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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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POAS4SPM Resource Report Resource Website 1+ mentions |
POAS4SPM (RRID:SCR_010469) | POAS4SPM | software resource | Software toolbox for SPM to denoise diffusion MRI data. Used for diffusion weighted magnetic resonance imaging data enhancement based on structural adaptive smoothing in both voxel space and diffusion-gradient space.Part of the ACID-toolbox. | denoise diffusion MRI data, diffusion weighted, magnetic resonance imaging data, MRI data, |
is related to: ACID works with: SPM |
Wellcome Trust ; Deutsche Forschungsgemeinschaft |
PMID:24993814 | nlx_157718 | http://www.diffusiontools.com/ | SCR_010469 | Position Orientation Adaptive Smoothing for SPM | 2026-08-01 12:03:52 | 4 | |||||
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ACT: Artemis Comparison Tool Resource Report Resource Website 10+ mentions |
ACT: Artemis Comparison Tool (RRID:SCR_004507) | ACT | software resource | A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | dna sequence, genome, synteny, pairwise comparison |
is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust | PMID:15976072 | GNU General Public License | OMICS_00928, nlx_48986 | SCR_004507 | Artemis Comparison Tool | 2026-08-01 12:02:42 | 46 | |||||
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European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2026-08-01 12:02:44 | 3696 | ||||||
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NeuronVisio Resource Report Resource Website 1+ mentions |
NeuronVisio (RRID:SCR_006839) | Neuronvisio | d visualization software | A Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections'''' properties and it offers easy integration with matplotlib for plotting the results. The geometry can be saved using NeuroML and the computational results in a customized and extensible HDF5 format; the results can then be reload in the software and analyzed in a later stage, without re-running the simulation. Featuring 3D visualization of the model with the possibility to change it runtime; creation of vectors to record any variables present in the section; pylab integration to plot directly the result of the simulation; exploration of the timecourse of any variable among time using a color coded scale; saving the results simulation for later analysis; automatic download and running of models in ModelDB. | 3d visualization, electrophysiological model, hdf storage, matplotlib integration, neuron model, visualization, neuron, visualization, electrophysiology |
is related to: INCF Software Center is related to: NEURON is related to: ModelDB has parent organization: European Bioinformatics Institute |
Wellcome Trust | PMID:22685429 | GNU General Public License, Acknowledgement requested | nlx_156723 | SCR_006839 | Neuron visio | 2026-08-01 12:03:18 | 3 | |||||
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InterMine Resource Report Resource Website 10+ mentions |
InterMine (RRID:SCR_001772) | software resource | An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust | PMID:24753429 | Free, Freely available | OMICS_03840, biotools:intermine | https://github.com/intermine/intermine, https://bio.tools/intermine | http://intermine.github.io/intermine.org/ | SCR_001772 | 2026-08-01 12:01:50 | 22 | |||||
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Wellcome Trust Case Control Consortium Resource Report Resource Website 100+ mentions |
Wellcome Trust Case Control Consortium (RRID:SCR_001973) | WTCCC | data or information resource | Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in African populations. The same approach has been used to type 2,000 cases of tuberculosis (TB) and 2,000 cases of malaria, as well as 2,000 shared controls. As well as addressing diseases of major global significance, and extending WTCCC coverage into the area of infectious disease, the inclusion of samples of African origin has obvious benefits with respect to methodological aspects of genome-wide association analysis. Second, the WTCCC has, for four additional diseases (autoimmune thyroid disease, breast cancer, ankylosing spondylitis, multiple sclerosis), completed an analysis of 15,000 SNPs designed to represent a large proportion of the known non-synonymous coding SNPs across the genome. This analysis has been performed at the WTSI using a custom Infinium chip (Illumina). Data release The genotypic data of the control samples (1958 British Birth Cohort and UK Blood Service) and from seven diseases analyzed in the main study are now available to qualified researchers. Summary genotype statistics for these collections are available directly from the website. Access to the individual-level genotype data and summary genotype statistics is by application to the Consortium Data Access Committee (CDAC) and approval subject to a Data Access Agreement. WTCCC2: A further round of GWA studies were funded in April 2008. These include 15 WTCCC-collaborative studies and 12 independent studies be supported totaling approximately 120,000 samples. