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http://aias.biol.uoa.gr/PredSL/
Web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. As input PredSL requires the protein's sequence in fasta format.
Proper citation: PredSL (RRID:SCR_000626) Copy
http://mullinslab.microbiol.washington.edu/publications/iyer_2012/
A set of perl programs that correct errors in 454 pyrosequences by identifying and flagging poor quality insertions, deletions and substitutions within an alignment. The algorithm utilizes the inherent base quality in sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors.
Proper citation: CorQ (RRID:SCR_000660) Copy
http://linus.nci.nih.gov./BRB-ArrayTools.html
A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.
Proper citation: Biometric Research Branch: ArrayTools (RRID:SCR_000778) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).
Proper citation: Computational Cancer Genomics Group (RRID:SCR_000772) Copy
An independent, privately-held online and print publisher based in New York that serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. GenomeWeb's editorial mission is to serve readers with exclusive, in-depth coverage of the technology, institutions, and scientists that make up the worldwide research enterprise of molecular biology. We operate the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics. Our expert editors report and write with precision and clarity. GenomeWeb users can be found in major scientific organizations around the world, including biopharmaceutical companies, important research universities, biomedical institutes, and government laboratories. Our advertisers include leading suppliers of research tools, analytical instruments, and information technology. Getting started is easy - just register, and use your workplace e-mail address to maximize your access to content. Once you're logged in, you'll have complete free access to GenomeWeb Daily News, The Daily Scan, all of Genome Technology magazine, every GenomeWeb blog, and much more. GenomeWeb Free Content * GenomeWeb Daily News offers breaking news as well as feature articles on genomics, proteomics, bioinformatics, and more. Daily News covers not only the science and business news, but also regulatory and policy updates. Published online and twice daily by e-mail bulletin. * The Daily Scan is a roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin. * Genome Technology: GenomeWeb's magazine covers news, trends, people, and technologies in the systems biology field. It also includes Tech Guides, which feature expert troubleshooting advice on specific lab challenges, and Research Trend Digests. Published 10 times per year. Subscriptions to the print edition are free to active researchers in the US and $29 per year for non-scientists or anyone outside the US. Non-US researchers are eligible for a free subscription to the digital edition of Genome Technology. We may contact subscribers from time to time to requalify for the magazine, in compliance with our third-party readership audit. * Careers: Our Careers page includes content to help scientists in their jobs, with links to relevant external blog posts, profiles of alternative job paths, and more. Careers also includes our Job Listings board, where anyone can post job ads for free. * Cancer Minute: Updated daily and published by e-mail bulletin weekly, Cancer Minute rounds up the latest oncology peer-reviewed literature as well as news and blog posts. * Informatics Iron: This blog covers high-performance computing and the hardware side of bioinformatics, from GPUs to compute clusters and more. * The Sample: This blog focuses on a range of topics of interest to clinical labs, including the adoption of molecular tools, issues related to lab management, in-depth coverage of the major reference labs, and more. GenomeWeb Premium Content All GenomeWeb premium content provides readers with in-depth, exclusive coverage in key technology or application areas. These publications include business, technology, and research news; patent and IP information; product launches and upgrades; and hirings, promotions, and other people news.
Proper citation: GenomeWeb (RRID:SCR_000650) Copy
http://www.geuvadis.org/web/geuvadis/home
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GEUVADIS (RRID:SCR_000684) Copy
http://www.genet.sickkids.on.ca/cftr/
Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.
Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy
http://hirisplex.erasmusmc.nl/
An interactive software tool that predicts hair and eye color based on genetics. The website includes both the IrisPlex system and the HIrisPlex system.
Proper citation: HIrisPlex system (RRID:SCR_014058) Copy
http://www.knockoutmouse.org/about/eucommtools
Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vector reagents which enable the construction of new useful knock-in alleles such as fluorescent and other reporters, site specific recombinases, and mutant cDNAs. These novel alleles can be constructed either by re-utilizing existing IKMC modular vector resources or directly modifying existing targeted IKMC ES cell lines by RMCE.
Proper citation: EUCOMMTOOLS (RRID:SCR_000676) Copy
A neuroscience network providing access to a database of brain, cognitive, genomic and clinical data for research and scientific publication. Data include genomic information, electrical measures of brain and body function, structural and functional MRI, and cognitive and medical history. All data are collected using a standardized assessment protocols. These data are from healthy people and those experiencing a range of brain-related illnesses.
