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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Brain Imaging Data Structure (BIDs) Resource Report Resource Website 100+ mentions |
Brain Imaging Data Structure (BIDs) (RRID:SCR_016124) | BIDS | narrative resource, data or information resource, portal, standard specification | Standard specification for organizing and describing outputs of neuroimaging experiments. Used to organize and describe neuroimaging and behavioral data by neuroscientific community as standard to organize and share data. BIDS prescribes file naming conventions and folder structure to store data in set of already existing file formats. Provides standardized templates to store associated metadata in form of Javascript Object Notation (JSON) and tab-separated value (TSV) files. Facilitates data sharing, metadata querying, and enables automatic data analysis pipelines. System to curate, aggregate, and annotate neuroimaging databases. Intended for magnetic resonance imaging data, magnetoencephalography data, electroencephalography data, and intracranial encephalography data. | Data storing structure, neuroimaging, standardized template, data sharing, MRI data, MEG data, EEG data, iEEG data, FASEB list |
is used by: OpenNeuro is used by: SPARC Portal is used by: SPARC Data Standard is listed by: FAIRsharing is related to: BIDS-Matlab is related to: NiPoppy works with: MNE-BIDS |
International Neuroinformatics Coordinating Facility ; Laura and John Arnold Foundation ; NIGMS P20 GM103472; Wellcome Trust ; NIAAA U01 AA021697; NIMH Intramural Research Program ; German federal state of Sachsen-Anhalt ; European Regional Development Fund ; Medical Research Council United Kingdom ; NSF 1429999 |
PMID:27326542 PMID:29917016 PMID:31239435 PMID:31239438 PMID:37744469 |
Free, Freely available | https://bids-specification.readthedocs.io/en/stable/, https://doi.org/10.25504/FAIRsharing.rd1j6t | SCR_016124 | Brain Imaging Data Structure, BIDS, Brain Imaging Data Structure (BIDS), Brain Imaging Data Structure v1.4.0 | 2026-08-03 09:36:18 | 212 | |||||
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Stimfit Resource Report Resource Website 10+ mentions |
Stimfit (RRID:SCR_016050) | software resource, data processing software, software application, data analysis software | Software for viewing and analyzing electrophysiological data. It features an embedded Python shell that allows you to extend the program functionality by using numerical libraries such as NumPy and SciPy. | electrophysiology, python, numpy, scipy, numerical, library, stimulus, analysis |
uses: NumPy uses: SciPy |
European Research Council ; Wellcome Trust ; Gatsby Charitable Foundation |
PMID:24600389 | Free, Available for download | SCR_016050 | 2026-08-03 09:36:14 | 38 | ||||||||
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Clonalframe Resource Report Resource Website 100+ mentions |
Clonalframe (RRID:SCR_016060) | sequence analysis software, software application, data processing software, data analysis software, software resource | Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance. | analysis, sequence, inference, bacteria, microevolution, multilocus, clonal, sample, chromosome, homologuous, recombination, disrupted, inheritance, DNA, genome |
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 | DOI:10.1534/genetics.106.063305 | Free, Available for download | OMICS_14623 | https://github.com/xavierdidelot/ClonalFrameML, https://sources.debian.org/src/clonalframe/ | SCR_016060 | ClonalFrameML | 2026-08-03 09:36:14 | 379 | |||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | sequence analysis software, software application, data processing software, data analysis software, data analytics software, software resource | Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions. | protein, secondary, structure, prediction, amino, acid, sequence, accurate, JNet algorithm, solvent, accessibility, coiled, coil, region | Biotechnology and Biological Sciences Research Council ; Wellcome Trust 355804783; Wellcome Trust WT092340; Wellcome Trust WT083481; Wellcome Trust 106370Z14 |
DOI:10.1093/nar/gkn238 | Free, Available for download, Freely available,Tutorial available | SCR_016504 | Jprotein secondary structure PREDiction | 2026-08-03 09:36:27 | 126 | ||||||||
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Potassium Channel Database Resource Report Resource Website 1+ mentions |
Potassium Channel Database (RRID:SCR_011960) | KDB | data or information resource, data set | A Database of Potassium Ion Channel Homology Models & Molecular Dynamics Simulations. | potassium ion channel, homology model, crystal structure, molecular dynamics, simulation, structure, image |
is listed by: OMICtools has parent organization: University of Oxford; Oxford; United Kingdom |
BBSRC ; Wellcome Trust |
OMICS_01609 | SCR_011960 | Potassium Channel Database - Structures and Simulations | 2026-08-03 09:34:54 | 2 | |||||||
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Wellcome Trust Centre for Human Genetics Resource Report Resource Website 10+ mentions |