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC2 will perform genome-wide association studies in 13 disease conditions: Ankylosing spondylitis, Barrett's oesophagus and oesophageal adenocarcinoma, glaucoma, ischaemic stroke, multiple sclerosis, pre-eclampsia, Parkinson's disease, psychosis endophenotypes, psoriasis, schizophrenia, ulcerative colitis and visceral leishmaniasis. WTCCC2 will also investigate the genetics of reading and mathematics abilities in children and the pharmacogenomics of statin response. Over 60,000 samples will be analyzed using either the Affymetrix v6.0 chip or the Illumina 660K chip. The WTCCC2 will also genotype 3,000 controls each from the 1958 British Birth cohort and the UK Blood Service control group, and the 6,000 controls will be genotyped on both the Affymetrix v6.0 and Illumina 1.2M chips. WTCCC3: The Wellcome Trust has provided support for a further round of GWA studies in January 2009. These include 5 WTCCC-collaborative studies to be carried out in WTCCC3 and 5 independent studies, across a range of diseases. Many of the studies represent major international collaborative networks that have together assembled large sample collections. WTCCC3 will perform genome-wide association studies in the following 4 disease conditions: primary biliary cirrhosis, anorexia nervosa, pre-eclampsia in UK subjects, and the interactions between donor and recipient DNA related to early and late renal transplant dysfunction. The WTCCC3 will also carry out a pilot in a study of the genetics of host control of HIV-1 infection. Over 40,000 samples will be analyzed using the Illumina 660K chip. The WTCCC3 will utilize the 6,000 control genotypes generated by the WTCCC2. | gene, genomic, genetics, microarray, genome-wide association study, snp, genome-wide association, blood, dna, genotype, variation, genome, sequence variant, copy number variation, genetic variation, phenotype, disease |
is related to: Psychiatric Genomics Consortium has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Bipolar disorder, Coronary artery disease, Crohn's disease, Rheumatoid arthritis, Type 1 diabetes, Type 2 diabetes, Hypertension, Control, Multiple sclerosis, Breast cancer, Ankylosing spondylitis, Autoimmune thyroid disease, Malaria, Tuberculosis, Inflammatory bowel disease, Barrett's esophagus, Esophageal adenocarcinoma, Glaucoma, Ischemic stroke, Pre-eclampsia, Parkinson's disease, Psychosis endophenotypes, Psoriasis, Schizophrenia, Ulcerative colitis, Visceral leishmaniasis, Primary biliary cirrhosis, Anorexia nervosa, Human immunodeficiency virus, Renal transplant dysfunction, Diabetes | Wellcome Trust ; Bill and Melinda Gates Foundation ; Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:17554300 | Access to summary data and individual-level genotype data is available by application to the Wellcome Trust Case Control Consortium Data Access Committee. Access to data will be granted to qualified investigators for appropriate use. | nif-0000-10551 | SCR_001973 | Wellcome Trust Case-Control Consortium (WTCCC) | 2026-08-01 12:01:40 | 213 | ||||
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Burroughs Wellcome Fund Resource Report Resource Website 100+ mentions |
Burroughs Wellcome Fund (RRID:SCR_005772) | BWF | institution | The Burroughs Wellcome Fund is an independent private foundation dedicated to advancing the biomedical sciences by supporting research and other scientific and educational activities. Within this broad mission, BWF has two primary goals: * To help scientists early in their careers develop as independent investigators * To advance fields in the basic biomedical sciences that are undervalued or in need of particular encouragement BWF''s financial support is channeled primarily through competitive peer-reviewed award programs. * BWF''s endowment: $586.8 million at the end of FY 2009 * BWF approved $26.4 million in grants during FY 2009 BWF makes grants primarily to degree-granting institutions on behalf of individual researchers, who must be nominated by their institutions. To complement these competitive award programs, BWF also makes grants to nonprofit organizations conducting activities intended to improve the general environment for science. A Board of Directors comprising distinguished scientists and business leaders governs BWF. BWF was founded in 1955 as the corporate foundation of the pharmaceutical firm Burroughs Wellcome Co. In 1993, a generous gift from the Wellcome Trust in the United Kingdom, enabled BWF to become fully independent from the company, which was acquired by Glaxo in 1995. BWF has no affiliation with any corporation. | biomedical sciences, research, science, education | Wellcome Trust | nlx_149371, grid.427464.7, Wikidata: Q5000488, ISNI: 0000 0000 8727 8697, Crossref funder ID: 100000861 | https://ror.org/01d35cw23 | SCR_005772 | 2026-08-01 12:02:59 | 103 | ||||||||
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ISOLDE Resource Report Resource Website 1+ mentions |
ISOLDE (RRID:SCR_025577) | software resource, software application | Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data. | software environment, model building, building macromolecular models, low resolution electron density maps, experimental maps, | is a plug in for: UCSF ChimeraX | Wellcome Trust | PMID:29872003 | Free, Freely available | SCR_025577 | 2026-08-01 12:13:21 | 8 | ||||||||
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XTRACT Resource Report Resource Website 1+ mentions |
