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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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UW Department of Biochemistry Resource Report Resource Website |
UW Department of Biochemistry (RRID:SCR_000149) | university | A department within the University of Washington which focuses on both undergraduate and postgraduate education in biochemistry. | biochemistry, undergraduate, graduate, university, washington | has parent organization: University of Washington; Seattle; USA | Public, Academic | nlx_149153 | SCR_000149 | University of Washington Department of Biochemistry, UW Department of Biochemistry | 2026-08-01 12:01:08 | 0 | ||||||||
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EdgeBio Resource Report Resource Website |
EdgeBio (RRID:SCR_000183) | EdgeBio | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider. | contract research organization, CRO, genomics, genome, sequencing, bioinformatics, NGS data analysis, whole exome sequencing, research, Illumina NGS | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_203 | https://www.edgebio.com/ | SCR_000183 | Edge Bio, EdgeBio.com | 2026-08-01 12:01:10 | 0 | ||||||
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MIMOSA Resource Report Resource Website |
MIMOSA (RRID:SCR_000184) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23887981 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mimosa, OMICS_05642 | https://bio.tools/mimosa | SCR_000184 | MIMOSA - Mixture Models for Single-Cell Assays, MIMOSA: Mixture Models For Single Cell Assays | 2026-08-01 12:01:09 | 0 | ||||||
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MODENT - A Tool For Reconstructing Gene Regulatory Networks Resource Report Resource Website 1+ mentions |
MODENT - A Tool For Reconstructing Gene Regulatory Networks (RRID:SCR_000220) | ModEnt | software resource | A computational tool that reconstructs gene regulatory networks from high throughput experimental data. | gene regulatory network, experimental data, computation, computational tool, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tel Aviv University; Ramat Aviv; Israel |
PMID:22216865 | Free, Available for download, Freely available | biotools:modent, OMICS_01685 | https://bio.tools/modent | SCR_000220 | 2026-08-01 12:01:09 | 1 | ||||||
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GOLD Resource Report Resource Website 10+ mentions |
GOLD (RRID:SCR_000188) | GOLD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures. | virtual screening, binding, active molecules, ligand-protein bonding, computation, protein structures, lead optimization |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01602 | SCR_000188 | 2026-08-01 12:01:12 | 18 | ||||||||
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Context Likelihood of Relatedness Resource Report Resource Website 1+ mentions |
Context Likelihood of Relatedness (RRID:SCR_000216) | CLR | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles. | transcription factors, gene expression profile, regulatory interactions, likelihood, relatedness | is listed by: OMICtools | PMID:17214507 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01682 | http://gardnerlab.bu.edu/software&tools.html, | SCR_000216 | 2026-08-01 12:01:11 | 1 | ||||||
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Council for Scientific and Industrial Research; Gauteng; South Africa Resource Report Resource Website 1+ mentions |
Council for Scientific and Industrial Research; Gauteng; South Africa (RRID:SCR_000214) | CSIR | nonprofit organization | A leading scientific and technology research, development and implementation organization in Africa that undertakes directed research and development for socio-economic growth and improving the quality of life of South African citizens. | south africa, global economy, south african parliament, quality of life | is related to: Pharma-Planta Consortium | nlx_158309, Crossref funder ID: 501100001332, ISNI: 0000 0004 0607 1766, grid.7327.1, Wikidata: Q849145 | https://ror.org/05j00sr48 | SCR_000214 | CSIR South Africa, Council for Scientific and Industrial Research | 2026-08-01 12:01:09 | 3 | |||||||
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GENIE3 Resource Report Resource Website 10+ mentions |
