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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | data or information resource, database | An information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these have indexes. Each of the Summary pages offers links to supplementary pages. About 3000 individual peptidases and inhibitors are included in the database, and there is a Summary page describing each one. You can navigate to this by any of several routes. There are indexes of Name, MEROPS Identifier and source Organism on the menu bar. Each Summary page describes the classification and nomenclature of the peptidase or inhibitor, and provides links to supplementary pages showing sequence identifiers, the structure if known, literature references and more. | peptidase, protease, proteinase, proteolytic enzyme, protein, inhibitor, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: TopFIND has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust WT077044/Z/05/Z | PMID:19892822 | biotools:merops, r3d100012783, nif-0000-03112 | https://bio.tools/merops, https://doi.org/10.17616/R33225, https://doi.org/10.17616/R33225 | SCR_007777 | MEROPS- the Peptidase Database, MEROPS - the Peptidase Database, MEROPS database, MEROPS fam | 2026-09-19 12:57:10 | 762 | |||||
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Genes to Cognition Database Resource Report Resource Website |
Genes to Cognition Database (RRID:SCR_002735) | G2Cdb | data or information resource, database | Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain. | allele, gene list, mouse line, human disease, phenotyping, plasticity, behavior, proteonomics, brain, cognition, cognition disorder, learning, memory, neuroscience, experimental protocol, synapse proteomics, synapse | Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
PMID:18984621 | Free, Freely available | nif-0000-02864 | http://www.genes2cognition.org/cgi-bin/SearchView | SCR_002735 | Genes-to-Cognition Database | 2026-09-19 12:56:37 | 0 | |||||
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MLST Resource Report Resource Website 1000+ mentions |
MLST (RRID:SCR_010245) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms via the internet. The aim of MLST is to provide a portable, accurate, and highly discriminating typing system that can be used for most bacteria and some other organisms. It is envisaged that this approach will be particularly helpful for the typing of bacterial pathogens. To achieve this aim we have taken the proven concepts of multilocus enzyme electrophoresis (MLEE) and have adapted them so that alleles at each locus are defined directly, by nucleotide sequencing, rather than indirectly from the electrophoretic moblity of their gene products. MLST was developed in the laboratories of Martin Maiden, Dominique Caugant, Ian Feavers, Mark Achtman and Brian Spratt. This site is hosted at Imperial College with funding from the Wellcome Trust. The location of the subsites for the individual species are shown on their respective front pages. | has parent organization: Imperial College London; London; United Kingdom | Wellcome Trust | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_156883 | SCR_010245 | 2026-09-19 12:57:21 | 1242 | |||||||||
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Human Developmental Biology Resource Resource Report Resource Website 100+ mentions |
Human Developmental Biology Resource (RRID:SCR_006326) | HDBR | biomaterial supply resource, material resource | Collection of human embryonic and fetal material (Tissue and RNA) ranging from 3 to 20 weeks of development available to the international scientific community. Material can either be sent to registered users or our In House Gene Expression Service (IHGES) can carry out projects on user''''s behalf, providing high quality images and interpretation of gene expression patterns. Gene expression data emerging from HDBR material is added to our gene expression database which is accessible via our HUDSEN (Human Developmental Studies Network) website. A significant proportion of the material has been cytogenetically karyotyped, and normal karyotyped material is provided for research. | development, fetal material, fetus, embryonic human, fetus human, karyotype, gene expression, image, imaging, FASEB list |
is listed by: One Mind Biospecimen Bank Listing is related to: HUDSEN Human Gene Expression Spatial Database has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom has parent organization: University College London; London; United Kingdom |
Normal | MRC ; Wellcome Trust |
Public: Intended for use primarily by academic researchers. Every effort is made to ensure that optimal use is made of donated tissue, Both in terms of the aims and quality of the research for which it is used and avoidance of duplication/wastage. Applications by pharmaceutical or biotechnology companies for access to the Resource are considered, Provided that the tissue itself is not used directly for financial gain. | nlx_152030 | SCR_006326 | MRC-Wellcome Trust Human Developmental Biology Resource | 2026-09-19 12:57:53 | 316 | |||||