Wellcome Trust Centre for Human Genetics (RRID:SCR_003307) | WTCHG | topical portal, data or information resource, portal | An international leader in genetics, genomics and structural biology, and research institute of the Nuffield Department of Medicine at the University of Oxford, whose objective is to extend our understanding on how genetic inheritance makes us who we are in order to gain a clearer insight into mechanisms of health and disease. Looking across all three billion letters of the human genetic code, they aim to pinpoint variant spellings and discover how they increase or decrease an individual's risk of falling ill. They collaborate with research teams across the world on a number of large-scale studies in these areas. | genetics, genomics, structural biology |
has parent organization: University of Oxford; Oxford; United Kingdom is parent organization of: Happy is parent organization of: Wellcome-CTC Mouse Strain SNP Genotype Set is parent organization of: CHAoS is parent organization of: Platypus is parent organization of: Stampy is parent organization of: GWAMA is parent organization of: cortex var |
University of Oxford; Oxford; United Kingdom ; Wellcome Trust ; other sponsors |
Free, Freely available | nif-0000-31897 | SCR_003307 | 2026-08-03 09:32:14 | 49 | |||||||
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Proteomics Identifications (PRIDE) Resource Report Resource Website 500+ mentions |
Proteomics Identifications (PRIDE) (RRID:SCR_003411) | PRIDE | data repository, data or information resource, database, storage service resource, service resource | Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester. | proteomics, protein, peptide, mass spectrometry, annotation, standard, spectra, protein-protein interaction, amino acid, amino acid sequence, post-translational modification, biomart, bio.tools |
is used by: ProteomeXchange is used by: BioSample Database at EBI is recommended by: NIDDK Information Network (dkNET) is listed by: Biositemaps is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: HUPO Proteomics Standards Initiative is related to: ProteomeXchange has parent organization: European Bioinformatics Institute |
Wellcome Trust WT085949MA; European Union FP7 LSHG-CT-2006-036814; European Union FP7 260558; European Union FP7 262067; European Union FP7 202272; BBSRC BB/I024204/1 |
PMID:23203882 PMID:19662629 |
Free, Available for download, Freely available | nif-0000-03336, biotools:pride, r3d100011515 | https://www.ebi.ac.uk/pride/archive/, https://bio.tools/pride, https://doi.org/10.17616/R3F330 | SCR_003411 | PRoteomics IDEntifications database, PRIDE Archive - proteomics data repository, PRIDE Archive, PRIDE, Proteomics Identifications, Proteomics Identifications (PRIDE), PRoteomics IDEntifications database (PRIDE) | 2026-08-03 09:32:07 | 642 | ||||
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Wellcome Images Resource Report Resource Website |
Wellcome Images (RRID:SCR_004181) | Wellcome Images | image collection, data repository, data or information resource, database, image repository, storage service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.Digital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individuals | biomedical, clinical, disease, surgery, healthcare, genetics, neuroscience, imaging, science, medicine, history, painting, manuscript | Wellcome Trust | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100010779, nlx_143611 | https://doi.org/10.17616/R3HS58 | SCR_004181 | 2026-08-03 09:32:37 | 0 | |||||||
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GeneDB Spombe Resource Report Resource Website |
GeneDB Spombe (RRID:SCR_010639) | GeneDB_Spombe, GeneDB Spombe, GeneDB S. pombe | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE documented June 6, 2013 Database of all S. pombe (fission yeast) known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs. Curation of new and existing literature is ongoing and changes are incorporated weekly. User feedback is welcome. The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824, has been sequenced and annotated. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization. | fission yeast |
is related to: PomBase has parent organization: GeneDB |
Wellcome Trust | PMID:11859360 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_62442 | SCR_010639 | Schizosaccharomyces pombe GeneDB, GDB S. pombe | 2026-08-03 09:34:48 | 0 | |||||
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Genomics of Drug Sensitivity in Cancer Resource Report Resource Website 1000+ mentions |
Genomics of Drug Sensitivity in Cancer (RRID:SCR_011956) | Genomics of Drug Sensitivity in Cancer | data or information resource, database | A genomics database project is an academic research program to identify molecular features of cancers that predict response to anti-cancer drugs. | compound, gene, molecule, drug, FASEB list |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust | OMICS_01581 | SCR_011956 | 2026-08-03 09:34:54 | 1418 | |||||||
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SHERPA RoMEO Resource Report Resource Website |
