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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pavlovia Resource Report Resource Website 100+ mentions |
Pavlovia (RRID:SCR_023320) | web application, software resource | 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, | Wellcome Trust ; University of Nottingham; Nottingham; United Kingdom |
Restricted | SCR_023320 | 2026-08-04 09:45:13 | 191 | ||||||||||
|
PhenStat Resource Report Resource Website 1+ mentions |
PhenStat (RRID:SCR_021317) | data processing software, data analysis software, software resource, software application, software toolkit | Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data. | Statistical analysis, phenotypic data, standardized analysis, bio.tools, Bioconductor |
is listed by: Bioconductor is listed by: bio.tools |
Wellcome Trust ; NHGRI U54 HG006370 |
PMID:26147094 | Free, Available for download, Freely available | biotools:phenstat | https://bio.tools/phenstat | SCR_021317 | 2026-08-04 09:44:47 | 8 | ||||||
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KymoButler Resource Report Resource Website 1+ mentions |
KymoButler (RRID:SCR_021717) | data processing software, software application, software resource, data analysis software | Software tool as deep learning software for automated kymograph analysis. Uses artificial intelligence to trace lines in kymograph and extract information about particle movement. Speeds up analysis of kymographs by between 50 and 250 times, and comparisons show that it is as reliable as manual analysis. | automated kymograph analysis, kymograph, particle movement | Wellcome Trust ; Herchel Smith Foundation ; Isaac Newton Trust ; Biotechnology and Biological Sciences Research Council ; European Research Council |
PMID:31405451 | Free, Available for download, Freely available | https://github.com/elifesciences-publications/KymoButler, https://gitlab.com/deepmirror/kymobutler, https://www.wolframcloud.com/objects/deepmirror/Projects/KymoButler/KymoButlerForm | SCR_021717 | 2026-08-04 09:44:53 | 6 | ||||||||
|
mRnd Resource Report Resource Website 100+ mentions |
mRnd (RRID:SCR_022156) | data access protocol, software resource, web service | Web tool for calculations for Mendelian Randomization. Power calculations for Mendelian Randomization. Used to calculate statistical power for Mendelian Randomization study, using Non Centrality Parameter based approach. | calculations for Mendelian Randomization, Mendelian Randomization, calculate statistical power, Mendelian Randomization study, Non Centrality Parameter | Wellcome Trust ; Leducq Foundation ; Australian National Health and Medical Research Council ; EU 7th Framework Programme |
PMID:24159078 | Free, Freely available | https://github.com/kn3in/mRnd | SCR_022156 | 2026-08-04 09:44:57 | 205 | ||||||||
|
BioMart Project Resource Report Resource Website 100+ mentions |
BioMart Project (RRID:SCR_002987) | portal, web service, software resource, data access protocol, project portal, data or information resource | 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 |
Wellcome Trust ; Spanish Government ; Sandra Ibarra Foundation for Cancer ; Breast Cancer Campaign Tissue Bank ; U.S. Department of Energy ; NSF NRF 2013M3A6A4043695; Center for Genome Regulation ; Center for Mathematical Modelling ; European Molecular Biology Laboratory |
PMID:21930506 PMID:19144180 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30184 | SCR_002987 | BioMart software | 2026-08-04 09:40:47 | 284 | ||||||
|
ClonalOrigin Resource Report Resource Website 1+ mentions |
ClonalOrigin (RRID:SCR_016061) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 |
Wellcome Trust WT082930MA; National Science Foundation DBI-0630765; Science Foundation of Ireland 05/FE1/B882 |
PMID:20923983 DOI:10.1534/genetics.110.120121 |
Free, Available for download | OMICS_18881 | https://sources.debian.org/src/clonalorigin/ | SCR_016061 | 2026-08-04 09:43:48 | 8 | ||||||
|
Roary Resource Report Resource Website 500+ mentions |
Roary (RRID:SCR_018172) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:44:17 | 602 | ||||||
|
xiSEARCH Resource Report Resource Website 10+ mentions |
xiSEARCH (RRID:SCR_018395) | data processing software, data analysis software, algorithm resource, software resource, software application | Software and algorithm for analyzing protein protein cross linking mass spectrometry data. Library of routines for peptide based mass spectrometry. Contains search engine for identification of crosslinked peptides. | Protein analysis, mass spectrometry, protein cross linking, XL-MS, cross-linking mass spectrometry, data analysis, peptide mass spectrometry, crosslinked peptide identification | Wellcome Trust | PMID:26719564 | Free, Available for download, Freely available | https://github.com/Rappsilber-Laboratory/xisearch | SCR_018395 | 2026-08-04 09:44:20 | 22 | ||||||||
|
Recombination Detection Program Resource Report Resource Website 100+ mentions |
Recombination Detection Program (RRID:SCR_018537) | RDP | data processing software, software application, software resource, data analysis software | Software package to analyse nucleotide sequence data and identify evidence of genetic recombination. RDP3 is version of RDP program for characterizing recombination events in DNA-sequence alignments. RDP4 is version of RDP program for detection and analysis of recombination patterns in virus genomes. | DNA sequence, alignment, phylogenetic tree, nucleotide analysis, sequence data analysis, genetic recombination identification, DNA sequence alignment, recombinant pattern analysis, virus genome | Wellcome Trust ; Fund for Scientific Research Flanders ; South African Centre of High Performance Computing ; European Research Council ; Spanish Ministry of Science and Education ; South African National Research Foundation ; University of Cape Town ; Polyomielitis Research Foundation ; Carnergie Corporation ; NIAID AI090970; NIGMS U01 GM110749; NIAID AI100665 |
PMID:27774277 PMID:20798170 |
