Continuing to identify existing software tools and resources valuable to this community, NITRC’s goal is to support its researchers dedicated to enhancing, adopting, distributing, and contributing to the evolution of neuroimaging analysis tools and resources. Registration not required.
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Fiji (Fiji is Just ImageJ) is an image processing package based on ImageJ and is currently the tool of choice in analysis of electron- microscopy data.Fiji is effectively an open-source distribution of ImageJ that includes a great variety of organized libraries, plugins relevant for biological research Registration not required.
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ColorBrewer is an online tool from Pennsylvania State University designed to help people select good color schemes for maps and other graphics. Registration not required.
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ITK-SNAP is an interactive software application that allows users to navigate three-dimensional medical images, manually delineate anatomical regions of interest, and perform automatic image segmentation. It provides semi-automatic segmentation using active contour methods, as well as manual delineation and image navigation. Indeed, the main purpose is to make it easy for researchers to delineate anatomical structures and regions of interest in imaging data Registration not required.
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The academy provides concise videos that present the practical information needed to establish and sustain an effective safety culture. The detailed, engaging videos cover topics ranging from selecting the correct gloves for a task to building strong safety leadership. The modules cover four major areas: safety orientation and training, which proposes general approaches to avoiding incidents and injuries; specialized topics, which covers issues that arise in working with particular kinds of equi... Registration required.
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discuss online published papers
Category: Literature search
PubPeer allows: to discuss papers
PubPeer is a forum for free-ranging discussion of published papers. It allows to search for scientific articles and to post anonymous comments on them. See Science 341:606, 2013) Registration not required.
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Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language and most bioconductor components are distributed as R packages, which are add-on modules for R. It is open source and open development. Boconductor core team is based primarily at the Fred Hutchinson Cancer Research Center (http://en.wikipedia.org/wiki/Bioconductor) Registration not required.
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The International Max Planck Research School for Molecular and Cellular Life Sciences: From Biology to Medicine, (IMPRS-LS), jointly conducted by Munich based Max Planck Institutes and Universities, is an internationally recognized center of scientific and educational excellence. Registration required.
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The International PhD Programme at the MDC was established in 2003 as collaboration of the Max Delbrück Centre for Molecular Medicine (MDC) and the Humboldt-Universität zu Berlin (HU). The graduate school currently supports 350 PhD students, one third of whom come from abroad. Research areas include cancer biology, immunology, cardiovascular research, metabolic research, developmental biology, medical systems biology, bioinformatics, structural biology and molecular neurobiology. Registration not required.
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This website from Dr, Hossein Arsham of the University of Baltimora, offers the opportunity to calculate several probabilistic models and statistical analyses on line. Although mainly business oriented, is very useful also for biomedical scientists. Registration not required.
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VecScreen quickly identifies contaminating vectors in your sequence. VecScreen is a system that quickly finds segments of a nucleic acid sequence that may be of vector origin. It helps researchers identify and remove any segments of vector origin before they analyze or submit sequences. Registration not required.
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Well organized web site with a multitude of statistical tests. Registration not required.
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Fully-funded four year PhD programme in an international scientific environment. The Copenhagen Bioscience PhD programme recruits up to 16 motivated international students annually to launch their careers in the vibrant scientific environment of the Novo Nordisk Foundation Research Centers in Copenhagen.
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A database of behavioral and structural anatomy of Caenorhabditis Elegans Registration not required.
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The TRIP Database is a clinical search engine designed to allow clinicians to quickly find answers to their clinical questions using the best available evidence. The creation of the TRIP Database allowed the simultaneous searching of multiple sites, hence speeding up the question answering process. The evolution of the TRIP Database has been guided by the desire to answer real clinical questions using the principles of evidence based medicine. TRIP Database Ltd’s involvement in clinical quest... Registration not required.
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OECD Series on Principles of Good Laboratory Practice and Compliance Monitoring. List of documents to be retrieved in pdf format. Registration not required.
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commercially available antibodies for research purposes
Category: Biomedical products search
AbMiner (NIH) is a tool that allows users to search for appropriate, commercially available antibodies for research purposes, and to match each antibody to its respective genomic identifiers. The unique feature of this anitibody collection is that all antibodies are screened by Western blot and the results are provided in AbMiner. The sample used for antibody screening was a pool of the NCI-60 cancer cell lines, comprised of 60 different cell lines from 9 different tissues of origin (more info?)... Registration not required.
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Orphanet is a database of information on rare diseases and orphan drugs for all publics. Its aim is to contribute to the improvement of the diagnosis, care and treatment of patients with rare diseases. Orphanet includes a Professional Encyclopaedia, which is expert-authored and peer-reviewed, a Patient Encyclopaedia and a Directory of expert Services. This Directory includes information on relevant clinics, clinical laboratories, research activities and patient organisations. Registration not required.
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The National Comprehensive Cancer Network® (NCCN®) is a not-for-profit alliance of 31 leading cancer centers devoted to patient care, research, and education. NCCN is dedicated to improving and facilitating quality, effective, equitable, and accessible cancer care so all patients can live better lives. Registration not required.
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The site provides full of information on heart, lung and blood diseases for patients and professionals. Registration not required.
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MicroArray Genome Imaging and Clustering Tool (MAGIC Tool)
Category: DNA microarray software
MAGIC Tool is an integrated microarray data analysis free software with open source. Registration not required.
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The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing. Registration not required.
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The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the Seattle Proteomics Center. Registration not required.
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BSP-SLIM is a blind molecular docking method on low-resolution protein structures. The method first identifies putative ligand binding sites by structurally matching the target to the template holo-structures. The ligand-protein docking conformation is then constructed by local shape and chemical feature complementarities between ligand and the negative image of binding pockets. Registration not required.
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NW-align is simple and robust alignment program for protein sequence-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. The mutation matrix is from BLOSUM62 with gap openning penaly=-11 and gap extension panalty=-1. The source code of this program can be downloaded at the bottom of the NW-align website, which can be easily modified for different purposes. Registration not required.
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EDTSurf is a open source program to construct triangulated surfaces for macromolecules. It can generate three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface (solvent-excluded surface), and identify cavities which are inside of macromolecules. Registration not required.
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The Cancer Genome Atlas (TCGA) Data Portal provides a platform to retrieve information on somatic mutations, or other data types such as copy number, DNA methylation, and gene expression, for a number of tumor types. It contains clinical information, genomic characterization data, and high-throughput sequencing analysis of the tumor genomes.TCGA updates as soon as new data become available. Registration not required.
