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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GEROprotectors Resource Report Resource Website 10+ mentions |
GEROprotectors (RRID:SCR_016737) | data or information resource, database | Collection of structured and manually curated data of current therapeutic interventions in aging and age-related disease. Describes compounds and mechanisms using multiple chemical and biological databases. | geroprotector, data, collection, current, thearpeutic, prevention, aging, disease, geriatic |
uses: PubChem uses: ChemSpider uses: DrugBank uses: ChEMBL uses: CHEBI uses: UniProt uses: GenAge |
Wellcome Trust ; Israel Ministry of Science and Technology ; Fund in Memory of Dr. Amir Abramovich |
PMID:26342919 | Public, Free, Freely available | SCR_016737 | Geroprotectors | 2026-02-11 10:59:31 | 11 | |||||||
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BIGSdb Resource Report Resource Website 1+ mentions |
BIGSdb (RRID:SCR_023551) | data or information resource, database | Platform for gene-by-gene bacterial population annotation and analysis. Designed to store and analyse sequence data for bacterial isolates. Used for scalable analysis of bacterial genome variation at population level. | sequence data, bacterial isolates, gene-by-gene bacterial population, annotation and analysis, bacterial genome variation, | Wellcome Trust | PMID:21143983 | Free, Freely available | https://bigsdb.readthedocs.io/en/latest/ | SCR_023551 | Bacterial Isolate Genome Sequence Database | 2026-02-11 11:00:42 | 1 | |||||||
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DECIPHER Resource Report Resource Website 1000+ mentions |
DECIPHER (RRID:SCR_006552) | DECIPHER | data or information resource, database | Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes. | chromosomal imbalance, phenotype, chromosome, gene, genome, deletion, duplication, copy number, genotype, polymorphism, FASEB list |
is used by: MARRVEL is listed by: OMICtools is related to: Deciphering Developmental Disorders is related to: Ensembl has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Developmental disorder, Microdeletion Syndrome, Overgrowth syndrome, Microduplication syndrome, Deletion syndrome, Duplication syndrome, Wolf-Hirschhorn Syndrome, Williams-Beuren Syndrome, Smith-Magenis Syndrome, Etc | Wellcome Trust WT077008 | PMID:19344873 | Acknowledgement required | nlx_151653, OMICS_00265 | SCR_006552 | Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources, Database of Chromosomal Imbalance Phenotype in Humans using Ensembl Resources, Decipher | 2026-02-11 10:57:25 | 1797 | ||||
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Zebrafish Brain Atlas Resource Report Resource Website 1+ mentions |
Zebrafish Brain Atlas (RRID:SCR_000606) | Zebrafish Brain Atlas | data repository, service resource, image repository, storage service resource, atlas, data or information resource | Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish. | brain, neuroanatomy, developing, transgene, antibody, confocal, section, reconstruction, high-resolution, developmental stage, embryo, brain structure, confocal imaging, comparative anatomy, transgenic, 3d spatial image, video, embryonic zebrafish, development, annotation, narrative resource, training material, cell repository |
recommends: Zebrafish Anatomical Ontology is listed by: One Mind Biospecimen Bank Listing has parent organization: University College London; London; United Kingdom |
European Union ; Wellcome Trust ; BBSRC |
Public, (Transgenic lines), Freely available for academic use, Creative Commons license, (pending verification), The community can contribute to this resource | nlx_149455 | http://zebrafishucl.org/ | http://www.ucl.ac.uk/zebrafish-group/zebrafishbrain/index.php | SCR_000606 | , zebrafishbrain.org, Zebrafish Brain Atlas | 2026-02-12 09:43:00 | 3 | ||||
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Genes to Cognition - Biological Resources Resource Report Resource Website 1+ mentions |
Genes to Cognition - Biological Resources (RRID:SCR_001675) | G2C Biological Resources | organism supplier, material resource, biomaterial supply resource | Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J | transgenic, mutant mouse strain, c57bl/6j, 129s5, transgenic mouse line, vector, es cell line, transgenic mouse |
is listed by: One Mind Biospecimen Bank Listing has parent organization: University of Edinburgh; Scotland; United Kingdom |
Wellcome Trust ; MRC ; BBSRC ; Gatsby Charitable Foundation ; Human Frontiers Science Programme ; European Union ; Framework Programme ; EPSRC ; NSF |
Free, Freely Available | nif-0000-10163 | http://www.genes2cognition.org/mice_resources/ | http://www.genes2cognition.org/resources.html | SCR_001675 | G2C Mice Resources, G2C Biological Resources, G2C-Biological Resources, G2C - Biological Resources | 2026-02-12 09:43:12 | 2 | ||||