XTRACT (RRID:SCR_024933) | software resource, software application | Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain. | automated tractography, tractography, human, macaque, brain | is a plug in for: FSL | Medical Research Council PhD Studentship UK ; Marie Skłodowska-Curie Individual Fellowship Grant ; Biotechnology and Biological Sciences Research Council ; Netherlands Organization for Scientific Research NWO Netherlands ; Sir Henry Dale Wellcome Trust Fellowship UK ; MRC Career Development Fellowship UK ; Wellcome Trust Collaborative Award UK ; UK Engineering and Physical Sciences Research Council ; Wellcome Trust grant UK ; Human Connectome Project ; NIMH 1U54MH091657; McDonnell Center for Systems Neuroscience at Washington University ; NIH ; UK Biobank Resource ; Wellcome Trust |
PMID:32407993 | Free, Freely available | SCR_024933 | 2026-08-01 12:13:08 | 2 | ||||||||
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Sanger Mouse Resources Portal Resource Report Resource Website 50+ mentions |
Sanger Mouse Resources Portal (RRID:SCR_006239) | Sanger Mouse Portal, WTSI Mouse Resources Portal, WTSI Mouse Resource Portal | biomaterial supply resource, material resource | Database of mouse research resources at Sanger: BACs, targeting vectors, targeted ES cells, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. The Wellcome Trust Sanger Institute generates, characterizes, and uses a variety of reagents for mouse genetics research. It also aims to facilitate the distribution of these resources to the external scientific community. Here, you will find unified access to the different resources available from the Institute or its collaborators. The resources include: 129S7 and C57BL6/J bacterial artificial chromosomes (BACs), MICER gene targeting vectors, knock-out first conditional-ready gene targeting vectors, embryonic stem (ES) cells with gene targeted mutations or with retroviral gene trap insertions, mutant mouse lines, and phenotypic data generated from the Institute''''s primary screen. | bacterial artificial chromosome, vector, embryonic stem cell, mutant mouse line, phenotype, gene, knockout, gene expression, genetics, chromosome, mutant, mouse line, mammal, marker symbol |
is listed by: One Mind Biospecimen Bank Listing is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Wellcome Trust 079643; Wellcome Trust 098051; NHGRI UO1-HG004080; NCRR 1-U42RR033192; European Union LSHG-CT-2006-037188; European Union 227490; European Union 312325; European Union 261492 |
For the scientific community | nlx_151819 | SCR_006239 | Mouse Resources Portal, Wellcome Trust Sanger Institute Mouse Resources Portal | 2026-08-01 12:10:52 | 51 | ||||||
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HipSci Resource Report Resource Website 100+ mentions |
HipSci (RRID:SCR_003909) | HipSci | biomaterial supply resource, material resource | A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation. | stem cell, genomic variation, cellular phenotype, disease mechanism, phenotype, disease, clinical data, clinical, genetics, male, female, cell line, induced pluripotent stem cell |
is listed by: One Mind Biospecimen Bank Listing has parent organization: European Bioinformatics Institute |
Healthy, Genetic disease | Wellcome Trust ; MRC |
Acknowledgement required, Free, Public | nlx_158252 | SCR_003909 | Human Induced Pluripotent Stem Cells Initiative | 2026-08-01 12:10:48 | 115 | |||||
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neuroConstruct Resource Report Resource Website 10+ mentions |
neuroConstruct (RRID:SCR_007197) | neuroConstruct | simulation software, software resource, software application | Software for simulating complex networks of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductance, implemented in Java and generates script files for the NEURON and GENESIS simulators, with support for other simulation platforms (including PSICS and PyNN) in development. neuroConstruct is being developed in the Silver Lab in the Department of Neuroscience, Physiology and Pharmacology at UCL and uses the latest NeuroML specifications, including MorphML, ChannelML and NetworkML. Some of the key features of neuroConstruct are: Creation of networks of biologically realistic neurons, positioned in 3D space. Complex connectivity patterns between cell groups can be specified for the networks. Can import morphology files in GENESIS, NEURON, Neurolucida, SWC and MorphML format for inclusion in network models. Simulations can be run on the NEURON or GENESIS platforms. Cellular processes (synapses/channel mechanisms) can be imported from native script files or created in ChannelML. Recording of simulation data generated by the simulation and visualization/analysis of data. Stored simulation runs can be viewed and managed through the Simulation Browser interface. | cell, cellular, channel, conductance, data, dendrite, java, mechanism, membrane, model, morphology, network, neuron, neuronal network, pharmacology, physiology, simulation, software, synapse, visualization |
is listed by: 3DVC is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: NEURON is related to: Open Source Brain is related to: NeuroML has parent organization: University College London; London; United Kingdom |
Wellcome Trust ; MRC |