Proper citation: BRAINnet-Brain Research And Integrative Neuroscience Network (RRID:SCR_000712) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14, 2025.NIH-RAID makes available at no cost to researchers and organizations certain critical resources needed for the development of new therapeutic agents. This program, part of the Translational Research component of Reengineering the Clinical Research Enterprise, uses resources of NCI's Developmental Therapeutics Program and the National Heart Lung and Blood Institutes (NHLBI) Gene Therapy Resource Program. The services provided will depend upon the stage of the project and the strength of the preliminary data. Services available include: production, bulk supply, GMP manufacturing, formulation, development of an assay suitable for pharmacokinetic testing, and animal toxicology. Assistance also will be provided in the regulatory process, through access to independent product development planning expertise. Proposals in support of animal efficacy studies or synthesis and formulation of recombinant proteins or monoclonal antibodies will not be accepted. NIH-RAID is not a grant program. Successful projects will gain access to the governments contract resources, as well as the assistance of the NIH in establishing and implementing a product development plan. Funds to support individual projects will come both from the Roadmap and from individual Institutes, with Institutes assuming the bulk of support in the specific disease areas germane to their mission. This co-sponsorship is critical because of the resource and expertise needs and because NIH-RAID cannot support the full developmental pipeline; an Institute partnership may therefore be important for subsequent translational efforts. To obtain access to NIH-RAID resources, applications must be submitted electronically through Grants.gov using SF424. Applications are initially screened to determine whether the resources requested are appropriate for this program. Then they are reviewed by the NIH Center for Scientific Research. The results of that evaluation along with supplemental information from the lead investigator will guide final Institute and Roadmap resource allocation. The services provided will depend upon the stage of the project and the strength of the preliminary data. When a lead therapeutic agent has been selected and proposed for preclinical development, the following services are available: For small molecules, natural products, peptides, oligonucleotides, and gene vectors: Synthesis, Scale-up production, Development of analytical methods, Development of suitable formulations, Isolation and purification of natural products, Pharmacokinetic/ADME studies including bioanalytical method development, Range-finding initial toxicology, IND-directed toxicology, Manufacture of clinical trial supplies, Product development planning and advice in IND preparation For recombinant proteins and monoclonal antibodies: Pharmacokinetic/ADME studies including bioanalytical method development, Range-finding initial toxicology, IND-directed toxicology, Product development planning and advice in IND preparation When a lead therapeutic agent has not yet been selected and proposed for preclinical development, the following services are available: For small molecules, natural products, peptides, oligonucleotides, and gene vectors: Synthesis, Development of analytical methods, Isolation and purification of natural products, Preliminary Pharmacokinetic/ADME studies, including bioanalytical method development, Preliminary toxicology For recombinant proteins and monoclonal antibodies, Preliminary Pharmacokinetic/ADME studies, including bioanalytical method development, Preliminary toxicology In some cases the NIH-RAID program will support only one or two key steps for preclinical development, while in other cases it may be possible to provide assistance with most of the development tasks needed to file an Investigational New Drug (IND) application to the Food and Drug Administration (FDA). When the NIH-RAID program does not provide all of the remaining services required for IND submission, it is expected that other resources will be in place to complete development steps not supported by NIH-RAID. Funding Resource,.
Proper citation: NIH - Rapid Access to Interventional Development (RRID:SCR_000713) Copy
http://sourceforge.net/projects/denovogear/
A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations.
Proper citation: DeNovoGear (RRID:SCR_000670) Copy
Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.
Proper citation: MEGA (RRID:SCR_000667) Copy
A genetic testing company for rare and complex disorders and syndromes. The company specializes in retinal disorders, reproductive medicine and oncology. They also offer custom genotyping services.