|
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 | 2026-02-11 10:58:19 | 0 | |||
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Flybrain at Stanford Resource Report Resource Website 1+ mentions |
Flybrain at Stanford (RRID:SCR_001877) | Flybrain(at)Stanford, FlybrainatStanford | software resource, software application, data processing software, data or information resource, image collection, image analysis software | Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer. | brain, cell, neuron, neuropil, olfactory, pheromone, confocal image, antennal lobe, axon trace, forum, neuronal tracing, image registration tool, analysis script, single-cell labeling, image registration, mushroom body, lateral horn, olfactory receptor neuron | has parent organization: Stanford University; Stanford; California | Wellcome Trust WT076726; Damon Runyon Cancer Research Foundation DRG-1766-03; NIAAA AA05965; NIAAA AA13521; NIDCD R01-DC005982 |
PMID:17382886 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10437 | SCR_001877 | Flybrain (at) Stanford - A warped brain is a good thing, Flybrain (at) Stanford | 2026-02-12 09:43:15 | 6 | |||||
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OME-TIFF Format Resource Report Resource Website |
OME-TIFF Format (RRID:SCR_002636) | OME-TIFF | data or information resource, standard specification, narrative resource | A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane. | microscopy, format, archiving, data management, annotation, mark up, metadata standard, standard, tiff, ome-xml |
is listed by: FORCE11 is related to: JCB DataViewer is related to: Cell Image Library (CIL) is related to: HMS LINCS Database is related to: Stowers Original Data Repository is related to: Bio-Formats has parent organization: OME - Open Microscopy Environment |
Wellcome Trust 68046 | PMID:15892875 | Free, Available for download, Freely available | nlx_156061 | SCR_002636 | OME-TIFF: Open Microscopy Environment Tagged Image File Format, Open Microscopy Environment Tagged Image File Format | 2026-02-12 09:43:25 | 0 | |||||
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Bio-Formats Resource Report Resource Website 50+ mentions |
Bio-Formats (RRID:SCR_000450) | Bio-Formats | standalone software, software toolkit, software resource, software application, software library | Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard. | Java library, reading microscopy image data files, writing image data, standardized format, open format, |
is listed by: FORCE11 is listed by: Debian is related to: OMERO is related to: OME-TIFF Format has parent organization: OME - Open Microscopy Environment |
Wellcome Trust | Free, Available for download, Freely available | nif-0000-30175 | http://www.force11.org/node/4810 http://www.loci.wisc.edu/software/bio-formats https://sources.debian.org/src/libbio-formats-java/ |
SCR_000450 | , BioFormats, Bio-Formats Library, The Bio-Formats Library | 2026-02-12 09:42:58 | 60 | |||||
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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 | 2026-02-12 09:46:22 | 155 | ||||||
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Ariba Resource Report Resource Website 100+ mentions |
Ariba (RRID:SCR_015976) | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | 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 |
Wellcome Trust 206194; Biotechnology and Biological Sciences Research Council BB/M014088/1 |
PMID:29177089 DOI:10.1099/mgen.0.000131 |
Free, Available for download, Freely available | OMICS_17327 | https://sources.debian.org/src/artemis/ | SCR_015976 | 2026-02-12 09:46:40 | 197 | ||||||
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GENCODE Resource Report Resource Website 5000+ mentions Rating or validation data |
GENCODE (RRID:SCR_014966) | data or information resource, portal, project portal, dataset | Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation. | human, mouse, genome, annotation, sequence, gene features, bio.tools |
is listed by: Debian is listed by: bio.tools is affiliated with: ENCODE |
NHGRI 5U54HG004555; Wellcome Trust WT098051 |
PMID:22955987 | Free | biotools:GENCODE | https://bio.tools/GENCODE | SCR_014966 | ENCODE | 2026-02-12 09:46:06 | 7700 | |||||
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NS-Forest Resource Report Resource Website 1+ mentions |