nif-0000-00105 | http://www.nitrc.org/projects/neuroconstruct | SCR_007197 | neuroConstruct: Biophysical Neural Network Modeling Software | 2026-08-02 09:04:54 | 10 | ||||||
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bulkAnalyseR Resource Report Resource Website |
bulkAnalyseR (RRID:SCR_027647) | software toolkit, software resource | Software R package for most bulk sequencing datasets. Creates shiny app for interactive data analysis and visualisation. Used for analysing and sharing bulk sequencing results. | bulk sequencing results, analysing and sharing results, sequencing data, | uses: Shiny | Wellcome Trust | PMID:36583521 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/bulkAnalyseR/ | SCR_027647 | 2026-08-02 09:09:29 | 0 | |||||||
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Deciphering Developmental Disorders Resource Report Resource Website 10+ mentions |
Deciphering Developmental Disorders (RRID:SCR_006171) | DDD | portal, disease-related portal, service resource, topical portal, biospecimen repository, material storage repository, storage service resource, research forum portal, data or information resource | The Deciphering Developmental Disorders (DDD) study aims to find out if using new genetic technologies can help doctors understand why patients get developmental disorders. To do this we have brought together doctors in the 23 NHS Regional Genetics Services throughout the UK and scientists at the Wellcome Trust Sanger Institute, a charitably funded research institute which played a world-leading role in sequencing (reading) the human genome. The DDD study involves experts in clinical, molecular and statistical genetics, as well as ethics and social science. It has a Scientific Advisory Board consisting of scientists, doctors, a lawyer and patient representative, and has received National ethical approval in the UK. Over the next few years, we are aiming to collect DNA and clinical information from 12,000 undiagnosed children in the UK with developmental disorders and their parents. The results of the DDD study will provide a unique, online catalogue of genetic changes linked to clinical features that will enable clinicians to diagnose developmental disorders. Furthermore, the study will enable the design of more efficient and cheaper diagnostic assays for relevant genetic testing to be offered to all such patients in the UK and so transform clinical practice for children with developmental disorders. Over time, the work will also improve understanding of how genetic changes cause developmental disorders and why the severity of the disease varies in individuals. The Sanger Institute will contribute to the DDD study by performing genetic analysis of DNA samples from patients with developmental disorders, and their parents, recruited into the study through the Regional Genetics Services. Using microarray technology and the latest DNA sequencing methods, research teams will probe genetic information to identify mutations (DNA errors or rearrangements) and establish if these mutations play a role in the developmental disorders observed in patients. The DDD initiative grew out of the groundbreaking DECIPHER database, a global partnership of clinical genetics centres set up in 2004, which allows researchers and clinicians to share clinical and genomic data from patients worldwide. The DDD study aims to transform the power of DECIPHER as a diagnostic tool for use by clinicians. As well as improving patient care, the DDD team will empower researchers in the field by making the data generated securely available to other research teams around the world. By assembling a solid resource of high-quality, high-resolution and consistent genomic data, the leaders of the DDD study hope to extend the reach of DECIPHER across a broader spectrum of disorders than is currently possible. | microarray, sequencing, child, genome, chromosome, dna sequencing, ethics, interview, dna, saliva, clinical, genetics, gene, diagnosis, phenotype, clinical data, FASEB list |
is related to: DECIPHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Genetic disorder, Parent, Neurodevelopmental disorder, Congenital anomaly, Abnormal growth, Dysmorphic feature, Unusual behavioral phenotype | Wellcome Trust ; Health Innovation Challenge Fund |
PMID:21679367 | nlx_151673 | SCR_006171 | Deciphering Developmental Disorders (DDD) | 2026-08-03 09:33:00 | 42 | |||||
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NEMBASE Resource Report Resource Website 10+ mentions |