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Stan is a probabilistic programming language implementing statistical inference with Markov chain Monte Carlo sampling (NUTS, HMC) and ptimization-based point estimation (BFGS) Stan interfaces with the most popular data analysis languages (R, Python, shell, MATLAB, Julia, Stata) and runs on all major platforms (Linux, Mac, Windows).Stan is freedom-respecting, open-source software. Registration not required.
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This site provides an interactive short course on experimental design for research scientists working with laboratory animals. The aim is to reduce the number of animals which are used, improve the quality of the science and save time, money and other scientific resources. Registration not required.
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SRMAtlas is a database of selected reaction monitoring (SRM) transitions and mass spectra derived from synthetic peptides created for SRM assay development and analyzed on the types of mass spectrometers most frequently used for SRM/MRM experiments— triple quadrupole, Orbitrap, and quadrupole–time-offlight instruments. Users can search SRMAtlas using a protein accession number or peptide sequence, or by uploading a text file containing a list of protein names or peptide sequences Registration not required.
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CZ CELLxGENE from The Chan Zuckerberg Initiative, is a free-to-use online data portal collecting free and open-source tools for finding, querying, analysing, downloading and publishing single-cell data. As of April 2024, it includes some 85 million single cells 248 and 1,317 data sets covering 844 cell types. Most of the data represent single-cell RNA sequencing information from healthy human tissues, but non-human and cell-line data, as well as molecular-profiling data obtained using spatial tr... Registration not required.
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The Comprehensive Enzyme Information System Registration not required.
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The Research Institute of Molecular Pathology (IMP) is a basic biomedical research center sponsored largely by the pharmaceutical company Boehringer Ingelheim, and located in the Campus Vienna Biocenter (VBC. Registration not required.
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REACTOME is an online, expert-authored, peer-reviewed knowledgebase of human reactions and pathways encompassing many areas of human biology. It functions as a data mining resource and electronic textbook. Registration not required.
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BrainMaps is an interactive multiresolution next-generation brain atlas that is based on over 20 million megapixels of sub-micron resolution, annotated, scanned images of serial sections of both primate and non-primate brains and that is integrated with a high-speed database for querying and retrieving data about brain structure and function over the internet. Registration not required.
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eSkeletons provides an interactive environment in which to examine and learn about skeletal anatomy. The purpose of this site is to enable you to view the bones of both human and non-human primates and to gather information about them from our osteology database. Registration not required.
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LOVD provides a flexible, freely available tool for Gene-centered collection and display of DNA variations.A flexible, freely available tool for genomic variant and phenotype collection, display and curation. LOVD allows both patient-centered and gene-centered views. Registration not required.
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Cyflogic is a flow cytometry data analysis tool for Microsoft Windows enviroment. It has all regular analysis capabilities, such as dot plot, histogram and statistics. Registration required.
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This is the high throughput PCR primer design software that is used at the J. Craig Venter Institute. See: Li K, et al. Novel computational methods for increasing PCR primer design effectiveness in directed sequencing. BMC Bioinformatics 2008, 9:191. Registration not required.
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Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences Registration not required.
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AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 30-untranslated regions (UTRs. In its current version AREsite uses Ensembl release 56 as data basis (Gruber et al., Nucleic Acid Res 39:D66, 2011). Registration not required.
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REMO is a new algorithm for constructing protein atomic structures from C-alpha traces by optimizing the backbone hydrogen-bonding networks. References: Yunqi Li and Yang Zhang. REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins, 2009, 76: 665-676. Registration not required.
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COTH (CO-THreader) is a multiple-chain protein threading algorithm to identify and recombine the protein complex structures from both tertiary and complex structure libraries. It first generates complex query-template alignments by sequence profile-profile alignment assisted by the ab initio binding-site predictions from BSpred. The monomer structures from tertiary template library are then combined into the complex framework by structure superposition. Registration not required.
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PROVEAN (Protein Variation Effect Analyzer) is a software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify nonsynonymous or indel variants that are predicted to be functionally important. The performance of PROVEAN is comparable to popular tools such as SIFT or PolyPhen-2. Registration not required.
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ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others).ANNOVAR is written in Perl and can be run as a standalone application on diverse hardware systems where standard Perl modules are installed. Registration not required.
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RegulomeDB identifies binding sites and other elements in non-coding DNA.Use RegulomeDB to identify DNA features and regulatory elements in non-coding regions of the human genome by entering dbSNP IDs, Single nucleotides, a chromosomal region. Registration not required.
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The UC Santa Cruz Xena (Cancer Genomics Browser) is a suite of web-based tools to visualize, integrate and analyze cancer genomics and its associated clinical data. It displays side-by-side heat maps of genomic data such as gene expression and copy number changes, and clinical data for a long list of cancer data sets, along with a feature that enables researchers to look for genomic variations that correlate with clinical outcomes. Registration not required.
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The International Cancer Genome Consortium (ICGC) Data Portal allows researchers to access mutation and expression data for specific genes, or to scroll through data sets collected so far on 24 types of cancers by project teams in 9 countries. It represents a good starting point to check for known mutations and other aberrations in a gene of interest. Registration not required.
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MyBioSoftware provides a list with links of several software tools used in Bioinformatics. Registration not required.
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Circadian rhythms drive daily oscillations in many different physiologies, including blood pressure, body temperature and behavior. In addition, disruptions of the circadian clock contribute to the pathologies of metabolic disorders as well as cardiovascular disease and cancer. Our lab is interested in the mechanism by which circadian oscillations drive these processes. We are using microarray analysis in combination with curve-fitting and Fourier-transform based statistical algorithms to search... Registration not required.
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Category: Statistics software
Minim: allocation by minimisation in clinical trials allows: Random, clinical trials
Minim is an MS-DOS program for running minimisation in clinical trials. For Windows 7, an emulation program called DOSBox has been used successfully to run Minim. Registration not required.
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ClinVar is a unified, curated, publicly available database about sequence variation and its relationship to health. It aggregates information about sequence variation and its relationship to human health. Registration not required.
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The database provides enhancer annotation in nine species, including human (hg19), mouse (mm9), fly (dm3), worm (ce10), zebrafish (danRer10), rat (rn5), yeast (sacCer3), chicken (galGal4), and boar (susScr3)(Andersson et al.Nature 507,455–461, 2014, Gao & Qian, Nucleic Acids Research, 48, D58, 2020). Registration not required.
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The International Cell Line Authentication Committee aims to make false or misidentified cell lines more visible, and promote awareness and authentication testing as effective ways to combat the problem. It provides a database listing cell lines that are currently known to be cross-contaminated or misidentified. Registration not required.
