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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ARNIE Resource Report Resource Website |
ARNIE (RRID:SCR_000514) | ARNIE | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided. | network, orthologue, paralogue, gene, orthologue, protein interaction, protein, blast, extracellular, expression profiling, interaction network, ligand, interaction, signaling |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
MRC ; Wellcome Trust |
PMID:20802085 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01529 | SCR_000514 | AVEXIS Receptor Network with Integrated Expression | 2026-07-28 09:40:00 | 0 | |||||
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BioLexicon Resource Report Resource Website 1+ mentions |
BioLexicon (RRID:SCR_000589) | data or information resource, database | A large-scale English terminological database that contains over 2.2.M lexical entries (3.3M semantic relations), terminological variants and rich linguistic information (subcategorization frames) which supports text mining systems. It is primarily intended to support text mining and information retrieval in the biomedical domain. The BioLexicon provides specific information to help determine the relevant facts to be extracted. BioLexicon is available in a relational database format (MySQL dump format) and it adheres to the EAGLES/ISO standards for lexical resources. | text mining, biomedical, terminology, semantics, terminological variant, linguistic, information retrieval, computational linguistics |
uses: MEDIE is used by: Europe PubMed Central is listed by: FORCE11 has parent organization: National Centre for Text Mining |
Europe PubMed Central ; Wellcome Trust ; Economic and Social Research Council |
PMID:21992002 PMID:20183880 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_54008 | SCR_000589 | BOOTStrep Bio-Lexicon | 2026-07-28 09:40:01 | 4 | ||||||
|
COSMIC - Catalogue Of Somatic Mutations In Cancer Resource Report Resource Website 1000+ mentions |
COSMIC - Catalogue Of Somatic Mutations In Cancer (RRID:SCR_002260) | COSMIC | data or information resource, database |
Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines. |
cancer, mutation, somatic mutation, tumor, cancer genome, genome, gene, dna, tissue, histology, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Cancer | Wellcome Trust 077012/Z/05/Z | PMID:20952405 | Free | nif-0000-02690, biotools:cosmic, OMICS_00082 | http://www.sanger.ac.uk/perl/CGP/cosmic, https://bio.tools/cosmic | SCR_002260 | Catalogue Of Somatic Mutations In Cancer | 2026-07-28 09:40:23 | 4486 | |||
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ShARM Resource Report Resource Website 1+ mentions |
ShARM (RRID:SCR_003120) | ShARM | tissue bank, biomaterial supply resource, material resource | A not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA). | data sharing, female, male, gut, heart, kidney, livers, lung, mammary fat, muscle, pancreas, bat, bladder, bone, brain, femur, skin, spleen, thymus, tibia, wat, aged tissue, aged mouse, murine model | is listed by: One Mind Biospecimen Bank Listing | Aging, Control, Young control | Wellcome Trust | PMID:24085518 | Free, Freely available | nlx_156767 | SCR_003120 | Shard Ageing Research Models | 2026-07-28 09:40:36 | 4 | ||||
|
ChEMBL Resource Report Resource Website 1000+ mentions |
ChEMBL (RRID:SCR_014042) | data or information resource, database | Collection of bioactive drug-like small molecules that contains 2D structures, calculated properties and abstracted bioactivities. Used for drug discovery and chemical biology research. Clinical progress of new compounds is continuously integrated into the database. | database, compound, data, bioassay, bioactive, molecule, drug, discovery |
is used by: GEROprotectors is used by: PubChem is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
Wellcome Trust ; EMBL Member States ; Medicines for Malaria Ventures ; EU Innovative Medicines Initiative ; GSK ; Syngenta ; Pfizer |
PMID:21948594 | Public, Free, Freely available, Acknowledgement requested | r3d100010539 | https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320, https://doi.org/10.17616/R3C320 | SCR_014042 | ChEMBLdb, Chembl, ChEMBL Database | 2026-07-28 09:43:41 | 2433 | |||||
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Open Source Brain Resource Report Resource Website 10+ mentions |
Open Source Brain (RRID:SCR_001393) | OSB | service resource, data or information resource, data repository, database, storage service resource | A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome. | model, neuroml, pynn, computational model, neural system, neuron, disease, data analysis service, visualization, 3d explorer, network, ion channel distribution, ion channel, microcircuit |