GENIE3 (RRID:SCR_000217) | GENIE3 | software resource | An algorithm for the inference of gene regulatory networks from expression data. | javascript, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20927193 | Free, Available for download, Freely available | biotools:genie3, OMICS_01683 | https://bio.tools/genie3 | http://www.montefiore.ulg.ac.be/~huynh-thu/software.html | SCR_000217 | 2026-08-01 12:01:09 | 10 | |||||
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Inferelator Resource Report Resource Website 1+ mentions |
Inferelator (RRID:SCR_000218) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | modeling, inference algorithm, halobacterium, genetic regulatory network, learning regulatory network, model gene regulatory network | is listed by: OMICtools | PMID:23525069 PMID:16686963 PMID:19964678 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01684 | SCR_000218 | 2026-08-01 12:01:13 | 3 | ||||||||
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c3net Resource Report Resource Website 1+ mentions |
c3net (RRID:SCR_000212) | software resource | Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET. | gene regulation, microarray expression, c3net | is listed by: OMICtools | PMID:20920161 | Free, Available for download, Freely available | OMICS_01681 | SCR_000212 | 2026-08-01 12:01:11 | 4 | ||||||||
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GraBCas Resource Report Resource Website |
GraBCas (RRID:SCR_000205) | GraBCas | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites. | matlab, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:15980455 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01674, biotools:grabcas | https://bio.tools/grabcas | SCR_000205 | 2026-08-01 12:01:13 | 0 | ||||||
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GPS-Calpain Cleavage Detector Resource Report Resource Website 1+ mentions |
GPS-Calpain Cleavage Detector (RRID:SCR_000202) | GPS-CCD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites. | calpain, cleavage detector, prediction | is listed by: OMICtools | PMID:21533053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01673 | SCR_000202 | Calpain Cleavage Detector | 2026-08-01 12:01:11 | 4 | ||||||
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Queensland Cyber Infrastructure Foundation Ltd Resource Report Resource Website |
Queensland Cyber Infrastructure Foundation Ltd (RRID:SCR_000208) | QCIF | nonprofit organization | Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services. | bioinformatics, contract, software, infrastructure, proteomics, metabolomics, clinical, dataset, analysis |
is listed by: ScienceExchange has parent organization: University of Queensland; Brisbane; Australia is parent organization of: QFAB Bioinformatics |
Queensland Government Department of Employment Economic Development and Innovation ; Commonwealth Government of Australia ; funded through its members |
Available to the research community in Australia | SciEx_4541 | http://www.scienceexchange.com/facilities/4541 | SCR_000208 | Queensland Parallel Supercomputing Foundation, qcif, the Queensland Cyber Infrastructure Foundation | 2026-08-01 12:01:09 | 0 | |||||
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Multiple Myeloma Research Foundation Resource Report Resource Website 1+ mentions |
Multiple Myeloma Research Foundation (RRID:SCR_000207) | MMRF | institution | Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer. | drug, treatment, cancer | is parent organization of: MMRF CoMMpass Study | Multiple myeloma | ISNI: 0000 0000 9350 5788, Crossref funder ID: 100001253, nlx_157895, Wikidata: Q6934894, grid.429426.f | https://ror.org/03ww1bx13 | SCR_000207 | 2026-08-01 12:01:11 | 9 | |||||||
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Burroughs Wellcome Fund Resource Report Resource Website 100+ mentions |
Burroughs Wellcome Fund (RRID:SCR_005772) | BWF | institution | The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation. | biomedical sciences, research, science, education | Wellcome Trust | nlx_149371, grid.427464.7, Wikidata: Q5000488, ISNI: 0000 0000 8727 8697, Crossref funder ID: 100000861 | https://ror.org/01d35cw23 | SCR_005772 | 2026-08-01 12:02:59 | 103 | ||||||||
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CSIBS Resource Report Resource Website |