Free, Available for download, Freely available | SCR_018537 | Recombination Detection Program, RDP4, RDP3 | 2026-08-04 09:44:25 | 483 | |||||||
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University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility Resource Report Resource Website |
University of Edinburgh Wellcome Trust Centre for Cell Biology Bioinformatics Core Facility (RRID:SCR_017151) | University of Edinburgh WTCCB Bioinformatics Core Facility | access service resource, core facility, service resource | Facility provides regular training sessions, tools, advice and data analysis services to Centre members. | core, facility, bioinformatics | has parent organization: University of Edinburgh; Scotland; United Kingdom | Wellcome Trust | Restricted | SCR_017151 | 2026-08-04 09:44:07 | 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 set, data or information resource | 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 | 2026-08-04 09:40:51 | 3 | |||||||
|
Africa Centre for Health and Population Studies Resource Report Resource Website 1+ mentions |
Africa Centre for Health and Population Studies (RRID:SCR_008964) | Africa Centre Datasets, Africa Center Datasets, AfricaCentre Datasets | data set, data or information resource | Longitudinal datasets of demographic, social, medical and economic information from a rural demographic in northern KwaZulu-Natal, South Africa where HIV prevalence is extremely high. The data may be filtered by demographics, years, or by individuals questionnaires. The datasets may be used by other researchers but the Africa Centre requests notification that anyone contact them when downloading their data. The datasets are provided in three formats: Stata11 .dta; tables in a MS-Access .accdb database; and worksheets in a MS-Excel .xlsx workbook. Datasets are generated approximately every six months containing information spanning the whole period of surveillance from 1/1/2000 to present. | medicine, hiv infection, economic, demography, biology, social, longitudinal |
is listed by: re3data.org is listed by: DataCite has parent organization: University of KwaZulu-Natal; Durban; South Africa |
HIV | Wellcome Trust ; Agence Nationale de Recherches sur le Sida et les Hepatites Virales ; Department for International Development ; USAID ; EDCTP ; South African MRC ; National Research Foundation ; CSIR ; UNFPA ; CIDA |
Open unspecified license, Data Use Agreement, Approval required | nlx_152006 | SCR_008964 | Africa Centre for Health and Population Studies Datasets, Africa Center for Health and Population Studies | 2026-08-04 09:42:16 | 4 | |||||
|
DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | database, data or information resource | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-08-04 09:41:38 | 1797 | ||||
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Brain Intensity AbNormality Classification Algorithm Resource Report Resource Website 1+ mentions |
Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) | BIANCA | segmentation software, data processing software, software resource, software application, image analysis software | Software tool for automated segmentation of white matter hyperintensities. Classifies image’s voxels based on their intensity and spatial features, and the output image represents the probability per voxel of being WMH. Flexible in terms of MRI modalities to use and offers different options for weighting spatial information, local spatial intensity averaging, and different options for choice of number and location of training points. | images voxels classification, automated segmentation of white matter hyperintensities, white matter hyperintensities, | is a plug in for: FSL | Wellcome Trust ; Wolfson Foundation ; UK Stroke Association ; NIHR Oxford Biomedical Research Centre |
PMID:27402600 | Free, Freely available | SCR_024928 | BIANKA:Brain Intensity AbNormality Classification Algorithm | 2026-08-04 09:45:38 | 3 | ||||||
|
BIGSdb Resource Report Resource Website 1+ mentions |
BIGSdb (RRID:SCR_023551) | database, data or information resource | 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 | 2026-08-04 09:45:17 | 1 | |||||||
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Open Trials Resource Report Resource Website 1+ mentions |
Open Trials (RRID:SCR_015570) | database, data or information resource | 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 | 2026-08-04 09:43:41 | 3 | |||||||
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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 | Knut and Alice Wallenberg Foundation ; Swedish Foundation for Strategic Research ; Wellcome Trust ; Swedish Research Council ; SSF ; Cancerfonden ; EU ; Hjärnfonden ; SFO Strat Regen ; European Research Council ; Ollie and Elof Ericssons Foundation ; Åke Wiberg Foundation |
PMID:30096314 | Free, Available for download, Freely available | SCR_018356 | SCR_016999 | Linnarsson lab Mouse Brain Atlas | 2026-08-04 09:44:02 | 111 | ||||||
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GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | database, data or information resource | 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 |
Wellcome Trust ; Israel Ministry of Science and Technology ; Fund in Memory of Dr. Amir Abramovich |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-08-04 09:43:59 | 11 | |||||||
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MEROPS Resource Report Resource Website 500+ mentions |
MEROPS (RRID:SCR_007777) | MEROPS, MEROPS fam | database, data or information resource | 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 | 2026-08-04 09:41:59 | 736 | |||||
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MLST Resource Report Resource Website 1000+ mentions |
MLST (RRID:SCR_010245) | database, data or information resource | 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 | 2026-08-04 09:42:37 | 1230 |
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