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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VasoTracker Resource Report Resource Website 1+ mentions |
VasoTracker (RRID:SCR_017233) | data acquisition software, data analysis software, data processing software, software application, software resource | Open source and stand alone software for assessing vascular reactivity. Used in pressure myograph system. | vascular, reactivity, pressure, myograph, system |
is related to: Durham University; Durham; England has parent organization: University of Strathclyde; Glasgow; United Kingdom |
British Heart Foundation ; Wellcome Trust |
PMID:30846942 | Free, Available for download, Freely available | https://github.com/VasoTracker/VasoTracker | SCR_017233 | 2026-09-05 06:28:20 | 5 | |||||||
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Physiome Model Repository Resource Report Resource Website 1+ mentions |
Physiome Model Repository (RRID:SCR_017374) | PMR | data or information resource, data repository, dynamic model, model, service resource, storage service resource | Repository of mainly CellML models powered by collection of software tools and libraries with PMR2 software suite as core power. Third party integration suites are RICORDO, Virtuoso, BiVeS/BudHat, OpenCOR, CombineArchive Web, WebCAT, Morre/MaSyMoS. | Physiology, repository, CellML, cell, model, file, metadata, PMR2 |
is used by: SPARC Portal is related to: CellML is related to: International Union of Physiological Sciences: Physiome Project |
Auckland Bioengineering Institute ; British Heart Foundation ; Maurice Wilkins Centre for Molecular Biodiscovery ; Virtual Physiological Human Network of Excellence ; Wellcome Trust |
DOI:10.1093/bioinformatics/btq723 | Free, Available for download, Freely available | http://www.cellml.org/tools/pmr/, http://models.cellml.org/ | SCR_017374 | Physiome Repository, PMR2 | 2026-09-05 06:28:23 | 5 | |||||
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Accessible Resource for Integrated Epigenomics Studies Resource Report Resource Website 50+ mentions |
Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) | data access protocol, data or information resource, portal, software resource, topical portal, web service | Portal for epigenomic information on range of human tissues, including DNA methylation data on peripheral blood at multiple time points across lifecourse. Provides web interface to browse methylation variation between groups of individuals and across time. | Epigenomic, human, tissue, DNA, methylation, data, peripheral, blood | BBSRC ; Medical Research Council ; University of Bristol ; Wellcome Trust |
PMID:25991711 | Free, Freely available | http://www.bristol.ac.uk/alspac/ | SCR_017492 | ARIES | 2026-09-05 06:28:25 | 50 | |||||||
|
Seq-Gen Resource Report Resource Website 100+ mentions |
Seq-Gen (RRID:SCR_014934) | simulation software, software application, software resource | Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. | simulator, simulation software, molecular evolution, nucleotide, amino acid, sequence, phylogeny, phylogenetic tree |
is listed by: Debian is listed by: OMICtools has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; BBSRC ; Fogarty ; The Royal Society |
DOI:10.1093/bioinformatics/13.3.235 | Available for download | OMICS_15373 | https://sources.debian.org/src/seq-gen/ | SCR_014934 | 2026-09-05 06:27:52 | 158 | ||||||
|
Tracer Resource Report Resource Website 1000+ mentions |
Tracer (RRID:SCR_019121) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software tool for analysing trace files generated by Bayesian MCMC runs. Software package for visualising and analysing MCMC trace files generated through Bayesian phylogenetic inference. Provides kernel density estimation, multivariate visualisation, demographic trajectory reconstruction, conditional posterior distribution summary and more. | Analysing trace files, files generated by Bayesian MCMC runs, MCMC trace files, conditional posterior distribution summary, demographic trajectory reconstruction, Bayesian phylogenetic inference, kernel density estimation, multivariate visualisation | European Union Seventh Framework Programme ; NIAID R01 AI107034; NIAID U19 AI135995; NSF DMS 1264153; Wellcome Trust |
PMID:29718447 | Free, Available for download, Freely available | https://github.com/beast-dev/tracer, http://gensoft.pasteur.fr/docs/Tracer/v1.6, http://beast.community/tracer, https://github.com/beast-dev/tracer/releases/tag/v1.7.1 | SCR_019121 | Tracer v1.7.1, Tracer v1.6 | 2026-09-05 06:28:46 | 1598 | |||||||
|
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 | 2026-09-05 06:30:07 | 8 | ||||||
|
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 | 2026-09-05 06:30:19 | 3 | |||||||||
|
Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Analysis software that identifies antibiotic resistance genes by running local assemblies. It can also be used for MLST calling. | software, analysis, tool, sequence, antibiotic, resistance, assembly, local, mlst |
is listed by: Debian is listed by: OMICtools |
Biotechnology and Biological Sciences Research Council BB/M014088/1; Wellcome Trust 206194 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-09-05 06:28:01 | 220 | ||||||
|
HumanNet Resource Report Resource Website 100+ mentions |
HumanNet (RRID:SCR_016146) | data analysis software, data or information resource, data processing software, database, software application, software resource, web application | Database of human protein-encoding genes that is constructed by a modified Bayesian integration of 'omics' data from multiple organisms. Each data type is weighted according to how well it links genes that are known to function together in humans, and each interaction has an associated log-likelihood score (LLS) that measures the probability of an interaction representing a true functional linkage between two genes. | probability, gene, protein, encode, statistic, likelihood, network, bayesian, omic, pathway, guilt by association, FASEB list |
has parent organization: University of Texas at Austin; Texas; USA has parent organization: Yonsei University; Seoul; South Korea |
Korean government (MEST) 2010-0017649; National Research Foundation of Korea (NRF) ; Packard Foundations ; POSCO TJ ; U.S. Army Research 58343-MA; Welch F1515; Wellcome Trust 076113; Wellcome Trust 085475 |
Freely available | SCR_016146 | 2026-09-05 06:28:04 | 135 | |||||||||