CSIBS (RRID:SCR_005889) | CSIBS | software resource | A software tool designed to aid researchers in browsing through scientific literature. As one reads an online article and encounters a citation that looks important, CSIBS creates a preview summary of the cited document. The key innovation is the contextual tailoring of the automatically generated summaries using the citation and its surrounding text. As this context changes, so too does the citation-specific summary portion of the preview, which contains contextually-relevant sentences extracted from the cited document. The CSIBS preview presents relevant information required to appraise the citation, containing meta-data about the reference, the abstract and the citation-specific summary. Thus, CSIBS, alleviates information overload by enabling the reader to determine whether or not to invest time in exploring the cited article further. Reference, http://www.sciencedirect.com/science/article/pii/S1570826810000181 | elsevier grand challenge, natural language processing, text summarization, document browsing aid, contextual summary, computational linguistics, text mining, metadata |
is listed by: FORCE11 has parent organization: ICT Centre has parent organization: Macquarie University; Sydney; Australia |
Prototype | nlx_149460 | http://www.force11.org/node/4689 | SCR_005889 | CSIBS: The Citation-Sensitive In-Browser Summarizer, Citation-Sensitive In-Browser Summarizer | 2026-08-01 12:03:03 | 0 | ||||||
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GlycoPeptideSearch Resource Report Resource Website |
GlycoPeptideSearch (RRID:SCR_005767) | GPS | software resource | GlycoPeptideSearch (GPS) simplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format. Accelerate and simplify interpretation of N-glycopeptide CID MS/MS spectra using GlycoPeptideSearch (GPS). This tool is designed for tandem mass-spectra acquired from proteolytic digests of purified glycoproteins modified with N-glycans and analyzed by LC-MS/MS and CID. The search yields an Excel spreadsheet of N-glycopeptide matches consistent with the spectra. GPS requires two files as input - an mzXML (or other open spectral format) file of glycopeptide CID tandem mass-spectra and a text file (.txt) of peptide sequences containing the N-linked glycosylation motif NXS/T. Spectral datafiles must be converted from raw vendor formats, such as .RAW or .wiff, to an open peak list format (mzXML preferred). In addition to these two input files, the user must specify one or more glycan databases (provided in the software package). The database(s) selected by the user will be used to match glycan structures in the glycopeptide spectra. The output is an Excel spreadsheet with one or more rows for spectra within the dataset that contain evidence of glycoprotein fragmentation, paired with one or more proposed glycopeptide matches for each spectrum. Glycopeptide matches consist of a peptide-glycan pair, with the peptide drawn from the user-supplied peptide file, and the glycan selected from a glycan database(s). The human subset of the GlycomeDB glycan database is provided, and N-linked glycans are automatically selected from it. GPS interprets glycopeptide CID MS/MS spectra by first requiring MS/MS spectra contain evidence of glycopeptide fragmentation - the oxonium ion peaks (m/z 204 - Hex, m/z 366 - HexNAc), and N-glycopeptide core specific peaks (peptide, peptide + HexNAc, peptide + HexNAc-HexNAc, peptide + HexNAc-HexNAc-Hex). For spectra that meet these initial criteria, for a particular peptide, a mass-based search of one or more glycan databases looks for glycans which capture the remaining mass of the spectral precursor. Additional spectral information may be used to narrow the number of matches, and equivalent glycan topologies may be collapsed to a single peptide-glycan pair. GPS also provides N-glycan compositions with the necessary additional mass, even if no glycan with the composition is present in the glycan database(s). GPS can either be run from the command-line or by using its graphical user interface. We recommend the msconvert (or MSConvertGUI) software from the ProteoWizard project to convert spectral datafiles from vendor formats such as .wiff and .RAW into mzXML. | peptide, glyopeptide, glycoprotein, mass-spectra, ms/ms spectra | has parent organization: Edwards Lab | PMID:22239659 | nlx_149231 | SCR_005767 | 2026-08-01 12:02:59 | 0 | ||||||||
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Finnish Cancer Registry Resource Report Resource Website 1+ mentions |