SHERPA RoMEO (RRID:SCR_013815) | data or information resource, database | A database which houses publisher policies regarding the self- archiving of journal articles on the web and in Open Access repositories. RoMEO contains publishers' general policies on self-archiving of journal articles and certain conference series. Each entry provides a summary of the publisher's policy, including what version of an article can be deposited, where it can be deposited, and any conditions that are attached to that deposit. | database, publisher policy, open access |
is listed by: Connected Researchers is related to: Connected Researchers has parent organization: University of Nottingham; Nottingham; United Kingdom |
JISC ; Wellcome Trust |
Free, Public | SCR_013815 | RoMEO | 2026-08-03 09:35:32 | 0 | ||||||||
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CoCoMac Resource Report Resource Website 50+ mentions |
CoCoMac (RRID:SCR_007277) | CoCoMac | data or information resource, database | Online access (html or xml) to structural connectivity ("wiring") data on the Macaque brain. The database has become by far the largest of its kind, with data extracted from more than four hundred published tracing studies. The main database, contains data from tracing studies on anatomical connectivity in the macaque cerebral cortex. Also available are a variety of tools including a graphical simulation workbench, map displays and the CoCoMac-Paxinos-3D viewer. Submissions are welcome. To overcome the problem of divergent brain maps ORT (Objective Relational Transformation) was developed, an algorithmic method to convert data in a coordinate- independent way based on logical relations between areas in different brain maps. CoCoMac data is used to analyze the organization of the cerebral cortex, and to establish its structure- function relationships. This includes multi-variate statistics and computer simulation of models that take into account the real anatomy of the primate cerebral cortex. This site * Provides full, scriptable open access to the data in CoCoMac (you must adhere to the citation policy) * Powers the graphical interface to CoCoMac provided by the Scalable Brain Atlas * Sports an extensive search/browse wizard, which automatically constructs complex search queries and lets you further explore the database from the results page. * Allows you to get your hands dirty, by using the custom SQL query service. * Displays connectivity data in tabular form, through the axonal projections service. CoCoMac 2 was initiated at the Donders Institute for Brain, Cognition and Behaviour, and is currently supported by the German neuroinformatics node and the Computational and Systems Neuroscience group at the Juelich research institute. | brain, macaque, non-human primate, connectivity, microcircuitry, prefrontal cortex, neural network, structure, function, neuroanatomy, brain circuitry, axonal projection, data repository, visualization, atlas application, computational neuroscience, magnetic resonance, ontology, php, tractography, web environment, software, FASEB list |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Scalable Brain Atlas has parent organization: German Neuroinformatics Node (G-Node) is parent organization of: CoCoMac-Paxinos3D viewer |
DFG ; Heinrich-Heine University of Dusseldorf; Dusseldorf; Germany ; Wellcome Trust |
PMID:23293600 PMID:11545697 PMID:15319511 PMID:15971361 PMID:10703043 |
Open Access | nif-0000-00022 | http://www.nitrc.org/projects/cocomac, http://134.95.56.239/home.asp | http://cocomac.org/, http://cocomac.g-node.org/drupal/ | SCR_007277 | CoCoMac Brain Connectivity Database, Collations of Connectivity Data on the Macaque Brain, CoCoMac (Collations of Connectivity Data on the Macaque Brain) | 2026-08-03 09:33:19 | 57 | |||
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Database of Spatially Interacting Motifs in Proteins Resource Report Resource Website |
Database of Spatially Interacting Motifs in Proteins (RRID:SCR_007735) | iMOTdb | data or information resource, database | Comprehensive collection of spatially interacting motifs in proteins. Interacting motif database lists interacting motifs that are identified for all structural entries in PDB. Conserved patterns or finger prints are identified for individual structural entries and also grouped together for reporting common motifs shared among all superfamily members. | Conserved patterns, spatially interacting motifs, finger prints, structural entries, protein | has parent organization: Tata Institute of Fundamental Research; Mumbai; India | Wellcome Trust | PMID:16381866 | Free, Freely available | nif-0000-03018, SCR_008194, nif-0000-21218 | SCR_007735 | 2026-08-03 09:33:40 | 0 | ||||||
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VGNC Resource Report Resource Website 10+ mentions |
VGNC (RRID:SCR_017514) | service resource, data or information resource, database | Software resource for vertebrate gene nomenclature. Database of gene symbols. Coordinates with vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), AGNC (Anole green lizard), XNC (Xenopus frog) and ZNC (zebrafish), to ensure genes are named in line with their human homologs. | Vertebrate, gene, nomenclature, data, symbol | is related to: HGNC | NHGRI U24 HG003345; Wellcome Trust |
Free, Freely available | SCR_017514 | Vertebrate Gene Nomenclature Committee | 2026-08-03 09:36:39 | 13 | ||||||||
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Alien-hunter Resource Report Resource Website 1+ mentions |
