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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ultimate Rough Aggregation of Metabolic Map Resource Report Resource Website |
Ultimate Rough Aggregation of Metabolic Map (RRID:SCR_014694) | data or information resource, database | Metabolic pathway map that collects metabolic data gathered from multiple public databases and organizes them in one central location. | database, metabolism, metabolic map, metabolic pathway, aggregation, public database |
uses: KEGG uses: HMDB uses: CHEBI |
Public | SCR_014694 | An Ultimate Rough Aggregation of Metabolic Map | 2026-08-29 11:30:17 | 0 | |||||||||
|
MicrocircuitDB Resource Report Resource Website |
MicrocircuitDB (RRID:SCR_014577) | data or information resource, database | A database for storing and efficiently retrieving realistic computational models of brain microcircuits and networks. The focus is on microcircuits that are based on experimentally demonstrated properties of neurons and their connectivity. | database, microcircuit, micro circuit, brain, neuron, connectivity |
works with: ModelDB works with: NeuronDB |
Researchers may contribute to this resource | SCR_014577 | 2026-08-29 11:30:44 | 0 | ||||||||||
|
RepOD Resource Report Resource Website 10+ mentions |
RepOD (RRID:SCR_014697) | data or information resource, database | An online platform for open source data/datasets created, collected or annotated for scientific research of all fields and disciplines. Registered users can share data relating to their research project and view data from other projects. Groups can combine datasets into collections associated with the group, in contrast to individual members of the group hosting their own data. | repository, open source, open data, research data, platform | Open source, Available to the research community, Registration required | r3d100011903 | SCR_014697 | Repository for Open Data, Repository for Open Data (RepOD) | 2026-08-29 11:30:17 | 12 | |||||||||
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Phi Toolbox Resource Report Resource Website 1+ mentions |
Phi Toolbox (RRID:SCR_015549) | software resource, software toolkit, source code | Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation. | matlab, integrated information, phi, Φ, neural data, computation | PMID:26796119 PMID:27930289 |
Open Source, Available for download | SCR_015549 | Φ toolbox, phi toolkit, integrated information matlab toolbox | 2026-08-29 11:30:19 | 1 | |||||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | software resource, software toolkit, source code | Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-08-29 11:30:45 | 64 | |||||
|
Astrocyte Reactivity RNA-Seq Browser Resource Report Resource Website 1+ mentions |
Astrocyte Reactivity RNA-Seq Browser (RRID:SCR_015033) | data or information resource, database | Database containing information about RNA-sequencing and astrocyte reactivity. Searching a gene through this engine provides differential expression data for various experimental conditions. | astrocyte, glia, reactivity, rna-seq, search engine | has parent organization: University of California Los Angeles Department of Neurobiology | NIH NS057624; NIH NS084030; NIH P30 NS062691; NIH NS060677; NIH MH099559A; NIH MH104069; Dr. Miriam and Sheldon G. Adelson Medical Foundation ; Wings for Life |
PMID:27027288 | Public | SCR_015033 | 2026-08-29 11:30:18 | 3 | ||||||||
|
Embassy-domsearch Resource Report Resource Website |
Embassy-domsearch (RRID:SCR_016086) | software resource, software toolkit, source code | Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt. | dhf, daf, redundancy, protein, domain, psi-blast, uniprot, molecular, biology |
is used by: RAVEN is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/embassy-domsearch/ | SCR_016086 | 2026-08-29 11:30:33 | 0 | |||||||||
|
WILD Resource Report Resource Website |
WILD (RRID:SCR_016240) | analysis service resource, material analysis service, production service resource, service resource | Service that distinguishes Isoleucine and Leucine using mass spectrometry experiments. | isoleucine, leucine, mass, spectrometry, ion, chemical, biochemistry | Commercially available, Free consultation | SCR_016240 | WILD (W-ion Isoleucine Leucine Determination), W-ion Isoleucine Leucine Determination | 2026-08-29 11:30:45 | 0 | ||||||||||
|
Glycan Mass Spectral Database (GMDB) Resource Report Resource Website |
Glycan Mass Spectral Database (GMDB) (RRID:SCR_014667) | GMDB | data or information resource, database | A multistage tandem mass spectral database using a variety of structurally defined glycans. It provides tools for glycomics research that enable users to identify glycans by spectral matching. The database stores MS2, MS3, and MS4 spectra of N-and O-linked glycans, and glycolipid glycans as well as the partial structures of these glycans. | glycomics, database, metagenomics, glycan, mass, spectral matching, tandem mass spectra | is listed by: Metabolomics Workbench | New Energy and Industrial Technology Development Organization ; Ministry of Education Culture Sports Science and Technology MEXT ; Tsukuba Advanced Computing Center of the National Institute of Advanced Industrial Science and Technology |
SCR_014667 | Glycan Mass Spectral Database | 2026-08-29 11:30:32 | 0 | ||||||||
|
Mass Spectral Library Resource Report Resource Website 10+ mentions |
Mass Spectral Library (RRID:SCR_014668) | data or information resource, database | A library containing spectra upwards of 200,000 chemical compounds. Spectra include metabolites, peptides, contaminants, and lipids. All spectra and chemical structures are examined by professionals. | library, database, spectra, mass spectrometry, metabolomics, metabolites, protein, lipid, contaminant | is listed by: Metabolomics Workbench | Available with the NIST MS Search Program for Windows | SCR_014668 | 2026-08-29 11:30:44 | 21 | ||||||||||
|
SEARCHBreast Resource Report Resource Website 1+ mentions |
SEARCHBreast (RRID:SCR_014826) | biomaterial supply resource, material resource, tissue bank | Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis. | breast cancer, database, tissue bank, in vivo, in vitro, mouse model | PMID:26062499 | Open to any UK based breast cancer researcher who uses in in vivo experimentation | SCR_014826 | 2026-08-29 11:30:18 | 8 | ||||||||||