Proper citation: Asper Biotech (RRID:SCR_000700) Copy
Gatsby is a Foundation set up by David Sainsbury to realize his charitable objectives. Gatsby works in areas that David Sainsbury and the Trustees are particularly passionate about and where they believe charitable funding can make a real difference. Gatsby is currently active in six tightly-focused areas: * Plant science research * Neuroscience research * Science and engineering education * Economic development in Africa * Public policy research and advice * The Arts We have also supported significant programs in mental health - in particular through the founding of the Centre for Mental Health - although we are no longer focusing on this area. Across all areas, we aim to be more than a funder. We act as an enabler for projects, designing, developing, overseeing and, in some cases, delivering activities. We are proactive in putting together projects to achieve our aims. Rather than wait for third-party proposals, we identify areas of need, commission research and design interventions in partnership with sector and industry experts. We take a long-term view as we do not think much can be achieved by short, one-off projects. We build long relationships with the organizations we support, allowing both them and us to learn from successes and failures and to develop sustainable change. We are particularly enthusiastic about supporting innovation. David Sainsbury has long believed that private foundations have an important role to play in testing imaginative models and new ideas that governments may see as too risky for public funding, even when they have significant potential to benefit the public if they succeed. Gatsby can incubate such models, giving them the support they need to prove themselves and build the track-records that will encourage others to scale them up. We will continue to support and undertake both large- and small-scale work, employing different methods and models depending on the different challenges, but always ultimately looking to deliver long-term, sustainable change. Registered Charity No. 251988
Proper citation: Gatsby Charitable Foundation (RRID:SCR_000618) Copy
http://vesalius.northwestern.edu/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 10,2026. English translation of Andreas Vesalius' Renaissance anatomical atlas On the Fabric of the Human Body (1543, 1555) and an explanation of the work in progress at Northwestern University to translate and annotate this historic work (by Daniel Garrison and Malcolm Hast). This detailed account of human anatomy transformed its subject and forever changed medical education in the West. Its woodcut illustrations became the basis of medical art and illustrations for generations to come, and continue to influence the way we look at the human body. * Book One -- The things that sustain and support the entire body, and what braces and attaches them all. (the bones and the ligaments that interconnect them) * Book Two -- All the ligaments and muscles, instruments of voluntary and deliberate motion * Book Three -- The series of veins and arteries throughout the body * Book Four -- The nerves * Book Five -- The organs of nutrition and generation * Book Six -- The heart and organs serving the heart (Chiefly the heart and lungs) * Book Seven -- The brain and organs of sense Note: Only introduction, images, and essays appear to be available.
Proper citation: De Humani Corporis Fabrica (RRID:SCR_000699) Copy
The John D. and Catherine T. MacArthur Foundation supports creative people and effective institutions committed to building a more just, verdant, and peaceful world. In addition to selecting the MacArthur Fellows, the Foundation works to defend human rights, advance global conservation and security, make cities better places, and understand how technology is affecting children and society. MacArthur is one of the nation's largest independent foundations. Through the support it provides, the Foundation fosters the development of knowledge, nurtures individual creativity, strengthens institutions, helps improve public policy, and provides information to the public, primarily through support for public interest media. The Foundation makes grants and loans through four programs. * International Programs focus on international issues, including human rights and international justice, peace and security, conservation and sustainable development, higher education in Nigeria and Russia, migration, and population and reproductive health. MacArthur grantees work in about 60 countries; the Foundation has offices in India, Mexico, Nigeria, and Russia. * U.S. Programs address issues in the United States, including community and economic development; housing, with a focus on the preservation of affordable rental housing; juvenile justice reform; education, with an emerging interest in digital media and learning; and policy research and analysis. * Media, Culture, and Special Initiatives support public interest media, including public radio, documentary programming, and work to explore the use of digital technologies to reach and engage the public. Grants are also made to arts and cultural institutions in the Chicago area and for special initiatives. * The MacArthur Fellows Program awards five-year, unrestricted fellowships to individuals across all ages and fields who show exceptional merit and promise of continued creative work. It is limited to U.S. citizens and residents. John D. MacArthur (1897-1978) developed and owned Bankers Life and Casualty Company and other businesses, as well as considerable property in Florida and New York. His wife Catherine (1909-1981) held positions in many of these companies and served as a director of the Foundation.
Proper citation: MacArthur Foundation (RRID:SCR_000612) Copy
http://www.nactem.ac.uk/Kleio/
An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008
Proper citation: KLEIO (RRID:SCR_000698) Copy
http://www.hiv.lanl.gov/content/index
Contains comprehensive data on HIV genetic sequences and immunological epitopes. This collection of databases contains tools to visualize and analyze HIV-related data.
Proper citation: HIV Databases (RRID:SCR_000614) Copy
http://sourceforge.net/projects/finesplice/
A software pipeline based on TopHat2 combined with a splice junction detection algorithm.
Proper citation: FineSplice (RRID:SCR_000691) Copy
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