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The calculator (from University college, London) helps in calculating the probability that a results associated to asignificant P value, after doing a single unbiased experiment, is a false positive. False positive risk (FPR) is defined here as the probability that a result which is significant at a specified P value, is a false positive result. Registration not required.
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The web site provide a web application to construct high-quality estimation graphics, that displays an experimental dataset’s complete statistical information. Plots can be saved in image formats suitable for publication (PNG and SVG).With the web application and open-source libraries, DABEST caters to both scripting and spreadsheet workflows, empowering all researchers to rapidly adopt better data-analysis practices (see Ho et al., Nature Methods 16:565,2019). Registration not required.
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These utilities can be used to calculate required sample sizes to estimate a population mean or proportion, to detect significant differences between two means or two proportions or to estimate a true herd-level prevalence. Registration not required.
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These utilities can be used to calculate confidence limits and summarise a variety of categorical or continuous data. Registration not required.
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The Life Science and Med Tech track of the Full-time Business Management Master’s course in Bologna Business School is intended for young graduates wishing to start a managerial career in pharmaceutical and biotechnological sectors.The pharmaceutical, health and medical machineries and equipment industry is a strategical asset of international economy as well as one of the sectors in which the numbers are increasing both on the employment front and as regards investment and research.
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QUAREP-LiMi aims to define standard operating procedures and tools for device monitoring, benchmarking and quality management of light microscopy instruments and images that are aligned with existing ISO standards, as well as to develop in liaison with ISO or other stakeholders (corporate partners, funders and publishers) a community-based consensus around microscope and image data QC (see Boehm et al, Nature Meth 18:1418, 2021) Registration not required.
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The CPDB is an international resource of the results of thousands of chronic, long-term animal cancer tests on chemicals. The CPDB provides easy access to the bioassay literature, with qualitative and quantitative analyses of both positive and negative experiments that have been published over the past 50 years in the general literature through 2001 and by the National Cancer Institute/National Toxicology Program through 2004. Registration not required.
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NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines™) Registration required.
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Interactive version of IUPAC Compendium of Chemical Terminology, informally known as the Gold Book. On these pages you will find a browsable, interactive version of this publication. Registration not required.
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Description not available. Registration not required.
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In this site, maintained by the Public Health Agency of Canada, it's possible to retrieve essential information on the most common infectious diseases. Registration not required.
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ALFRED has been designed to make allele frequency data on anthropologically defined human population samples readily available to the scientific community and to link these polymorphism data to the molecular genetics-human genome databases.ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. Registration not required.
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The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Registration not required.
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SGDTM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast. Registration not required.
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The purpose of the MAQC project is to provide quality control tools to the microarray community in order to avoid procedural failures and to develop guidelines for microarray data analysis by providing the public with large reference datasets along with readily accessible reference RNA samples. Registration not required.
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Goals of Immunopaedia are to disseminate immunology information and to facilitate improvement in clinical practice. It uses a clinical case–based perspective to target interns in multiple clinical specialities. The Web site consists of three key components: Clinical Cases, Immunology Learning, and Treatment and Diagnostics. Registration required.
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Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Registration not required.
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MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included wit... Registration not required.
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Sybil is a web-based software package for comparative genomics. It was developed by the Bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute and Institute for Genome Sciences (IGS) at the University of Maryland Baltimore's School of Medicine. The project has been funded by a variety of sources including: The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Center... Registration not required.
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This graphics-rich site from Thomas Poon and Bradford Mundy More provides virtual flash cards with a dozen animated tutorials cover everything from drawing chemical structures, to the basics of mass spectrometry, to the reactions of aldehydes and ketones. Registration not required.
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The Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.8 comprises a full Knowledgebase update to the sixth version of our original web-accessible programs. DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
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G*Power is a tool to compute statistical power analyses for many different t tests, F tests, χ2 tests, z tests and some exact tests. G*Power can also be used to compute effect sizes and to display graphically the results of power analyses. Windows and Mac OS versions. Registration not required.
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SILVA is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data, free for academic use. SILVA provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Registration not required.
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The ICGC Goal is to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe. ICGC has been organized as an international effort to harmonize the large number of projects that are now, or shortly will be, underway that have the common aim of elucidating comprehensively the genomic changes present in many forms of cancer. Registration not required.
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ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm, and to the functional annotation of predicted isoforms (Martelli et al., Nucleic Acids Res 39:D80, 2011) Registration not required.
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ClinicalTrials.gov is a registry of federally and privately supported clinical trials conducted in the United States and around the world that offers up-to-date information for locating federally and privately supported clinical trials for a wide range of diseases and conditions. Registration not required.
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Free online Acronyms and Abbreviations Dictionary. Quickly define the meaning for all acronyms and abbreviations Registration not required.
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SPICKER is a clustering algorithm to identify the near-native models from a pool of protein structure decoys. The cluster is defined by the pair-wise RMSD metrics of the structural decoys. References: Y. Zhang, J. Skolnick, SPICKER: Approach to clustering protein structures for near-native model selection, Journal of Computational Chemistry, 2004 25: 865-871. Registration not required.
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The Mouse Genomes Project aims to use new sequencing technologies to sequence the genomes of 17 key mouse strains. We are releasing the raw sequence data, SNPs, short indels, structural variants and assemblies of each strain. Registration not required.
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BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads. Registration not required.
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Here you can view the current vacancies and find all of the information you need about working for the University of Cambridge, UK Registration not required.
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PHAST is a freely available software package (Cornell University) for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel).Like algorithms that assess protein-coding genes, they evaluate variants on the basis of how often the sequence changes between species
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From SourceForge
Category: Statistics software
MinimPy allows: Random, clinical trials
MinimPy is a desktop application program for sequential allocation of subjects to treatment groups in clinical trials by using the method of minimisation.It requires Python 2.7 with GTK libraries.
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National Toxicology Program
Category: Laboratory animals, Laboratory animal tutorials
This website from the US National Toxicology Program presents microscopic images of rodent organs and non-neoplastic lesions. The atlas is organized by organ system and is subdivided into chapters, each covering a single organ. Each chapter comprises a set of sections, each describing a single lesion. Each section includes histopathologic descriptions, high-quality images, diagnostic guideline recommendations, and references (Environmental Health Perspectives 122:A76, March 2014). Registration not required.
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TumorPortal, developed and maintained by the Broad Institute of Harvard and MIT, hosts a ‘pan-cancer’ data set from several tumor types. It provides visualization of computationally processed gene information. It shows which genes are mutated in many tumor samples and types. Registration not required.
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The Antibody Registry was created to give researchers a way to universally identify antibodies used in in the course of their research. The Antibody Registry assigns unique and persistent identifiers to each antibody so that they can be referenced within publications. Unlike antibody names or catalog numbers, these identifiers only point to a single antibody, so that the actual antibody used in your research research can be identified by humans and search engines. Registration not required.