|
Datasets2Tools Resource Report Resource Website 1+ mentions |
Datasets2Tools (RRID:SCR_016174) | data or information resource, database | Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools. | biomedical, digital, bioinformatics, dataset, rna seq, computation, microarray, proteomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Public, Freely available | biotools:datasets2tools | https://bio.tools/datasets2tools | SCR_016174 | 2026-08-29 11:30:21 | 1 | ||||||||
|
cwltool Resource Report Resource Website 10+ mentions |
cwltool (RRID:SCR_015528) | software resource, software toolkit, source code | Reference implementation of the Common Workflow Language standards. It provides complete features and tools and comprehensive validation of CWL. The reference implementation consists of two packages. The cwltool package is the primary Python module containing the reference implementation in the cwltool module and console executable by the same name. The cwlref-runner package is optional and provides an additional entry point under the alias cwl-runner, which is the implementation-agnostic name for the default CWL interpreter installed on a host. | language, reference implementation, python |
uses: Python Programming Language is listed by: Debian is listed by: OMICtools |
DOI:10.6084/m9.figshare.3115156.v2 | Available for download | OMICS_28977 | https://sources.debian.org/src/cwltool/ | SCR_015528 | CWLtool, Common Workflow Language Tool | 2026-08-29 11:30:19 | 25 | ||||||
|
Soma-Segmentation Resource Report Resource Website 1+ mentions |
Soma-Segmentation (RRID:SCR_015649) | algorithm resource, software resource, source code | Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results. | soma, segmentation method, touching soma distribution, rayburst sampling algorithm, soma detection, matlab | uses: MATLAB | Free, Available for download | SCR_015649 | 2026-08-29 11:30:45 | 1 | ||||||||||
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UManitoba - JHU Functionally Defined Human White Matter Atlas Resource Report Resource Website 1+ mentions |
UManitoba - JHU Functionally Defined Human White Matter Atlas (RRID:SCR_015525) | atlas, data or information resource | Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates. | white matter, dti tractography, resting state brain network, group probability map |
works with: MRI Studio works with: SPM works with: 3D Slicer |
PMID:26578930 | Acknowledgement requested, Freely available, Available for download | SCR_015525 | UManitoba JHU Functionally Defined Human White Matter Atlas, UManitoba-JHU Functionally-Defined Human White Matter Atlas | 2026-08-29 11:30:33 | 1 | ||||||||
|
Reefgenomics Resource Report Resource Website 10+ mentions |
Reefgenomics (RRID:SCR_015009) | data or information resource, database | Database for marine genomics data. Users can access genomics datasets from various organisms as well as carry out BLAST and submit genomics information of their own. Data sets include coral, aiptasia, sponges, and sybiodinium. | marine genomics, genomics database, blast | has parent organization: King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia | DOI:10.1093/database/baw152 | Available to the research community, The community can contribute to this resource | SCR_015009 | reefgenomics.org | 2026-08-29 11:30:33 | 43 | ||||||||
|
Chemical Translation Service Resource Report Resource Website 10+ mentions |
Chemical Translation Service (RRID:SCR_014681) | CTS | data or information resource, database, service resource | A translation service which contains a registry of pubicly available chemical information such as structures, chemical names, chemical synonyms, database identifiers, molecular masses, XlogP and proton-donor/acceptor data for compound-specific, structure-based cross references. It offers single ID conversion, batch ID conversion, InChI code conversion, and other services. | translation service, chemical translation, metabolomics, metabolomics tool, chemical properties, chemical structure, compound, chemical registry, cross reference |
is listed by: Metabolomics Workbench has parent organization: Metabolomics Fiehn Lab |
Available to public, A web GUI is used and a soap-based application-programming interface was implemented for automated access | SCR_014681 | Chemical Translation Service (CTS) | 2026-08-29 11:30:44 | 25 | ||||||||
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Mamit tRNA Resource Report Resource Website 1+ mentions |
Mamit tRNA (RRID:SCR_015493) | data or information resource, database | Compilation of mammalian mitochondrial tRNA genes. Sequences are classified into families according to the amino acid specificity of the different tRNAs as defined by the anticodon triplets. Each sequence is displayed linearly with color codes indicating secondary structural domains. | mammal mitochondria dna, mammal mitochondria gene, mammal mitochondria trna | PMID:11073213 | SCR_015493 | Mamit-tRNA | 2026-08-29 11:30:45 | 2 | ||||||||||
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CATALYSTLite Resource Report Resource Website |
CATALYSTLite (RRID:SCR_017126) | analysis service resource, data analysis service, production service resource, service resource | Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package. | interactive, Shiny, website, application, interface, mass, cytometry, data, processing, pipeline |
is used by: CATALYST is related to: Bioconductor has parent organization: University of Zurich; Zurich; Switzerland |
Free, Freely available | SCR_017126 | 2026-08-29 11:30:24 | 0 | ||||||||||
|
Genes, Genome Features and Maps Resource Report Resource Website 1+ mentions |
Genes, Genome Features and Maps (RRID:SCR_017524) | data or information resource, database | Searchable database of mouse genes, DNA segments, cytogenetic markers and QTLs. MGI provides access to integrated data on mouse genes and genome features, from sequences and genomic maps to gene expression and disease models. | Data, mouse, gene, DNA, segment, cytogenetic, marker, MGI, genome, feature, sequenced, genomic, map, expression, disease, model | Free, Freely available | SCR_017524 | 2026-08-29 11:30:34 | 6 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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