Finnish Cancer Registry (RRID:SCR_005881) | Finnish Cancer Registry | institution | The Finnish Cancer Registry maintains a nation-wide database on all cancer cases in Finland going back to 1953. It is also an internationally active institute for statistical and epidemiological cancer research. The Mass Screening Registry is a department of the Finnish Cancer Registry, and is responsible of planning and evaluating national cancer screening programs in Finland. The site contains information on cancer research and up to date statistics on the prevalence of different types of cancer in Finland, the Nordic countries and on a global level. The web pages include information for participants in cancer screening and for professionals involved in organizing such screening. | Cancer | Cancer Society of Finland | grid.424339.b, nlx_149446, ISNI: 0000 0000 8634 0612 | https://ror.org/00j15sg62 | SCR_005881 | 2026-08-01 12:03:00 | 8 | ||||||||
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MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-08-01 12:02:58 | 456 | |||||
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Icahn School of Medicine at Mount Sinai; New York; USA Resource Report Resource Website 1+ mentions |
Icahn School of Medicine at Mount Sinai; New York; USA (RRID:SCR_005793) | ISMMS, MSSM | university | Icahn School of Medicine at Mount Sinai, formerly Mount Sinai School of Medicine, is graduate medical school in Manhattan, New York City. Leader in medical and scientific training and education, biomedical research and patient care. | medicine, medical, school, university, doctorate, phd |
uses: Scizzle is affiliated with: BioJupies is related to: Alzheimers Disease Genetics Consortium is related to: Beta Cell Biology Consortium is related to: Clinical and Translational Science Awards Consortium is related to: proMODMatcher is parent organization of: Enrichr is parent organization of: Neuropathology of CTE and Delayed Effects of TBI: Toward In-Vivo Diagnostics is parent organization of: NeuronStudio is parent organization of: Rayburst Open-Source Code is parent organization of: Volume Integration and Alignment System is parent organization of: Volume Integration and Alignment System Source Code is parent organization of: NeuroGL is parent organization of: TIFF Stack Sub-Sampler is parent organization of: Cre-X-Mice: A Database of Cre Transgenic Lines is parent organization of: Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory is parent organization of: Mount Sinai Biobank is parent organization of: ChEA is parent organization of: Kismeth is parent organization of: Lists2Networks is parent organization of: Mount Sianai Department of Neuroscience is parent organization of: NetworKIN is parent organization of: Mount Sinai Alzheimer's Disease Research Center is parent organization of: Manhattan HIV Brain Bank is parent organization of: Computational Neurobiology and Imaging Center is parent organization of: L1000 Characteristic Direction Signature Search Engine is parent organization of: L1000 Fireworks Display is parent organization of: Drug Gene Budger is parent organization of: COVID-19 Crowd Generated Gene and Drug Set Library is parent organization of: GeneOverlap is parent organization of: Datanator is parent organization of: BioSimulations is parent organization of: DE-Sim is parent organization of: Appyters is parent organization of: ezTrack project is parent organization of: Minian is parent organization of: TargetRanger is parent organization of: GeneRanger is parent organization of: Kinase Enrichment Analysis 3 is parent organization of: X2K Web is parent organization of: Diabetes Data and Hypothesis Hub is parent organization of: Icahn School of Medicine at Mount Sinai Microscopy and Advanced Bioimaging Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Transgenic and Genome Editing Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Stem Cell Engineering Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Metabolomics Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Neuropathology Brain Bank and Research CoRE Facility is parent organization of: Icahn School of Medicine at Mount Sinai RNA Nanocore Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Human Immune Monitoring Center Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Center for Advanced Genomics Technology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Biorepository and Pathology Core Facility is parent organization of: Icahn School of Medicine at Mount Sinai Mount Sinai Cryo-EM CoRE Core Facility |
nlx_55912, grid.59734.3c, Crossref funder ID:100007277, ISNI:0000 0001 0670 2351, Wikidata:Q1950740 | https://ror.org/04a9tmd77 | SCR_005793 | Mount Sinai School of Medicine, Icahn School of Medicine, Icahn School of Medicine at Mount Sinai | 2026-08-01 12:02:59 | 6 |
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