uses: PyNN uses: NeuroML is used by: NIF Data Federation is listed by: Integrated Models is related to: neuroConstruct is related to: NWB Explorer is related to: Allen Institute for Brain Science has parent organization: University College London; London; United Kingdom |
Wellcome Trust | Free, Freely Available | nlx_152590 | SCR_001393 | OpenSourceBrain | 2026-07-28 09:40:15 | 26 | ||||||
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SpydrPick Resource Report Resource Website 1+ mentions |
SpydrPick (RRID:SCR_018176) | software application, software resource, data analysis software, data processing software | Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree. | Direct coupling analysis, aligned categorical datasets, analysis, genome, bacteria, phylogenetic signal, correction, phylogenetic tree, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
COIN Center of Excellence ; Academy of Finland ; Wellcome Trust ; European Research Council |
PMID:31361894 | Free, Available for download, Freely available | biotools:SpydrPick | https://anaconda.org/bioconda/spydrpick, https://bio.tools/SpydrPick | SCR_018176 | 2026-07-28 09:44:51 | 2 | ||||||
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SuperDCA Resource Report Resource Website 1+ mentions |
SuperDCA (RRID:SCR_018175) | software application, software resource, data analysis software, data processing software | Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis. | Protein, sequence, alignment, analysis, genome, loci, epistasis | Academy of Finland ; Wellcome Trust ; Royal Society ; European Research Council |
PMID:29813016 | Free, Available for download, Freely available | SCR_018175 | Super Direct Coupling Analysis | 2026-07-28 09:44:42 | 1 | ||||||||
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genomics resource for animal lectins Resource Report Resource Website 1+ mentions |
genomics resource for animal lectins (RRID:SCR_018122) | data or information resource, topical portal, portal | Resource presents information about animal lectins involved in various sugar recognition processes. | Genomic, animal lectin, sugar recognition process | has parent organization: Imperial College London; London; United Kingdom | BBSRC ; Wellcome Trust ; Consortium for Functional Glycomics |
Free, Freely available | SCR_018122 | 2026-07-28 09:44:41 | 3 | |||||||||
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EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data or information resource, database, data access protocol, software resource, web service | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-07-28 09:44:53 | 233 | |||||||
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xiNET Resource Report Resource Website 10+ mentions |
xiNET (RRID:SCR_021010) | software application, data access protocol, software resource, data processing software, data visualization software, web service | Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains. | Crosslinking mass spectrometry data visualization, linkage sites, linked peptides, crosslinking reaction product display, crosslink network maps, maps with residue resolution | Wellcome Trust | PMID:25648531 | Free, Available for download, Freely available | http://github.com/colin-combe/crosslink-viewer | SCR_021010 | Crosslink Network Maps With Residue Resolution | 2026-07-28 09:45:09 | 19 | |||||||
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Jpred Resource Report Resource Website 100+ mentions |
Jpred (RRID:SCR_016504) | software application, data analysis software, sequence analysis software, software resource, data processing software, data analytics software | 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 | 2026-07-28 09:44:19 | 126 | ||||||||
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riboWaltz Resource Report Resource Website 10+ mentions |
riboWaltz (RRID:SCR_016948) | software application, data analysis software, software resource, data processing software, data visualization software | Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates. | calculation, optimal, Psite, offset, diagnostic, analysis, visual, inspection, ribosome, profiling, data, read, alignment, transcript, coordinate |
uses: ggplot2 uses: Biostrings uses: GenomicFeatures uses: GenomicRanges uses: IRanges uses: devtools is related to: R Project for Statistical Computing |
Autonomous Province of Trento ; Wellcome Trust |
PMID:30102689 | Free, Available for download, Freely available | SCR_016948 | 2026-07-28 09:44:26 | 21 | ||||||||
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ALSPAC Resource Report Resource Website 100+ mentions |