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Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | data or information resource, database | Database that contains data such as registry entries, portions of regulatory documents describing individual trials, structured data on methods and results, and researchers and papers from and/or related to clinical trials. The initiative aims to locate, match, and share all publicly accessible data and documents, on all trials conducted, on all medicines and other treatments, globally. | clinical trial, clinical trial database, clinical trial data, open database, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Oxford; Oxford; United Kingdom |
Laura and John Arnold Foundation ; Wellcome Trust ; World Health Organisation ; West of England Academic Health Science Network |
Open source | biotools:opentrials | https://bio.tools/opentrials | SCR_015570 | 2026-09-19 12:57:35 | 3 | |||||||
|
mousebrain.org Resource Report Resource Website 100+ mentions |
mousebrain.org (RRID:SCR_016999) | atlas, data or information resource | Atlas of brain cell types, derived from single cell RNA-Seq data from Linnarsson Lab. Can be browsed by taxon, cell type, tissue, and gene, with information on enriched genes, specific markers, anatomical location and more. Single cell gene expression atlas of mouse nervous system. | Atlas, brain cell, cell type, single cell RNA seq data, taxon, tissue, gene, marker, anatomical location, data | has parent organization: Karolinska Institute; Stockholm; Sweden | Åke Wiberg Foundation ; Cancerfonden ; European Research Council ; EU ; Hjärnfonden ; Knut and Alice Wallenberg Foundation ; Ollie and Elof Ericssons Foundation ; SFO Strat Regen ; SSF ; Swedish Foundation for Strategic Research ; Swedish Research Council ; Wellcome Trust |
PMID:30096314 | Free, Available for download, Freely available | SCR_018356 | SCR_016999 | Linnarsson lab Mouse Brain Atlas | 2026-09-19 12:57:36 | 135 | ||||||
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GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | data or information resource, database | Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases. | geroprotector, data, collection, current, thearpeutic, prevention, aging, disease, geriatic |
uses: PubChem uses: ChemSpider uses: DrugBank uses: ChEMBL uses: CHEBI uses: UniProt uses: GenAge |
Fund in Memory of Dr. Amir Abramovich ; Israel Ministry of Science and Technology ; Wellcome Trust |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-09-19 12:57:36 | 13 | |||||||
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BIGSdb Resource Report Resource Website 1+ mentions |
BIGSdb (RRID:SCR_023551) | data or information resource, database | Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level. | sequence data, bacterial isolates, gene-by-gene bacterial population, annotation and analysis, bacterial genome variation, | Wellcome Trust | PMID:21143983 | Free, Freely available | https://bigsdb.readthedocs.io/en/latest/ | SCR_023551 | Bacterial Isolate Genome Sequence Database | 2026-09-19 12:57:39 | 1 | |||||||
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Pavlovia Resource Report Resource Website 100+ mentions |
Pavlovia (RRID:SCR_023320) | software resource, web application | Web application as repository and launch platform for Psychopy experiments and other open-source tools. | Open Science Tools Limited, Psychopy experiments, repository and launch platform, behavioural sciences, | University of Nottingham; Nottingham; United Kingdom ; Wellcome Trust |
Restricted | SCR_023320 | 2026-09-19 12:55:33 | 282 | ||||||||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
Austrian Science Fund J-3401; Dutch Brain Foundation ; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NHGRI F32HG007805; NHGRI HG007022; NHGRI R01 HG006399; NHLBI HL117626; NIMH R01 MH101244; NWO 480-05-003; Wellcome Trust WT098051 |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-09-19 12:58:14 | 57 | |||||
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fragon Resource Report Resource Website |
fragon (RRID:SCR_019158) | software resource, software toolkit | Software tool for rapid high resolution structure determination from ideal protein fragments. Pipeline to determine crystal structures using molecular replacement with small fragments followed by density modification. It is available through CCP4. | Density modification, molecular replacement, protein fragments, crystal structure determination | is related to: CCP4 | Wellcome Trust | PMID:29533228 | Free, Freely available | SCR_019158 | 2026-09-19 12:58:18 | 0 | ||||||||
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Wellcome-CTC Mouse Strain SNP Genotype Set Resource Report Resource Website 1+ mentions |
Wellcome-CTC Mouse Strain SNP Genotype Set (RRID:SCR_003216) | Wellcome-CTC Mouse Strain SNP Genotype Set | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34. | genome, genotype, snp, chromosome, haplotype, haplotype structure, recombinant inbred mouse strain | has parent organization: Wellcome Trust Centre for Human Genetics | Wellcome Trust ; NCRR R24RR015116; NIGMS R01GM072863; NIAAA U01AA014425; NINDS R01NS049445; NIMH P20-MH 62009; NIAAA U24AA13513 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156947 | SCR_003216 | 2026-09-19 12:58:35 | 3 | |||||||
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GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, dataset, portal, project portal | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-09-19 12:56:04 | 8811 | |||||
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NS-Forest Resource Report Resource Website 1+ mentions |
