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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Brainreader Resource Report Resource Website 1+ mentions |
Brainreader (RRID:SCR_017308) | software resource | Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain. | Company, Denmark, medical, image, analysis, processing, software, brain | is affiliated with: Neuroreader | SCR_017308 | brainreader, BrainReader | 2026-09-03 04:54:21 | 3 | ||||||||||
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Protein Circular Dichroism Data Bank (PCDDB) Resource Report Resource Website 1+ mentions |
Protein Circular Dichroism Data Bank (PCDDB) (RRID:SCR_017428) | PCDDB | data or information resource, data repository, database, service resource, storage service resource | Public repository for archiving circular dichroism spectroscopic data and associated bioinformatics and experimental metadata. For authors to deposit experimental data as well as detailed information on methods and calculations associated with published work. Includes links for each entry to bioinformatics databases. Data are freely available to accessors either as single files or as complete data bank downloads. |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases has parent organization: Birkbeck University of London; London; United Kingdom has parent organization: Queen Mary University of London; London; United Kingdom |
International Union of Pure and Applied Chemistry ; U.K. Biotechnology and Biological Research Council |
DOI:10.1093/nar/gkw796 | Restricted | r3d100010890 | http://pcddb.cryst.bbk.ac.uk/, https://doi.org/10.17616/R36W5H | SCR_017428 | Protein Circular Dichroism Data Bank, PCDDB, Protein Circular Dichroism Data Bank (PCDDB) | 2026-09-03 04:54:29 | 5 | |||||
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MoRDa Resource Report Resource Website 1+ mentions |
MoRDa (RRID:SCR_017278) | data analysis software, data or information resource, data processing software, database, software application, software resource, software toolkit | Software package for molecular replacement protein structure solution using X-ray data. Includes database and set of programs for structure solution. Automatic molecular replacement pipeline. | molecular, replacement, protein, structure, data, Xray, crystallography | uses: CCP4 | DOI:10.1107/S2053273315099672 | Restricted | https://ccp4serv7.rc-harwell.ac.uk/ccp4online/ | SCR_017278 | Automatic Molecular Replacement Pipeline | 2026-09-03 04:54:31 | 6 | |||||||
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IBIS Network Resource Report Resource Website 1+ mentions |
IBIS Network (RRID:SCR_017399) | IBIS | consortium, data or information resource, disease-related portal, organization portal, portal, topical portal | Research study of brain development in infants and children with autism. Consortium of researchers across North America that work together to discover early changes in brain development of young children with autism. Participants will travel to their closest study location to receive developmental and behavioral assessments, MRI scan of the brain. Participants will be reimbursed for travel and related expenses. Families of children at high risk for developing symptoms of autism will receive assistance with referrals for local services. check if data repository is in the papers | Brain, development, infant, child, autism, assessment, MRI, scan, brain, service | autism | NICHD R01 HD055741 | Restricted | SCR_017399 | The Infant Brain Imaging Study, Infant Brain Imaging Study | 2026-09-03 04:54:28 | 3 | |||||||
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ClustalW Resource Report Resource Website 10000+ mentions |
ClustalW (RRID:SCR_017277) | ClustalW of DDBJ | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan. | alignment, service, DNA, data, bank, Japan | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017277 | ClustalW of DNA Data Bank of Japan | 2026-09-03 04:54:21 | 10545 | ||||||||
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Brain Image Library Resource Report Resource Website 10+ mentions |
Brain Image Library (RRID:SCR_017272) | BIL | data or information resource, data repository, service resource, storage service resource | Public, NIH-funded repository and analysis ecosystem for brain microscopy data, designed to store, share, and process massive volumetric datasets. It enables researchers to access whole-brain images, neuron morphologies, and spatial data without needing to download, fostering collaborative discovery. Used to deposit, analyze, mine, share and interact with large brain image datasets. | archive, dataset, confocal, microscopy, brain, image, data, brain microscopy data, |
is used by: BICCN is used by: BRAIN Initiative Cell Atlas Network is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is listed by: DataCite is listed by: re3data.org is related to: BRAIN Initiative is related to: Allen Institute for Brain Science works with: CBI BrAinPI is organization facet of: BRAIN Initiative Cell Atlas Network |
BRAIN Initiative ; NIMH R24 MH114793 |
PMID:38187527 | Free, Available for download, Freely available | DOI:10.17616/R31NJN9G, DOI:10.35077, r3d100013956 | https://doi.org/10.17616/R31NJN9G, https://doi.org/10.17616/r31NJN9G, https://doi.org/10.35077/, https://dx.doi.org/10.35077/, https://doi.org/10.17616/R31NJN9G | SCR_017272 | Brain Image Library | 2026-09-03 04:54:26 | 20 | ||||
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LDMatrix Resource Report Resource Website 10+ mentions |
LDMatrix (RRID:SCR_017391) | data analysis software, data processing software, service resource, software application, software resource | Software tool to create interactive heatmap matrix of pairwise linkage disequilibrium statistics. | Interactive, heatmap, matrix, pairwise, linkage, disequilibrium, statistics | Free, Freely available | SCR_017391 | 2026-09-03 04:54:34 | 38 | |||||||||||