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IRB Barcelona is a world-class research centre devoted to understanding fundamental questions about human health and disease. IRB Barcelona is not a University and cannot grant PhD degrees. Registration not required.
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ProDeGe is the first fully automated computational protocol for decontamination of genomes. The protocol uses public databases to detect contamination in agenome assembly, then groups contigs into “Clean” or “Contaminant” groups. ProDeGe spits out lists that users can read through to identify contaminants and determine what they mightbe.The standalone software is freely available and can be run on any system that has Perl, R, Prodigal and NCBI Blast installed. (Tennessen et al., ISME J. ... Registration required.
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Publons allows researchers to post online profiles with bios and peer-review histories. Users receive Publons “merits” for their reviews and are incentivized by a leaderboard, with quarterly awards for the top three reviewers overall and the top reviewers in particular fields and institutions, Registration required.
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Enhancing the QUAlity and Transparency Of health Research
Category: Biomedical guidelines, Biomedical journals
The site contains a comprehensive searchable database of reporting guidelines and also links to other resources relevant to research reporting (Randomised trials; Observational studies; Systematic reviews; Study protocols; Diagnostic/prognostic studies; Case reports; Clinical practice guidelines; Qualitative research; Animal pre-clinical studies; Quality improvement studies; Economic evaluation). Registration not required.
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Consente di fare calcoli per semplici diluizioni. Si marca con il quadratino nero la voce da calcolare. Registration not required.
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The site is intended for use by epidemiologists and researchers involved in estimating disease prevalence or demonstrating freedom from disease through structured surveys, or in other epidemiological applications. Registration not required.
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Description not available. Registration not required.
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Instruct links many major structural-biology centres in Europe, allowing researchers to access a range of equipment and expertise in a single request. It has brought together representing all major infrastructure technologies that enable structure determination from macromolecular to atomic resolution of proteins, protein complexes and single particles. Registration required.
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List several sources of MSDSs available via the World Wide Web. Registration not required.
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CDC’s Office of Health and Safety list several information and links for for protecting workers and preventing exposures in biological laboratories. Printable as a *.pdf file. Registration not required.
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This site presents an introductory overview of GFP. Registration not required.
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The NIOSH Pocket Guide to Chemical Hazards (NPG) is intended as a source of general industrial hygiene information on several hundred chemicals/classes for workers, employers, and occupational health professionals. Registration not required.
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A Database of Drosophila Genes & Genomes Registration not required.
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This data base supported by NIH, provides international bibliographic information in the form of abstracts on dietary supplements. Registration not required.
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The Zebrafish Model Organism Database Registration not required.
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The purpose of the MAQC project is to provide quality control tools to the microarray community in order to avoid procedural failures and to develop guidelines for microarray data analysis by providing the public with large reference datasets along with readily accessible reference RNA samples. Registration not required.
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The LSRF solicits monies from industry, foundations and individuals to support postdoctoral fellowships in the life sciences. Each sponsor supports one or more designated individuals, chosen by the Foundation's Board on the basis of the merit of the proposed research and the quality of the individual's past performance, as judged by the Foundation's Peer Review Committee. Registration not required.
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The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regi... Registration not required.
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The National Human Genome Research Institute (NHGRI) model organism ENCyclopedia Of DNA Elements (modENCODE) Project will try to identify all of the sequence-based functional elements and the genome-wide patterns of regulatory interactions in the Caenorhabditis elegans and Drosophila melanogaster genome. Registration not required.
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NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs). Registration not required.
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The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), PDBe (Europe) and PDBj (Japan) whic act as data deposition, processing and distribution centers for PDB data (RP Josten et al, Nucleic Acid Res 39, D411, 2011). Registration not required.
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The Arabidopsis Gene Regulatory Information Server (AGRIS) is an information resource of Arabidopsis promoter sequences, transcription factors and their target genes. AGRIS provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thalian through the access to three interlinked databases, AtTFDB, AtcisDB and AtRegNet. Registration not required.
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The Participant Portal is the single-entry point for interactions with the research and innovation programmes of the European Commission. It offers you the possibility to use a great variety of services and tools that facilitate the monitoring and the management of your proposals and projects throughout their lifecycle. Registration required.
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FusionSeq programs are written in C and constitute a tri-modular computational framework to detect fusion transcripts from paired-end RNA-sequencing. Registration not required.
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Galaxy is an open, web-based platform for data intensive biomedical research, now available as a "cloud computing" resource Whether on this free public server or your own instance, you can perform, reproduce, and share complete analyses. Registration required.
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The Vertebrate Genome Annotation (VEGA) genome browser is a central repository for high quality manual annotation of vertebrate finished genome sequence. The majority of the annotation is from the HAVANA group at the Welcome Trust Sanger Institute. Registration not required.
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LRG sequence format has been designed for the specific purpose of gene variant reporting. LRGs have fixed sequences that are independent of the genome so that they provide a stable framework for reporting variants. The data base provides a single-file record containing a uniquely stable reference DNA sequence along with all relevant transcript and protein sequences essential to the description of gene variants.
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Resources provided by EMAP are the EMA Anatomy Atlas of Mouse Development and the EMAGE Gene Expression Database. The EMA Anatomy Atlas of Mouse Development uses embryological mouse models to provide a digital atlas of mouse development. EMAGE is a database of in situ gene expression data in the mouse embryo and an accompanying suite of tools to search and analyse the data.
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VarSifter is a graphical Java program designed to display, sort, filter, and generally sift variation data from massively parallel sequencing experiments. It is designed to read exome-scale variation data in either a tab-delimited text file with header, or an uncompressed VCF file. The program is written in Java, and should run on any platform with a current Java Virtual Machine. Registration not required.
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openBIS is an open, distributed system for managing biological information for Windows And Linux. The main goal is to support biological research data workflows from the source (i.e. the measurement instruments) to facilitate the process of answering biological questions by means of cross-domain queries against raw data, processed data, knowledge resources and its corresponding metadata. The openBIS software framework can be easily extended and has been customized for High Content Screening, Pro... Registration required.
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The open source SeqWare project is a portable software infrastructure designed to analyze massive genomics datasets produced by contemporary and emerging technologies, in particular Next Generation Sequencing (NGS) platforms. It consists of a comprehensive suite of infrastructure tools focused on enabling the end-to-end analysis of sequence data – from from raw base calling to analyzed variants ready for interpretation by users. SeqWare is designed to work in a 64-bit Linux environment. It can... Registration not required.