Alien-hunter (RRID:SCR_015967) | software resource, software application, standalone software | Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer. | Horizontal Gene Transfer, Interpolated Variable Order Motifs, gene, transfer, interpolated, variable, motif, prediction, hgt, ivom |
is listed by: Debian is listed by: OMICtools works with: Artemis: Genome Browser and Annotation Tool |
Wellcome Trust | PMID:16837528 DOI:10.1093/bioinformatics/btl369 |
Free, Available for download | OMICS_08280 | https://sources.debian.org/src/alien-hunter/, https://sources.debian.org/src/alien-hunter/ | SCR_015967 | 2026-08-03 09:36:12 | 5 | ||||||
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FLIMfit Resource Report Resource Website 1+ mentions |
FLIMfit (RRID:SCR_016298) | software toolkit, software resource, software application | Software package for quantitative analysis of large Fluorescence Lifetime Imaging Microscopy (FLIM) data, including global analysis. It is able to routinely analyse multi-well plate FLIM datasets on conventional PC workstations in a reasonable time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | fluorescence, lifetime, imaging, microscopy, dataset, global, analysis, multiwell, plate, routine | United Kingdom Biotechnology and Biological Sciences Research Council BBSRC BB/E003621/1; United Kingdom Technology Strategy Board Technology Award CHBT/007/00030; Wellcome Trust WT 095931/Z/11/Z |
PMID:23940626 DOI:10.1371/journal.pone.0070687 |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/flimfit/FLIMfit | SCR_016298 | 2026-08-03 09:36:42 | 3 | ||||||||
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Tract Based Spatial Statistics Resource Report Resource Website 1+ mentions |
Tract Based Spatial Statistics (RRID:SCR_024932) | TBSS | image analysis software, software resource, software application, data processing software | Software tool to improve sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies. | analysis of multi-subject diffusion imaging studies, imaging analysis, imaging, | is a plug in for: FSL | EPSRC ; BBSRC ; MRC ; Wellcome Trust ; Multiple Sclerosis Society |
PMID:16624579 | Free, Freely available | SCR_024932 | , Tract-Based Spatial Statistics, TBSS:Tract-Based Spatial Statistics | 2026-08-03 09:38:28 | 4 | ||||||
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ezBIDS Resource Report Resource Website |
ezBIDS (RRID:SCR_025563) | software resource, web application | Web-based BIDS conversion tool to convert neuroimaging data and associated metadata to BIDS standard. Guided standardization of neuroimaging data interoperable with major data archives and platforms. | Guided standardization, neuroimaging data, Brain Imaging Data Structure, BIDS conversion tool, convert neuroimaging data, associated metadata, interoperable, BIDS standard, | NINDS UM1NS132207; BRAIN CONNECTS ; NIBIB R01EB029272; NIBIB R01EB030896; NSF ; Kavli Foundation ; Wellcome Trust ; NIMH R01MH133701; Spanish Government |
PMID:38332144 | Free, Freely available | https://brainlife.io/ezbids/, | SCR_025563 | ez Brain Imaging Data Structure | 2026-08-03 09:38:49 | 0 | |||||||
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University College London Darwin Research Core Facility Resource Report Resource Website |
University College London Darwin Research Core Facility (RRID:SCR_026345) | service resource, access service resource, core facility | Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas. | ABRF, biochemistry, molecular, structural and cellular biology, service, |
is listed by: ABRF CoreMarketplace has parent organization: University College London; London; United Kingdom |
Wellcome Trust ; HEFCE ; University College London |
ABRF_3028 | https://coremarketplace.org/?FacilityID=3028&citation=1 | SCR_026345 | , UCL Darwin Research Facility, Darwin Research Facility, University College London Darwin Research Facility | 2026-08-03 09:38:46 | 0 | |||||||
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Metabolic Subphenotype Predictor Resource Report Resource Website 1+ mentions |
Metabolic Subphenotype Predictor (RRID:SCR_027192) | software resource, source code | Software repository contains code for Inference of T2D metabolic subphenotypes (MuscleIR, Beta-cell Function, Incretin Effect, Hepatic IR), Identification of dominant metabolic subphenotype, Feature extraction from glucose tiemseries, Extraction of reduced representation of glucose tiemseries,Visualization of metabolic phenotypes based on various glucose-related metrics,Concordance between CGM and Venous glucose values from at home and at clinical setting, Classification of metabolic subphenotypes. | Inference of T2D metabolic subphenotypes, identification of dominant metabolic subphenotype, extraction from glucose tiemseries, visualization of metabolic phenotypes, classification of metabolic subphenotype, s | NIDDK R01 DK110186; Stanford PHIND award ; Stanford Diabetes Research Center ; Wellcome Trust ; NIDDK U01 DK105535; NIDDK U01 DK085545; NIDDK UM1DK126185; NHLBI 2T32HL09804911 |
PMID:39715896 | Free, Available for download, Freely available | SCR_027192 | 2026-08-03 09:39:05 | 1 |
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