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http://www.mrc.ac.za/home.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Organization which focuses on the promotion of health and increased quality of life for South Africans through research, development and technology. This organization conducts basic laboratory investigations, clinical research and public health studies, and its research focuses around the study of TB, HIV, chronic diseases, alcohol and drug abuse, and women's health.

Proper citation: South African Medical Research Council (RRID:SCR_000159) Copy   

•   Source: SciCrunch Registry

http://gprox.sourceforge.net/

A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.

Proper citation: GProX (RRID:SCR_000273) Copy   

•   Source: SciCrunch Registry

http://peptideprophet.sourceforge.net/

Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

Proper citation: PeptideProphet (RRID:SCR_000274) Copy   

•   Source: SciCrunch Registry

http://www.mmnt.net/db/0/0/ftp-genome.wi.mit.edu/distribution/GISTIC2.0

Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.

Proper citation: GISTIC (RRID:SCR_000151) Copy   

•   Source: SciCrunch Registry

http://mor.nlm.nih.gov/perl/gennav.pl

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.

Proper citation: GenNav (RRID:SCR_000147) Copy   

•   Source: SciCrunch Registry

http://www.cs.utexas.edu/~bajaj/cvc/software/f2dockclient.shtml

A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results.

Proper citation: F2DockClient (RRID:SCR_000185) Copy   

•   Source: SciCrunch Registry

http://www.biosolveit.de/flexx/index.html?ct=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds.

Proper citation: FlexX (RRID:SCR_000186) Copy   

•   Source: SciCrunch Registry

http://pipmaker.bx.psu.edu

A portal for the Miller Lab at Penn State that does research in comparative genomics and bioinformatics. The website has resources such as web-based applications for genetic databases, software for genomic analysis and publications from the lab.

Proper citation: Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics (RRID:SCR_000222) Copy   

•   Source: SciCrunch Registry

http://www.crash.lshtm.ac.uk/TP_English_StudyDesgn.htm

Portal for placebo controlled trial of the effects of 48-hour infusion of corticosteroids on death and on neurological disability, among adults with head injury and some impairment of consciousness. The outcomes will be measured by rates of death and neurological disability. Patients are recruited (or entered by their doctors when informed consent is not obtainable due to impaired cognitive functioning) on a case-by-case basis as head injured patients come through emergency departments. Randomization is done via a 24-hour telephone line that will denote which pack of medication (either the corticosteroids or saline solution as control) to give.

Proper citation: CRASH (RRID:SCR_000221) Copy   

•   Source: SciCrunch Registry

http://environmentontology.org/

Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.

Proper citation: EnvO (RRID:SCR_000182) Copy   

•   Source: SciCrunch Registry

http://www.cs.toronto.edu/~hilal/rnacontext/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.

Proper citation: RNAcontext (RRID:SCR_000179) Copy   

•   Source: SciCrunch Registry

https://github.com/AliView

Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

Proper citation: AliView (RRID:SCR_002780) Copy   

•   Source: SciCrunch Registry

http://www.enzyme-database.org

Enzyme database developed as a way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards. A simple, easy to use, web-based query interface is provided (Search), along with an advanced search engine for more complex queries (Advanced Search). Forms are provided to submit suggestions for new enzyme entries or to report errors in existing entries. Downloads of the database are available via FTP as SQL or XML.

Proper citation: ExplorEnz (RRID:SCR_002665) Copy   

•   Source: SciCrunch Registry

http://www.cmhd.ca/genetrap/

Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Proper citation: Centre for Modeling Human Disease Gene Trap Resource (RRID:SCR_002785) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/ExomeDepth/

Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

Proper citation: ExomeDepth (RRID:SCR_002663) Copy   

•   Source: SciCrunch Registry

https://github.com/rcanovas/libCSAM

Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.

Proper citation: libCSAM (RRID:SCR_002766) Copy   

•   Source: SciCrunch Registry

http://stkctr.biol.sc.edu/

The deer mouse (Peromyscus maniculatus) and congeneric species are the most common native North American mammal. Laboratory stock of both wild-type and genetically variant Peromyscus are used for investigations in which laboratory-based studies can be interfaced with those of natural populations. The major function of the Stock Center is to provide genetically characterized types of Peromyscus in limited quantities to scientific investigators. It provides a reliable source of genetically defined and virus-free animals and related materials to the scientific and educational communities. The center currently keeps nine species and more than 27 distinctive mutant and other genetically defined stocks. Included among the species maintained are P. californicus, P. leucopus, P. eremicus, P. aztecus, P. melanophrys as well as two subspecies each of P. maniculatus and P. polionotus and three inbred lines of P. leucopus. Among the mutant stocks are 17 with altered coat phenotypes, 3 with neurological symptoms, and 6 others with developmental/physiological effects. One of these is a line deficient in alcohol dehydrogenase that has been widely used in studies of alcohol metabolism. The stock center also supplies biological materials, including fresh, frozen, and preserved tissues; molecular probes, and libraries. The center functions as a clearinghouse for information regarding this genus by sponsoring an Internet database and the semi-annual Peromyscus Newsletter. The center maintains a collection of over 3,000 Peromyscus-related reprints of published articles, books, and journals-photocopies of which are available upon request. Continuation of the center is dependent upon significant external utilization, therefore potential users are encouraged to take advantage of this resource. Sufficient animals of the mutant types generally can be provided to initiate a breeding stock. Some what larger numbers, up to about 50 animals, can be provided from the wild-type stocks. A user fee of $25.00 per wild-type animal and $33.00 per mutant or other special types is charged. The user assumes the cost of air shipment. Animals lost in transit are replaced without charge. Tissues, blood, skins, etc. can also be supplied at a modest fee. Arrangements for special orders will be negotiated. :Sponsors: The peromyscus genetic stock center is supported by the University of South Carolina, :a grant from the Special Projects Program of the National Science Foundation and a P40 grant ( grant number: P40 RR014279) from the National Institutes of Health. physiological, Developmental, Biological, Animal,

Proper citation: Peromyscus Genetic Stock Center (RRID:SCR_002769) Copy   

•   Source: SciCrunch Registry

https://simtk.org

A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

Proper citation: Simtk.org (RRID:SCR_002680) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/simvascular

Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC.

Proper citation: SimVascular (RRID:SCR_002686) Copy   

•   Source: SciCrunch Registry

http://bioportal.bioontology.org/

Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Proper citation: BioPortal (RRID:SCR_002713) Copy   

•   Source: SciCrunch Registry