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IARC awards between eight to eleven new fellowships per year, depending on availability of funds. Fellowships are tenable at the IARC in Lyon, France working in a research Group. Applicants are eligible from any country. The IARC is particularly keen to promote the development of expertise in cancer research in low- and medium-resource countries by training postdoctoral researchers from these countries who can return to apply their new skills and expertise. Registration required.
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GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles. Registration not required.
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The Probes & Drugs aggregates publicly available information to help researchers select which chemicals to use. This portal is a public resource joining together focused libraries of bioactive compounds (probes, drugs, specific inhibitor sets etc.) with commercially available screening libraries. The purpose of the portal is to reflect the current state of bioactive compound space and to enable its exploration from different points of view. Registration not required.
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updated data and charts in Italy and in the other European countries
Category: COVID19
COVID infection updated data and charts in Italy and in the other European countries by the Sole24ore group. Registration not required.
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Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data, including the Novel coronavirus (2019-nCoV). It provides a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. The goal is to aid epidemiological understanding and improve outbreak response. Registration not required.
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Useful collection of simple and exhaustive tutorials for statistical testing and data presentation in biomedical publishing. Registration not required.
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Scitility’s tool Argos identifies work with authors who have a record of misconduct scientific publishers and also journals that are worst affected by fraudulent or dubious research papers. Argos is one of a growing number of research-integrity tools that look for red flags in paper (see: Richard Van Noorden, Nature, 634, 1023, 2024). Registration required.
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PDQ® Cancer Information Summaries: Pediatric Treatment Registration not required.
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The EST database (NCBI) is a collection of short single-read transcript sequences from GenBank. These sequences provide a resource to evaluate gene expression, find potential variation, and annotate genes. Registration not required.
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ICLAS (International Council for Laboratory Animal Science) is a scientific organization dedicated to advancing human and animal health by promoting the ethical care and use of animals in research worldwide. Registration required.
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The US Occupational safety & Health Administration, recognizing the unique characteristics of the laboratory workplace, has tailored a standard for occupational exposure to hazardous chemicals in laboratories. Registration not required.
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This site maintained by research labs at UCSD provide and introduction tu muscle physiology and design. Registration not required.
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The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. As a curated database, it collects genomic gain/loss information of individual cancer and leukemia cases, published in peer reviewed journals. Registration not required.
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The Berkeley Drosophila Genome Project (BDGP) is a consortium of the Drosophila Genome Center whose goals are are to finish the sequence of the euchromatic genome of Drosophila melanogaster to high quality and to generate and maintain biological annotations of this sequence. Registration not required.
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The National Human Genome Research Institute's (NHGRI) Ethical, Legal and Social Implications (ELSI) Research Program was established in 1990 as an integral part of the Human Genome Project (HGP) to foster basic and applied research on the ethical, legal and social implications of genetic and genomic research for individuals, families and communities. The ELSI Research Program funds and manages studies, and supports workshops, research consortia and policy conferences related to these topics. Registration not required.
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Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, it is possible edit pages in Proteopedia. Registration not required.
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This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid. Registration not required.
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This comprehensive organic chemistry Web text from William Reusch of Michigan State University in East Lansing can enlighten not only students but also working chemists who need a refresher on the details of a particular reaction (Science 303, 115,2004) Registration not required.
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SPIKE (Signaling Pathways Integrated Knowledge Enginestore, stores, organizes and allows retrieval of pathway information (A Paz et .a, Nucleic Acid Res 39, D793, 2011). Registration not required.
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The International Knockout Mouse Consortium (IKMC) is a scientific endeavour to produce a collection of mouse lines, each lacking a protein-coding gene, using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells.(M Ringwald, Nucleic Acid Res 39, D849, 2011). Registration not required.
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NIF is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet. Registration not required.
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HAAD is a computer algorithm for constructing hydrogen atoms from protein heavy-atom structures. The hydrgen is added by minimizing atomic overlap and encouraging hydrogen bonding. References: Yunqi Li, Roy Ambrish and Yang Zhang, HAAD: A Quick Algorithm for Accurate Prediction of Hydrogen Atoms in Protein Structures, PLoS One, 2009 4: e6701 Registration not required.
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MVP (Macromolecular Visualization and Processing) is a convenient tool for visualizing macromolecular structures and their derived information. It supports PDB format and EM density maps and has many drawing styles and color modes. It contains lots of convenient features, including computations of triangulated surfaces, depth, principal axes and estimate the secondary structures for protein structures etc. References: Dong Xu, Yang Zhang (2009) Generating Triangulated Macromolecular Surfaces by ... Registration not required.
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ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content. Registration not required.
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MedlinePlus (NIH National Library of Medicine)is a free Web site that provides consumer health information for patients, families, and Health care providers. MedlinePlus brings together information from NIH, other federal agencies, and reputable health information providers. MedlinePlus covers a wide range of health conditions and wellness issues, and includes key resources to inform patients about their health. Registration not required.
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The RDXplorer (Read Depth eXplorer) is a computational tool based on LINUX/UNIX/MAC OS X for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. It requires SAMtools and Python programming language v 2.6 or further. Registration not required.
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OsiriX is an open-source image processing software dedicated to DICOM images (".dcm" / ".DCM" extension) produced by imaging equipment (MRI, CT, PET, PET-CT, SPECT-CT, Ultrasounds, ...). It is available in 32-bit and 64-bit format and is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is at the same time a DICOM PACS workstation for imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D i... Registration not required.
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myIDP is an online application designed to guide early-career scientists through a confidential, rigorous process of introspection to create a customized career plan. myIDP provides an individual development plan (IDP) to explore career possibilities and set goals to follow the career path that fits you best. After the user has identified a long-term career goal, myIDP walks her or him through the process of setting short-term goals directed toward accumulating new skills and experiences importa... Registration required.
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PDQ (Physician Data Query) is the National Cancer Institute’s source of comprehensive cancer information. It contains peer-reviewed, evidence-based cancer information summaries on treatment, supportive care, screening, prevention, genetics, and complementary and alternative medicine Registration not required.
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ResearchMatch has a simple goal – to bring together two groups of people who are looking for one another: (1) people who are trying to find research studies, and (2) researchers who are looking for people to participate in their studies. It is a free and secure registry that has been developed by major academic institutions across the country who want to involve you in the mission of helping today’s studies make a real difference for everyone’s health in the future Registration required.
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The Cancer Genome Atlas (TCGA), a landmark cancer genomics program, molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. This joint effort between NCI and the National Human Genome Research Institute began in 2006, bringing together researchers from diverse disciplines and multiple institutions. Registration required.
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Software Carpentry is a volunteer organization whose members teach basic software skills to researchers in science, engineering, and medicine. Registration required.