NEMBASE (RRID:SCR_006070) | NEMBASE | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | NEMBASE is a comprehensive Nematode Transcriptome Database including 63 nematode species, over 600,000 ESTs and over 250,000 proteins. Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal into extensively functionally annotated, EST-derived transcriptomes from over 60 species of nematodes, including plant and animal parasites and free-living taxa. Using the PartiGene suite of tools, we have assembled the publicly available ESTs for each species into a high-quality set of putative transcripts. These transcripts have been translated to produce a protein sequence resource and each is annotated with functional information derived from comparison with well-studied nematode species such as Caenorhabditis elegans and other non-nematode resources. By cross-comparing the sequences within NEMBASE4, we have also generated a protein family assignment for each translation. The data are presented in an openly accessible, interactive database. An example of the utility of NEMBASE4 is that it can examine the uniqueness of the transcriptomes of major clades of parasitic nematodes, identifying lineage-restricted genes that may underpin particular parasitic phenotypes, possible viral pathogens of nematodes, and nematode-unique protein families that may be developed as drug targets. | nematode, transcriptome, expressed sequence tag, protein, cluster, library, sequence, peptide prediction, functional annotation, gene family, gene, annotation, pathway, genome, partigene, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: nematodes.org |
Wellcome Trust ; Hospital for Sick Children ; BBSRC ; MRC ; NERC |
PMID:21550347 PMID:14681449 |
Public | nlx_151476, biotools:nembase4 | https://bio.tools/nembase4 | SCR_006070 | NEMBASE4, NEMBASE4 - Nematode Transcriptome Analyses | 2026-08-03 09:32:59 | 25 | ||||
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Virtual Fly Brain Resource Report Resource Website 10+ mentions |
Virtual Fly Brain (RRID:SCR_004229) | VFB | neurons, data or information resource, atlas, expression | An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain. | Drosophila, brain, neurons, innervation patterns, gene expression, transgene expression, phenotypes, neuroanatomy, neurobiology |
uses: Drosophila Gross Anatomy Ontology uses: Drosophila Development Ontology is related to: FlyBase is related to: Flycircuit is related to: Janelia Research has parent organization: University of Edinburgh; Scotland; United Kingdom has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: European Bioinformatics Institute |
Wellcome Trust | PMID:22180411 | nlx_143644 | http://www.virtualflybrain.org/site/vfb_site/home.htm | SCR_004229 | VirtualFlyBrain.org, VFB, Virtual Fly Brain | 2026-08-03 09:32:38 | 45 | |||||
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Roslin Wellcome Trust Tick Cell Biobank Resource Report Resource Website 1+ mentions |
Roslin Wellcome Trust Tick Cell Biobank (RRID:SCR_004228) | Roslin Wellcome Trust Tick Cell Biobank | material resource, biomaterial supply resource, cell repository | The world''s largest collection of tick cell lines, enabling scientists to carry out advanced research. This biobank is establishing a collection of all the continuous cell lines derived from ixodid and argasid ticks of medical and veterinary importance available worldwide now and in future. Ticks are blood feeding arthropods which transmit many human and animal diseases. Research into prevention and cure of these diseases, which are caused by viruses, bacteria and protozoa, is greatly assisted by the use of cell culture systems which enable study of both how tick cells function, and how and why ticks transmit these disease-causing pathogens. Cell lines will always be shipped to recipient laboratories as growing cultures, since we cannot guarantee successful resuscitation of frozen stabilates. Tick cells in culture can tolerate the range of temperatures experienced during transit by air for up to a week. Training: We will provide training in tick cell line care and maintenance. This is an essential component of successful transfer of tick cells to, and their establishment in, laboratories with little or no previous experience of tick cell culture. Recipient scientists (preferably the person who will actually look after the cells) can visit the biobank for between 2 days and 2 weeks, depending on their level of previous experience, to be trained in the specific approach and methods for tick cell cultivation. Establishment of new cell lines: In response to requests and on receipt of suitable starting material (engorged female or moulting nymphal ticks), we will attempt to establish new cell lines from tick species or strains which are not already represented in the collection. Deposition of new tick cell lines: We invite researchers anywhere in the world who have established new tick cell lines to deposit samples for safekeeping free of charge and, if requested, for distribution alongside the existing biobank portfolio. |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust | Public | nlx_24657 | http://tickcells.roslin.ac.uk/ | SCR_004228 | 2026-08-03 09:32:23 | 2 | |||||||
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ALSPAC Resource Report Resource Website 100+ mentions |
ALSPAC (RRID:SCR_007260) | ALSPAC | data or information resource, portal, project 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 | 2026-08-03 09:33:19 | 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) | data or information resource, portal, project 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 | 2026-08-03 09:35:30 | 0 | |||||||||
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EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | software resource, web application | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Connected Researchers is listed by: Debian is listed by: bio.tools is related to: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-08-03 09:35:19 | 3 |
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