NS-Forest (RRID:SCR_018348) | software application, software resource, data processing software | Software tool as method that takes cluster results from single cell nuclei RNAseq experiments and generates lists of minimal markers needed to define each cell type cluster. Utilizes random forest of decision trees machine learning approach. Used to determine minimum set of marker genes whose combined expression identified cells of given type with maximum classification accuracy. | Single cell, RNAseq experiment, generated gene list, minimum set, marker gene, define cell type cluster, random forest, decision tree, machine learning, identify cell, cell clasyfication | is related to: Allen Institute for Brain Science | Allen Institute for Brain Science ; JCVI Innovation Fund ; NIAID R21 AI122100; NIAID U19 AI118626; California Institute for Regenerative Medicine ; Wellcome Trust ; Chan Zuckerberg Initiative DAF |
PMID:29590361 | Free, Available for download, Freely available | SCR_018348 | Necessary and Sufficient Forest, NS-Forestversion 1.3, NS-Forest v2.0, NS-Forest version 1.0 | 2026-02-12 09:47:29 | 2 | |||||||
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PALM Resource Report Resource Website 10+ mentions |
PALM (RRID:SCR_017029) | PALM | software resource, software application, data analysis software, data processing software | Software tool for inference using permutation methods. Requires Matlab or Octave. Can be executed from inside either environment, or directly from the shell and can be called from scripts. For users who are familiar with statistics and willing to use experimental analysis tools. | statistics, permutation, bootstrap, non parametric, combination, inference |
requires: MATLAB is a plug in for: FSL |
GlaxoSmithKline ; Marie Curie ITN ; Medical Research Council ; Wellcome Trust ; NIBIB R01 EB015611; MRC G0900908; Brazilian National Research Council |
PMID:24530839 PMID:26074200 DOI:10.1002/hbm.23115 PMID:27288322 |
Free, Available for download, Freely available | https://github.com/andersonwinkler/PALM | SCR_017029 | PALM, Permutation Analysis of Linear Models | 2026-02-12 09:46:45 | 47 | |||||
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Physiome Model Repository Resource Report Resource Website 1+ mentions |
Physiome Model Repository (RRID:SCR_017374) | PMR | data repository, model, service resource, dynamic model, storage service resource, data or information 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 |
British Heart Foundation ; Maurice Wilkins Centre for Molecular Biodiscovery ; Virtual Physiological Human Network of Excellence ; Wellcome Trust ; Auckland Bioengineering Institute |
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 | 2026-02-12 09:46:33 | 5 | |||||
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VasoTracker Resource Report Resource Website 1+ mentions |
VasoTracker (RRID:SCR_017233) | software resource, data acquisition software, software application, data analysis software, data processing software | 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 |
Wellcome Trust ; British Heart Foundation |
PMID:30846942 | Free, Available for download, Freely available | https://github.com/VasoTracker/VasoTracker | SCR_017233 | 2026-02-12 09:46:51 | 5 | |||||||
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Accessible Resource for Integrated Epigenomics Studies Resource Report Resource Website 10+ mentions |
Accessible Resource for Integrated Epigenomics Studies (RRID:SCR_017492) | data access protocol, software resource, web service, topical portal, data or information resource, portal | 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 ; Wellcome Trust ; University of Bristol |
PMID:25991711 | Free, Freely available | http://www.bristol.ac.uk/alspac/ | SCR_017492 | ARIES | 2026-02-12 09:47:09 | 33 | |||||||
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NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software toolkit, software resource, software application, data analysis software, data processing software | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-02-12 09:46:59 | 2 | |||||
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Cytograph Resource Report Resource Website 1+ mentions |
Cytograph (RRID:SCR_023101) | software resource, software application, data analysis software, data processing software | 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 | Knut and Alice Wallenberg Foundation ; Swedish Foundation for Strategic Research ; Wellcome Trust ; Swedish Research Council ; European Research Council ; Ollie and Elof Ericssons Foundation ; Ake Wiberg Foundation |
PMID:30096314 | Free, Freely available | SCR_023101 | 2026-02-12 09:47:47 | 3 | |||||||||
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Pavlovia Resource Report Resource Website 100+ mentions |
Pavlovia (RRID:SCR_023320) | software resource, web application | Web application as repository and launch platform for Psychopy experiments and other open-source tools. | Open Science Tools Limited, Psychopy experiments, repository and launch platform, behavioural sciences, | Wellcome Trust ; University of Nottingham; Nottingham; United Kingdom |
Restricted | SCR_023320 | 2026-02-12 09:47:37 | 191 |
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