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Mendeley is a free desktop and web tool for research and literature management. It acts as reference manager and academic social network for for managing and sharing research papers,discovering research data and collaborating on line (Singh, J Pharmacol Pharmacotherap 1:62, 2010). Registration required.
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Skyline is a freely-available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS and DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data.Skyline helps users select peptides and transitions based on mass spectra from their own experiments or imported from public proteomics data repositories (MacLean et al., Bioinform... Registration required.
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From Novartis Institutes for Biomedical Research. Program provides postdoctoral scholars with a unique opportunity to perform innovative, fundamental research in a pharmaceutical setting. Postdocs design and conduct their research with guidance from a principal investigator at Novartis, and an academic advisor where appropriate. Topics cover several topics vary from cancer research to immunology, regenerative medicine etc. Registration required.
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An open-access database of publicly available antibodies against human protein targets. The site features user and provider data on antibody efficacy in a range of biochemical and cell biological techniques--so you can find the right antibody for the right application Registration not required.
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PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. Registration required.
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The GTEx Consortium adopts a strategy called expression quantitative trait loci (eQTL) mapping that allows the researchers to generate a comprehensive catalogue of associations between genetic variation and gene expression across many tissues in many individuals. The processed data are available in this website (see: Nat Genet. 2013 June ; 45(6): 580–585; Ward & Gilad Nature 550:190, 2017). Registration not required.
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A protein knowledge-base. It includes entries on more than 20,000 proteins and nearly 200,000 posttranslational modifications. Registration not required.
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Biorender is a web-based tool designed for life-science and medical illustration, is like a feature-lite version of Illustrator. It features an extensive library of scalable ‘icons’ from across the life sciences and medicine; researchers can drop these onto a canvas and manipulate them as if they were circles or polygons. Biorender is mainly utilized by researchers for professional-level illustrated explainers of proposed models, experimental methods or biochemical pathways (see Jeffrey M Pe... Registration required.
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The goal of the Dependency Map (DepMap) portal is to empower the research community to make discoveries related to cancer vulnerabilities by providing open access to key cancer dependencies analytical and visualization tools. It would systematically map cancer vulnerabilities by perturbing genes and proteins across many cancer types as well as across clinical stages and settings. The Cancer Dependency Map would collect different data and ask different questions from sequencing projects by lookin... Registration not required.
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Master research International Registration not required.
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In this site it is possible to post a job search or to individuate position offering, from research scientist to professor, restricting per area and discipline. Registration not required.
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Il sito consente una ricerca di vari mastere di primo e secono livello in Italia
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The FCS-free Database (RRID:SCR_018769), part of the 3Rs Database Programme, provides an overview of FCS-free media for cell-culture. A forum function for each record allows researchers to discuss the applicability of each product. The database is offered by the 3Rs-Centre ULS in collaboration with Animal Free Research UK.
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xCell is a webtool that performs cell type enrichment analysis from gene expression data for 64 immune and stroma cell types. xCell is a gene signatures-based method learned from thousands of pure cell types from various sources. (Aran et al., Genome Biology 18:220. 2017). Registration required.
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Lipidomics Gateway is a free, comprehensive website for researchers interested in lipid biology. Use the site to stay abreast of developments each month from across the field, and explore the rich information collections, tools and resources from the LIPID MAPS consortium Registration not required.
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Cytokines & Cells Online Pathfinder Encyclopedia: Angiogenesis, Apoptosis , CD antigens, Cell lines in cytokine research, Chemokines, Cytokines, Hematology, Hormones, Innate immunity & antimicrobial peptides, Metalloproteinases, Modulins & virulence factors, Protein domains. Registration not required.
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It is possible to toggle between definitions in English and Spanish Registration not required.
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The UCSF Occupational Health and Safety Program is intended to provide guidelines for establishing a high level of safety for all individuals who are involved in the care and use of research animals. This Program provides guidance in all areas of occupational health and safety and environmental protection. It is organized by types of hazards and risks, followed by the educational and preventive programs that address those hazards and risks. Registration not required.
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Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size esti... Registration not required.
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The IMPC envisages a ten year programme to undertake a broad-based, systematic genome-wide phenotyping project of knockout mice generated from the embryonic stem cell mutant resources developed by the International Knock-out Mouse Consortium (IKMC). It will produce knockout animals for each gene and analyze the phenotypic changes. Registration not required.
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PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences. Registration not required.
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Do-it-yourself, DIY BIO, is a biology movement dedicated to making biology an accessible pursuit for citizen scientists, amateur biologists and biological engineers who value openness and safety Registration not required.
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Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. It runs on Intel-based computers running Linux or Mac OS X and that have GCC 4.0 or greater... Registration not required.
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The GSEA algorithm implemented in MeV is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). GSEA software uses the Molecular Signatures Database (MSigDB), a collection of annotated gene sets. Registration required.
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The commercial company Jackson Laboratory JAX® Mice contains the most published and well characterized mouse models in the world. Registration not required.
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The Diversity Outbred (DO) stock from JAX is a genetically diverse mouse resource and may be used as a tool for high resolution genetic mapping and validation of previously identified quantitative trait loci (QTLs) linked to disease susceptibility, drug resistance or behavioral phenotypes. It represents 45 million single nucleotide polymorphisms (SNPs) and 4 million copy number variations. Registration not required.
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The Common Fund's Human Microbiome Project (HMP) aims to characterize the microbial communities found at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract, and to analyze the role of these microbes in human health and disease. HMP includes the following initiatives Registration not required.
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The server from MSKCC predicts the functional impact (high, medium, low, or neutral) of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. MutationAssessor looks at conservation across all the homologs of a protein and also it takes into account the conservation within just the closest homologs, which is called “specifici... Registration not required.
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This wiki is a community knowledge base for ImageJ and friends
Category: Imaging software
Image Net is a federally funded, multi-institution project to develop the next generation of ImageJ to include support for many features such as large multidimensional image support, a more flexible data model and improved developer resources. Registration required.
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CiteAb Ltd is a biotechnology company located in Bath, England that offers an antibody search facility. CieAb ranks antibodies by the number of times they have been cited. This allows researchers to easily find antibodies that have been used in peer-reviewed publications and the accompanying citations are listed, so users can check the data contained within the publications. This makes CiteAb a useful resource for identifying antibodies for experiments and also for finding information to demonst... Registration not required.
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PLINK is a popular and computationally efficient software program that offers a comprehensive and well-documented set of automated genome wide association quality control and analysis tools. It is a freely available open source software written in C++, which can be installed on Windows, Mac and Unix machines. The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from ra... Registration not required.