NS-Forest (RRID:SCR_018348) | data processing software, software application, software resource | Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy. | Single cell, RNAseq experiment, generated gene list, minimum set, marker gene, define cell type cluster, random forest, decision tree, machine learning, identify cell, cell clasyfication | is related to: Allen Institute for Brain Science | Allen Institute for Brain Science ; California Institute for Regenerative Medicine ; Chan Zuckerberg Initiative DAF ; JCVI Innovation Fund ; NIAID R21 AI122100; NIAID U19 AI118626; Wellcome Trust |
PMID:29590361 | Free, Available for download, Freely available | SCR_018348 | Necessary and Sufficient Forest, NS-Forestversion 1.3, NS-Forest v2.0, NS-Forest version 1.0 | 2026-09-19 12:56:09 | 2 | |||||||
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BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | data access protocol, data or information resource, portal, project portal, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse. | biology, data, management, data mining, search, descriptive, graphical, application, perl, java, gold standard |
is used by: Blueprint Epigenome is related to: Mouse Genome Informatics (MGI) is related to: biomaRt has parent organization: Ontario Institute for Cancer Research has parent organization: European Bioinformatics Institute |
Breast Cancer Campaign Tissue Bank ; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory ; NSF NRF 2013M3A6A4043695; Sandra Ibarra Foundation for Cancer ; Spanish Government ; U.S. Department of Energy ; Wellcome Trust |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-09-19 12:55:06 | 295 | ||||||
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Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes. | Genome analysis, prokaryote pan genome, pan genome, gene identification, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools works with: Scoary |
Wellcome Trust | PMID:26198102 | Free, Available for download, Freely available | OMICS_09491, biotools:roary | https://github.com/sanger-pathogens/Roary, https://bio.tools/roary, https://sources.debian.org/src/roary/ | SCR_018172 | 2026-09-19 12:55:17 | 710 | ||||||
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ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry. | comparative, analysis, sequence, bacteria, genome, reconstruct, recombination, events, ancestry, bayesian |
is listed by: Debian is listed by: OMICtools is related to: Imperial College London; London; United Kingdom is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882; Wellcome Trust WT082930MA |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-09-19 12:55:15 | 8 | ||||||
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Cytograph Resource Report Resource Website 1+ mentions |
Cytograph (RRID:SCR_023101) | data analysis software, data processing software, software application, software resource | Software multistage analysis pipeline which progressively discovers cell types or states while mitigating impact of technical artifacts.Used for single cell analysis. | cell types discovery, cell states discovery, single cell analysis | Ake Wiberg Foundation ; European Research Council ; Knut and Alice Wallenberg Foundation ; Ollie and Elof Ericssons Foundation ; Swedish Foundation for Strategic Research ; Swedish Research Council ; Wellcome Trust |
PMID:30096314 | Free, Freely available | SCR_023101 | 2026-09-19 12:55:28 | 3 | |||||||||
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NWB Explorer Resource Report Resource Website 1+ mentions |
NWB Explorer (RRID:SCR_021151) | data access protocol, software application, software resource, standalone software, web service | Web application and standalone application to read, visualize and explore content of NWB:N 2 files.Used to share neurophysiological data in Neurodata Without Borders format. | Read NWB files, visualize NWB files, explore NWB files, NWB, neurophysiology data sharing, Neurodata Without Borders format, neurophysiology data |
uses: Jupyter Notebook uses: PyNWB is listed by: Neurodata Without Borders is related to: Metacell is related to: Open Source Brain |
Wellcome Trust | Free, Available for download, Freely available | https://www.nwb.org/tools/ | SCR_021151 | 2026-09-19 12:54:49 | 1 | ||||||||
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SpikeInterface Resource Report Resource Website 1+ mentions |
SpikeInterface (RRID:SCR_021150) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool as unified framework for spike sorting. Python framework to unify preexisting spike sorting technologies into single codebase and to facilitate straightforward comparison and adoption of different approaches.Used to reproducibly run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs. | Spike sorting, Python framework, unify preexisting spike sorting, single codebase, spike sorting algorithms | is listed by: Neurodata Without Borders | ETH Zurich Postdoctoral Fellowship ; Norwegian Ministry of Education ; Research and Church Affairs ; University of Edinburgh ; University of Oslo ; Wellcome Trust |
PMID:33170122 | Free, Available for download, Freely available | https://www.nwb.org/tools/, https://github.com/SpikeInterface/spikeinterface/blob/master/doc/index.rst | SCR_021150 | 2026-09-19 12:54:49 | 4 |
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