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CLC Genomics Server Resource Report Resource Website 10+ mentions |
CLC Genomics Server (RRID:SCR_017396) | data analysis software, data processing software, software application, software resource | Commercially available software tool for high throughput sequencing analysis, designed for use on central compute cluster or server. Can handle data volumes beyond capacity of desktop systems and manages submission of many jobs via its own queuing system or through submission of jobs to third party grid scheduler. | high, throughput, sequencing, analysis, data | works with: CLC Genomics Workbench | Restricted | SCR_017396 | 2026-09-03 04:54:32 | 18 | ||||||||||
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DAQCORD Resource Report Resource Website 1+ mentions |
DAQCORD (RRID:SCR_017395) | DAQCORD | data or information resource, data set, portal | Software tool for practical self assessment and reporting method for clinical research studies, to capture key information about data acquisition and quality control measures. Linked to dataset so that potential research collaborators can determine if data meets their needs and expectations. | Assessment, reporting, method, clinical, study, data, acquisition, quality, control, information | Restricted | SCR_017395 | Data Access Quality and Curation for Observational Research Designs | 2026-09-03 04:54:27 | 2 | |||||||||
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Brain Observatory Storage Service and Database (BossDB) Resource Report Resource Website 10+ mentions |
Brain Observatory Storage Service and Database (BossDB) (RRID:SCR_017273) | BossDB, bossDB, BOSS DB | 3d spatial image, data or information resource, data repository, database, image, service resource, storage service resource | BossDB (Brain Observatory Storage Service and Database) is a cloud-based ecosystem for the storage and management of public large-scale volumetric neuroimaging and connectomics datasets. This includes volumetric Electron Microscopy and X-Ray Micro/Nanotomography data with support for multi-channel image data, segmentations, annotations, meshes, and connectomes. BossDB integrates with community resources for data access, processing, visualization, and analysis, and includes an API that enables metadata management, rendering, datatype conversions, and ingest. | Johns Hopkins University Applied Physics Laboratory, JHU/APL, database, electron microscopy, xray, data, storage, archive, BRAIN Initiative, EM, XRM, XNH, ecosystem |
is used by: BICCN is recommended by: National Library of Medicine is recommended by: BRAIN Initiative is related to: Scalable Analytics for Brain Exploration Research is related to: Ecosystem for Multi-modal Brain-behavior Experimentation and Research has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
BRAIN Initiative ; NIMH R24 MH114785 |
DOI:10.1101/217745 | Open | https://github.com/jhuapl-boss/boss/ | SCR_017273 | Brain Observatory Storage Service, bossDB, Block and Object Storage Service, BOSSDB, Block and Object Storage Service Database, Brain Observatory Storage Service and Database, BossDB | 2026-09-03 04:54:28 | 31 | |||||
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Galaxy scater Resource Report Resource Website 1+ mentions |
Galaxy scater (RRID:SCR_017394) | data analysis software, data processing software, sequence analysis software, service resource, software application, software resource, software toolkit, source code, training service resource | Software tool as Galaxy based training resource for single cell RNA-seq quality control and analyses. | scRNA-seq, single, cell, scater, Galaxy, training, quality, control, bio.tools |
is listed by: Debian is listed by: bio.tools |
BBSRC BBS/E/T/000PR9817; BBSRC BBS/E/T/000PR9818; BBSRC BBS/E/T/000PR9819; BBSRC CCG:BBS/E/T/000PR9816 |
DOI:10.1101/724047 | Free, Available for download, Freely available | biotools:Galaxy_scater | https://bio.tools/Galaxy_scater | SCR_017394 | 2026-09-03 04:54:26 | 1 | ||||||
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Strains, SNPs and Polymorphisms Resource Report Resource Website 1+ mentions |
Strains, SNPs and Polymorphisms (RRID:SCR_017518) | data or information resource, service resource | MGI integrates comparative data on inbred strain characteristics including SNPs, polymorphisms, and quantitative phenotypes. | Integrate, comparative, data, inbred, strain, SNP, polymorhism, quantitative, phenotype | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017518 | 2026-09-03 04:54:37 | 4 | ||||||||||
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Vertebrate Homology Resource Report Resource Website 50+ mentions |
Vertebrate Homology (RRID:SCR_017517) | data or information resource, service resource | MGI contains homology information for mouse, human, rat, chimp, dog and other species. Complete set of human, chimpanzee, rhesus macaque, dog, cattle, rat, chicken, western clawed frog and zebrafish Homology Classes for mouse genes. Report includes Chromosome and EntrezGene and OMIM IDs. Report of Human and Mouse Homology Classes sorted by HomoloGene ID includes associated nucleotide and protein sequences, Chromosome and OMIM IDs. Report of Human and Mouse Homology with phenotype annotations. Several additional MGI reports are available, including those for Gene Ontology, Phenotypes and Nomenclature. | Homology, class, mouse, human, rat, chimp, dog, rhesus macaque, cattle, chicken, zebrafish, frog | has parent organization: Mouse Genome Informatics (MGI) | Free, Available for download, Freely available | SCR_017517 | 2026-09-03 04:54:30 | 51 | ||||||||||