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The Agency for Toxic Substances and Disease Registry (ATSDR), based in Atlanta, Georgia, is a federal public health agency of the U.S. Department of Health and Human Services. ATSDR serves the public by using the best science, taking responsive public health actions, and providing trusted health information to prevent harmful exposures and diseases related to toxic substances. Registration not required.
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It is a project listing independent antibody reviews and encouraging people to review antibodies. Registration required.
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This site focuses on helping researchers make the most informed decisions possible about where to publish their work. It helps also to avoid fake journals. Through a range of tools and practical resources, this international cross-sector initiative aims to educate researchers, promote integrity, and build trust in credible research and publications.(BL Benderly, Science Careers, Octrober 13, 2015: 10.1126/science.caredit.a1500242). Registration not required.
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The Expression Atlas provides information on gene expression patterns under different biological conditions such as a gene knock out, a plant treated with a compound, or in a particular organism part or cell. It includes both microarray and RNA-seq data. The data is re-analysed in-house to detect interesting expression patterns under the conditions of the original experiment. There are two components to the Expression Atlas, the Baseline Atlas and the Differential Atlas. The Baseline Atlas displ... Registration not required.
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EBImage provides general purpose functionality for high-throughput image processing and analysis in fluorescence microscopy. In the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data (Paut et... Registration not required.
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Biobanking and BioMolecular Resources Research Infrastructure–European Research Infrastructure Consortium
Category: Biomedical products search
The BBMRI-ERIC Directory will help researches to spot relevant biobanks and get their contact information. It also list infrastructures to store samples for research. It has produced a database of European biorepositories that is based on the Minimum Information About Biobank Data Sharing (MIABIS) guidelines. Registration not required.
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CancerMine resource is a literature-mined and routinely updated database of drivers, oncogenes and tumor suppressors in different types of cancer. This resource provides information on genes that are drivers (frequently harbor cancer-promoting mutations), oncogenes (cancer-promoting) and tumor suppressors (protective against cancer) in a large number of different cancers. Context is key as some genes (e.g. NOTCH1) are oncogenes in one cancer and tumor suppressive in another. All data has been te... Registration not required.
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International mastera, including biomedicine and biotechnology Registration not required.
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Almost an encyclopedia of skin lesions. DermNet is the world’s free resource and authority on all things skin. We help thousands of people make informed, evidence-based decisions on how to care for skin conditions, by providing reliable information at the click of a button. Registration not required.
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l Master ha lo scopo di fornire una preparazione professionale per operare nell'ambito delle imprese che producono beni (elettromedicali, dispositivi medici, tecnologie, farmaci, presidi, biotecnologie, etc.) e servizi (sistemi informativi, servizi di supporto generali o tecnici) per le organizzazioni sanitarie pubbliche e private.
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The mission statement of the 3Rs-Centre is to stimulate the development, acceptance and implementation of methods which can Replace, Reduce and Refine (the 3Rs) animal experiments.The 3Rs-Centre stimulates the development, acceptance and implementation of 3Rs methods (Replacement, Reduction and Refinement of animal experiments), by advising and giving information to researchers.
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The Academic Phrasebank is a general resource/data base for academic writers. It aims to provide you with examples of some of the phraseological ‘nuts and bolts’ of writing organised according to the main sections of a research paper or dissertation. Other phrases are listed under the more general communicative functions of academic writing. The resource should be particularly useful for writers who need to report their research work. It contains more than 3,000 phrases harvested from papers... Registration not required.
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There are 214,684,311 structures available on the AlphaFold DB website, including 48 complete proteomes available for bulk download. Registration not required.
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Search for jobs from the world’s universities and research institutions and learn everything you need to succeed academic career. Registration not required.
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AI-based Elicit functionality automate time-consuming research tasks like summarizing papers, extracting data, and synthesizing your findings. Elicit can use a language model to sift through a mountain of texts and summarize the most important findings much faster than any human being. Registration required.
Click here for more informationsThis page contains links to free software packages that you can download and install on your computer for stand-alone (offline, non-Internet) computing. Registration not required.
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Databases and nomenclature for cytochromes P450 in nature Registration required.
Click here for more informationsDescription not available. Registration not required.
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United States Cancer Statistics (USCS: 1999–2006 Cancer Incidence and Mortality Data Registration not required.
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The Breast Cancer Now Tissue Bank is the UK’s largest unique collection of high-quality breast tissue, breast cells and blood samples from breast cancer patients. These samples are made available to researchers to give them the ability to study real breast cancer samples from different angles Registration required.
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The XCMS software for metatabolomic and lipidomic reads and processes LC/MS data stored in netcdf , mzXML, mzData and mzML files. It provides methods for feature detection, non-linear retention time alignment, visualization, relative quantization and statistics. XCMS is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples. Registration not required.
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Proteome Commons is a public proteomics database for annotations and other information linked to the Tranche data repository and to other resources. The site is a project management tool that functions like some social networking websites. Users register, sign into the system, create a new project, and then invite colleagues and collaborators to the project. Invitees are given permissions and responsibilities by the project’s creator. Registration required.
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The open source ISA metadata tracking tools facilitates standards compliant collection, curation, local management and reuse of datasets in an increasingly diverse set of life science domains. Built around the ‘Investigation’ (the project context), ‘Study’ (a unit of research) and ‘Assay’ (analytical measurement) metadata categories, the tools are designed to manage studies employing one or a combination of technologies. Registration required.
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The Genomics of Drug Sensitivity in Cancer project from Weelcome Trust is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. Participants are performing a large-scale drug screen incorporating detailed genomic and gene expression analyses to systematically identify drug response biomarkers. Registration not required.
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A quite comprehensive collection of medical calculator for several specialtises. Registration required.
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The Yeast Metabolome Database (Canadian Institutes of Health Research) is a manually curated database of small molecule metabolites found in or produced by Saccharomyces cerevisiae. This database covers metabolites described in textbooks, scientific journals, metabolic reconstructions and other electronic databases. Registration not required.
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In the effort to test the reproducibility of academic research using independent laboratories, The goal of the SC Reproducibility Committee is to encourage and promote reproducible research within the SC community. Registration required.
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The R package multiMiR, with web server is a comprehensive collection of predicted and validated miRNA-target interactions and their associations with diseases and drugs. Within this database, investigators can find clues to potential new treatments for various diseases, including cancer. In addition to helping researchers search for relationships between microRNAs and their genetic targets, multiMiR includes drugs that affect these microRNAs and lists associated diseases.The database combines n... Registration not required.