ALSPAC (RRID:SCR_007260) | ALSPAC | project portal, data or information resource, portal | A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally. | longitudinal, study, parent, child, health, research, mother, development, research, disease, genetic, environmental | has parent organization: University of Bristol; Bristol; United Kingdom | UK Medical Research Council ; Wellcome Trust ; University of Bristol |
Available to the research community | nif-0000-30224 | SCR_007260 | The Avon Longitudinal Study of Parents and Children, Avon Longitudinal Study of Parents and Children | 2026-07-28 09:41:56 | 460 | ||||||
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Predicting Language Outcome and Recovery After Stroke (PLORAS) Resource Report Resource Website |
Predicting Language Outcome and Recovery After Stroke (PLORAS) (RRID:SCR_014498) | project portal, data or information resource, portal | A research project investigating the difficulties of recovering language after stroke (aphasia). The overall aim of the study is to give future stroke survivors accurate predictions of their aphasia recovery by creating clinical tools and discerning why some patients recover from aphasia better than others. | stroke, aphasia, language, project portal, aphasia recovery, language outcome, recovery prediction | Aphasia, Stroke | Wellcome Trust ; Stroke Association |
Public | SCR_014498 | 2026-07-28 09:43:53 | 0 | |||||||||
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hMRI-toolbox Resource Report Resource Website 10+ mentions |
hMRI-toolbox (RRID:SCR_017682) | software application, software toolkit, software resource, data processing software | Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis. | Quantitative, MRI, data, processing, multi, parameter, qMRI, map, spatial, registration, statistical, analysis, histology, longitudinal, relaxation, rate R1 and R2, proton, density, magnetisation, transfer, MT saturation |
is related to: MATLAB is related to: SPM |
European Structural and Investment Fund ; European Regional Development Fund ; Belgian Walloon Government ; European Research Council ; Swiss State Secretariat for Education ; Research and Innovation ; German Research Foundation ; Swiss National Science Foundation ; Leenaards Foundation ; Roger De Spoelberch Foundation ; Wellcome Trust ; Emory Universitys Research Council ; Swedish Research Council |
DOI:10.1016/j.neuroimage.2019.01.029 | Free, Available for download, Freely available | https://github.com/hMRI-group/hMRI-toolbox | SCR_017682 | 2026-07-28 09:44:40 | 33 | |||||||
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BALBES Resource Report Resource Website 1+ mentions |
BALBES (RRID:SCR_018763) | software application, standalone software, software toolkit, software resource | Software system for solving protein structures using x-ray crystallographic data. Automatic molecular replacement pipeline for molecular replacement in CCP4. Integrates into one system all components necessary for solving crystal structure by Molecular Replacement. System is automated so that it needs no user intervention when running combination of jobs such as model searching, molecular replacement and refinement. | Molecular replacement pipeline, protein structure, solving protein structure, x-ray crystallographic data, molecular replacement, molecular replacement in CCP4, solving crystal structure, automated system, no user intervention, model searching, refinement |
uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: CCP4 |
Wellcome Trust ; NIGMS R01 GM069758 |
PMID:18094476 | Free, Available for download, Freely available | SCR_018763 | 2026-07-28 09:44:45 | 1 | ||||||||
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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) | access service resource, 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 | 2026-07-28 09:46:37 | 0 | |||||||
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Metabolic Subphenotype Predictor Resource Report Resource Website 1+ mentions |
Metabolic Subphenotype Predictor (RRID:SCR_027192) | source code, software resource | 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 | 2026-07-28 09:47:03 | 1 | |||||||||
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Souporcell Resource Report Resource Website 1+ mentions |
Souporcell (RRID:SCR_027462) | software application, source code, software resource | Software tool to cluster cells using the genetic variants detected within the scRNAseq reads. Robust clustering of single-cell RNA-seq data by genotype without reference genotypes. Used for clustering scRNAseq by genotypes. | Clustering scRNAseq by genotypes, cluster cells, genetic variants, scRNAseq reads, | Wellcome Trust ; UK Medical Research Council ; British Heart Foundation |
PMID:32366989 | Free, Available for download, Freely available | SCR_027462 | 2026-07-28 09:47:11 | 1 |
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