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Webcutter Resource Report Resource Website 10+ mentions |
Webcutter (RRID:SCR_017638) | analysis service resource, data access protocol, data analysis service, data analysis software, data processing software, production service resource, sequence analysis software, service resource, software application, software resource, web service | Software tool to find restriction endonucleases. Helps restriction map nucleotide sequences. Tool with customizable interface, platform independent accessibility, interfaces to NCBI's GenBank, DNA sequence database, and NEB's REBase, and restriction enzyme database. In addition to restriction site mapping, Webcutter 2 also performs degenerate digests, including option of finding restriction sites that can be introduced into sequence by silent mutagenesis. | Find, restriction, site, endonuclease, map, nucleotide, DNA, sequence, degenarte, digest, silent, mutagenesis |
has parent organization: Yale University; Connecticut; USA works with: GenBank works with: REBASE |
Free, Freely available | SCR_017638 | Webcutter 2.0, Webcutter 2 | 2026-09-03 04:54:36 | 15 | |||||||||
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DiseaseMeth Resource Report Resource Website |
DiseaseMeth (RRID:SCR_017488) | database, data or information resource | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | Human, disease, methylation, database, aberrant, methylome, data |
is listed by: OMICtools was submitted by: Resource Identification Portal |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; State Key Laboratory of Urban Water Resource and Environment and Scientific Research Fund of Heilongjiang Provincial Education Department |
PMID:22135302 PMID:27899673 |
Free, Available for download, Freely available | http://bio-bigdata.hrbmu.edu.cn/diseasemeth/visualize.jsp | SCR_017488 | DiseaseMeth, Disease Meth-The Human Disease Methylation Database, DiseaseMeth version 2.0 | 2026-09-03 04:54:32 | 0 | ||||||
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3D Genome Resource Report Resource Website 10+ mentions |
3D Genome (RRID:SCR_017525) | service resource | Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structure |
is related to: Encode has parent organization: Pennsylvania State University |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017525 | 2026-09-03 04:54:27 | 20 | ||||||||||
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Cardiff Study of all Wales and North West of England Twins Resource Report Resource Website |
Cardiff Study of all Wales and North West of England Twins (RRID:SCR_017480) | CaStANET | data or information resource | Study of twins and their families provides tool for disentangling genetic and environmental origins of traits. Study collected behavioral and psychopathological information using self-, parent and teacher reports, and focused on contributions of genetic and environmental risk factors to psychological health of young people. | Twins, family, genetic, environmental, origin, trait, collected, behavioral, psychopathological, data | PMID:17539361 | SCR_017480 | 2026-09-03 04:54:29 | 0 | ||||||||||
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Brain RNA-Seq Resource Report Resource Website 10+ mentions |
Brain RNA-Seq (RRID:SCR_017483) | database, data or information resource | Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain. | RNAseq, transcriptome, splicing, data, glia, neuron vascular, cell, cerebral, cortex, mouse, human, brain | has parent organization: Stanford University; Stanford; California | NIMH R01 MH09955501; NINDS R01 NS0817030; Stanford School of Medicine ; NIGMS R00 GM95713; Berry Postdoctoral Fellowship ; National Health and Medical Research Council of Australia C. J. Martin Fellowship ; National Institutes of Health and the Staman Ogilvie Fund–Memorial Hermann Foundation ; NIMH R01 MH099555; JPB foundation ; Walter V. and Idun Berry Fellowship ; NINDS K99 NS089780; NIGMS T32 GM007365 |
PMID:25186741 PMID:26687838 |
Free, Freely available | http://www.brainrnaseq.org/ | SCR_017483 | Barres Brain RNA-Seq | 2026-09-03 04:54:26 | 12 | ||||||
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DIANA-mirExTra Resource Report Resource Website 1+ mentions |
DIANA-mirExTra (RRID:SCR_017498) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software tool for analysis of expression data for microRNA function. | Analysis, expression, data, microRNA, function, DIANA tool | is provided by: DIANA Tools | Free, Freely available | http://diana.imis.athena-innovation.gr/DianaTools/ | SCR_017498 | Mirextra 2.0 | 2026-09-03 04:54:32 | 1 | ||||||||
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MCScan Resource Report Resource Website 10+ mentions |
MCScan (RRID:SCR_017650) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package to simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors.Used to identify conserved gene arrays both within same genome and across different genomes. Command line program to wrap dagchainer and combine pairwise results into multi alignments in column format. | Simultaneously, scan, multiple, genome, identify, homologous, chromosomal, region, align, gene, anchor, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Georgia; Georgia; USA |
Free, Available for downoad, Freely available | biotools:MCScan | http://chibba.agtec.uga.edu/duplication/mcscan/, https://bio.tools/MCScan | SCR_017650 | Multiple Collinearity Scan | 2026-09-03 04:54:43 | 42 |
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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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