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ChEMBL, an open-access database, contains more than 5 million interactions between proteins and ligands that have been published in peer-reviewed journals or reported by laboratories and screening centers . Under ChEMBL’s “Ligand Search” tab, you can enter a compound’s SMILES notation in the “List Search” box and click “Fetch Compounds.” On the next page, clicking on the ChEMBL compound identifier under the 2-D drawing takes you to the Compound Report Card page, which includes th... Registration not required.
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Idealist is an online job site that helps in finding the type of non-profit organizations that dovetail with one’s interests. Registration not required.
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The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry. It results from high-quality measurements of natural and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource for selected/multiple reaction monitoring (SRM/MRM)-based proteomic workflows (See Kusebauch, U. et al., Cell 166: 766, 2016; Doerr A, Nature Meth 13:712, 2016) Registration not required.
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bioRxiv (pronounced io-archive) is a free online archive and distribution service for unpublished preprints in the life sciences. It is operated by Cold Spring Harbor Laboratory, a not-for-profit research and educational institution. By posting preprints on bioRxiv, authors are able to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. Registration required.
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Microscopy Image Browser (MIB) is a high-performance Matlab-based software package for advanced image processing, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy dataset (see Belevich et al., PLoS Biol. 14, e1002340 (2016). Registration not required.
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Site to search for specific positions offered. Search is free. Advanced use requires registration and fee. Registration not required.
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This web site, part of the Human Cell Atlas, presents full single cell RNA-seq dataset of 428K intestinal cells from fetal, pediatric, adult donors, and up to 11 intestinal regions (Ref Elmentaite et al., Nature 597:250, 2021). Registration not required.
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Il Master Scienziati in Azienda ti darà accesso a competenze di alto profilo con le quali costruire la tua carriera nel settore dell’Healthcare e Life Science
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Il Master in Management della Filiera della Salute – Major in Management dei Prodotti Biomedicali (PROBIOMED) forma la figura professionale del Product Specialist, esperto di prodotti ad alta tecnologia, ampiamente diffusa nel settore biomedicale. PROBIOMED fornisce le competenze manageriali per operare nel settore biomedicale, permettendo ai partecipanti di acquisire competenze sui comportamenti e sulle procedure di acquisto nei mercati di riferimento.
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ISTUM Pharma è una divisione di ISTUM Istituto di Studi di Management altamente specializzata in campo farmaceutico. Le direzioni scientifiche dei master pharma e le faculty sono costituite da manager con significative esperienze nel contesto farmaceutico attuale e quindi capaci di comprendere le esigenze formative necessarie a sviluppare la propria carriera in ambito farmaceutico.I master in area pharma sono finalizzati a coprire diversi e specifici fabbisogni formativi: in ambito marketing & ...
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Grammarly helps you write mistake-free in Gmail, Facebook, Twitter, LinkedIn, and any other app you use. Even in text messages. Grammarly is available as a plug-in that is compatible with a range of apps and platforms — including Microsoft Office, Google Docs, Gmail, Slack and Overleaf (an online editor for the LaTeX typesetting language), as well as a keyboard app for mobile devices.It has both free and paid versions (A. Katsnelson, Nature, 609,208, 2022). Registration required.
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General information on various cancer topics Registration not required.
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Gene Set Enrichment Analysis (GSEA) is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes). Registration required.
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The information in the Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations
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Floreada.io is a web-based free flow cytometry analysis application. It is available from any platform with a web browser including phones and tablets. It is currently in very active development with a feature set that continues to grow. Registration required.
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A portal collecting several downloadable tools for the study of genomic structural & copy number variations. Software tools can be used to construct a personal diploid genome sequence by including personal variants into reference genome (vcf2diploid), to discover and genotype CNVs from genome sequencing (CNVnator), etc. Registration not required.
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The Bionimbus Protected Data Cloud (PDC), developed at the University of Chicago, is an open-source cloud-based infrastructure for managing, analyzing, and sharing large amounts of genomics and phenotypic data in a secure and compliant manner. Bionimbus is part of a larger project called the Open Science Data Cloud (OSDC) and there is a version of Bionimbus (Bionimbus Community Cloud) for open-access data and a version for controlled-access data (Bionimbus PDC). Bionimbus is based primarily upon... Registration required.
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A database to find commercial antibodies, peptides, kits, proteins, etc. Registration not required.
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The Exomiser is a Java applicationthat that finds potential disease-causing variants from whole-exome or whole-genome sequencing data. It is an opensource Java software package that can be downloaded and run on a single desktop computer. It filters and prioritizes candidate genes and variants from whole-exome or wholegenome sequencing data, with a special focus on phenotypic data. Users enter a patient’s clinical features and exome into the program, and Exomiser generates a scored list of cand... Registration not required.
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Mendeley is a free reference manager and an academic social network. Manage your research, showcase your work, connect and collaborate with over five million researchers worldwide (ref Singh J, J Pharmacol Pharmacother 2010 Jan;1(1):62-3) Registration required.
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medRxiv (pronounced med-archive) is a free online archive and distribution server for complete but unpublished manuscripts (preprints) in the medical, clinical, and related health sciences. Registration not required.
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Una buona scelta formativa con i Master in Management Sanitario, Marketing Farmaceutico o Economia e Management dei servizi sanitari. Formazione certificata in modalità Executive, Full Time con stage, Part Time ed Online per acquisire competenze specifiche e diventare esperto del settore sanitario e farmaceutico.
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Il Master in Management della Filiera della Salute – Major in Sperimentazione Clinica ha l’obiettivo di dotare i partecipanti degli strumenti teorici e pratici necessari per una corretta programmazione, conduzione e gestione di una sperimentazione clinica.
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This is a list of questionable, scholarly open-access publishers. Registration not required.
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OmicsPred is an open resource applied to genetic scores to predict multi-omic traits from genotype data, uncovering insights into disease biology (Xu et al., Nature https://doi.org/10.1038/s41586-023-05844-9, 2023; https://www.nature.com/articles/d41586-023-00721-x) Registration required.
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Jobs available in medicine, pharmacy, biomedical science
Category: Biomedical funding and jobs
Medicinoxy is an academic web portal for careers of professors, lecturers, researchers and academic managers in schools of medicine, pharmacy and biomedical sciences worldwide. Registration required.
Click here for more informationsDescription not available. Registration not required.
Click here for more informationsR is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. R is developed by Robert Gentleman and Ross Ihaka. Registration not required.
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Network of Excellence
Category: Biomedical communities
The Epigenome NoE allows: Epigenome
Biomedical search tools
Online genomic tools
Online proteomics tools
Calculators
Biomedical lab tools
Scientific writing/reading
Biomedical communities
Biomedical funding and jobs
Medical topics
Biomedical softwares