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Research Data Management Platform Resource Report Resource Website 1+ mentions |
Research Data Management Platform (RRID:SCR_016268) | RDMP | data management software, data or information resource, data repository, service resource, software application, software resource, software toolkit, storage service resource | Software toolkit which automates the loading, storage, linkage and provision of data sets. It also cleans, transforms and documents provenance meta-data and domain knowledge to make data sets “research ready”. | metadata, reproducibility, anonymization, security, audit, clinical, dataset, translational, research, data, management, catalogue, health, informatics, linkage | has parent organization: University of Dundee; Scotland; United Kingdom | EU Horizon 2020 633983; Medical Research Council (MRC) MR/M501633/1; Wellcome Trust WT086113 |
Free, Available for download | https://hic.dundee.ac.uk/Installers/RDMP/Stable/ | SCR_016268 | 2026-09-05 06:28:06 | 2 | |||||||
|
Gaussian-Copula Mutual Information (GCMI) Resource Report Resource Website 10+ mentions |
Gaussian-Copula Mutual Information (GCMI) (RRID:SCR_016450) | GCMI | data analysis software, data processing software, software application, software resource | Software package of functions for calculating mutual information and other information theoretic quantities using a parametric Gaussian copula. | gaussian, copula, parametric, equation, calculation, python, matlab, repository, statistic | European Research Council 646657; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/D01400X1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/J018929/1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/L027534/1; UK Biotechnology and Biological Sciences Research Council (BBSRC) BB/M009742/1; Wellcome Trust 098433; Wellcome Trust 107802 |
Free, Available for download | SCR_016450 | gcmi : Gaussian-Copula Mutual Information, Gaussian-Copula Mutual Information | 2026-09-05 06:28:09 | 11 | ||||||||
|
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 | 2026-09-05 06:33:24 | 3 | |||||||
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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 or information resource, data set | 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 | 2026-09-05 06:33:29 | 4 | |||||
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Retinal wave repository Resource Report Resource Website |
Retinal wave repository (RRID:SCR_010462) | Retinal wave repository | data or information resource, data set | A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged. | hdf5, development, neural circuit, retina, eye, multielectrode, array recording, spontaneous activity, reproducible research, retinal wave, electrophysiology, multielectrode array, developmental age, genotype |
has parent organization: GigaScience has parent organization: Code Analysis Repository and Modelling for e-Neuroscience has parent organization: University of Cambridge; Cambridge; United Kingdom |
Developing retina, Aging | EPSRC EP/E002331/1; BBSRC BB/H023577/1; BBSRC BB/I000984/1; Wellcome Trust 083205/B/07/Z |
PMID:24666584 | Registration required, (CARMEN), Acknowledgement required, The community can contribute to this resource | nlx_157664 | http://www.damtp.cam.ac.uk/user/eglen/waverepo/ | SCR_010462 | A data repository and analysis framework for spontaneous neural activity recordings in developing retina | 2026-09-05 06:33:44 | 0 | |||
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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 | 2026-09-05 06:33:00 | 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 | 2026-09-05 06:33:05 | 0 | ||||||||
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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 | 2026-09-05 06:32:37 | 316 | |||||
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UK Biobank Resource Report Resource Website 1000+ mentions |
UK Biobank (RRID:SCR_012815) | biobank, material storage repository, service resource, storage service resource | Biobank provides data collected at Assessment Center and via online questionnaires on participants aged 40-69 years recruited throughout United Kingdom and provides summary information to improve prevention, diagnosis and treatment of serious and life threatening illnesses. | Data, collected, United Kingdom, prevention, diagnosis, treatment, illness, questionnaire, blood, urine, saliva, cognitive function, psychological status, hearing test, interview, operation, medication, blood pressure, body measurementdie |
is listed by: One Mind Biospecimen Bank Listing is related to: AstraZeneca PheWAS Portal |
cancer, heart diseases, stroke, diabetes, arthritis, osteoporosis, eye disorders, depression, dementia. | MRC ; Scottish Government ; UK Department of Health ; Wellcome Trust ; Welsh Assembly Government |
grid.421945.f, nlx_95741, ISNI: 0000 0004 0396 0496, Wikidata: Q7864819 | https://ror.org/02frzq211 | SCR_012815 | 2026-09-05 06:33:58 | 3905 | |||||||
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Brain Intensity AbNormality Classification Algorithm Resource Report Resource Website 1+ mentions |
Brain Intensity AbNormality Classification Algorithm (RRID:SCR_024928) | BIANCA | data processing software, image analysis software, segmentation software, software application, software resource | 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 | NIHR Oxford Biomedical Research Centre ; UK Stroke Association ; Wellcome Trust ; Wolfson Foundation |
PMID:27402600 | Free, Freely available | SCR_024928 | BIANKA:Brain Intensity AbNormality Classification Algorithm | 2026-09-05 06:34:45 | 7 | ||||||
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IBEX Knowledge Base Resource Report Resource Website 1+ mentions |
IBEX Knowledge Base (RRID:SCR_025296) | knowledge base | Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase. | Antibody, validation, multiplexed imaging, | Chan Zuckerberg Initiative ; NCI ; NIAID ; Schroeder Allergy and Immunology Research Institute ; McMaster University ; CA ; Wellcome Trust |
Free, Freely available | https://zenodo.org/records/7693279 | SCR_025296 | Iterative Bleaching Extends Multiplexity (IBEX) Knowledge-Base | 2026-09-05 06:34:55 | 4 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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