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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
mirDIP Resource Report Resource Website 100+ mentions |
mirDIP (RRID:SCR_016770) | data or information resource, database, portal | microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies. | data, integral, portal, DIP, collect, predict, microRNA, gene, human | Krembil Foundation ; Ontario Research Fund ; Canadian Cancer Society Research Institute ; Natural Sciences Research Council ; Canada Foundation for Innovation |
PMID:29194489 | Free, Download available, Freely available, email address required to download, Acknowledgement requested | SCR_016770 | mirDIP 4.1, mirDIP, microRNA Data Integration Portal | 2026-07-28 09:44:27 | 187 | ||||||||
|
Optogenetics Resource at JAX Resource Report Resource Website |
Optogenetics Resource at JAX (RRID:SCR_017508) | data or information resource, portal | Mouse lines expressing proteins that activate, inhibit or detect neuronal activity are available from The Jackson Laboratory Repository. Many of these strains have been generated by HHMI Janelia Farm GENIE Project or by Allen Institute for Brain Science. | Data, mouse, line, expressing, protein, activate, inhibit, detect, neuronal, activity, JAX | Free, Freely available | SCR_017508 | 2026-07-28 09:44:36 | 0 | |||||||||||
|
Maestro Resource Report Resource Website 50+ mentions |
Maestro (RRID:SCR_016748) | data or information resource, portal | Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data. | molecular, modeling, environment, computation, data, analyze, organize |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Trial available | SCR_016748 | 2026-07-28 09:44:26 | 79 | ||||||||||
|
brainlife.io Resource Report Resource Website 1+ mentions |
brainlife.io (RRID:SCR_016513) | data or information resource, portal | Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain. | human, brain, life, data, application, technology, share, open, software, reproducible, code, dataset, |
has parent organization: Indiana University Bloomington; Indiana; USA works with: brainlife |
NSF BCS 1734853; NSF IIS 1636893 |
DOI:10.1038/s41597-019-0073-y | Public, Free, Freely available, Login required | https://github.com/brain-life | SCR_016513 | 2026-07-28 09:44:16 | 1 | |||||||
|
Data Browser Resource Report Resource Website 10+ mentions |
Data Browser (RRID:SCR_017561) | data or information resource, organization portal, portal | National research resource to provide interactive views of publicly available All of Us Research Program participant data including electronic health record data, biospecimens, surveys, and other measures taken at time of participant enrollment. Data platform will be open to researchers all over world and show data for groups of de-identified participants. Data is updated periodically. | All of Us Research, program, participant, data, surey, physical, measurement, electronic, health, record | SCR_017561 | 2026-07-28 09:44:31 | 23 | ||||||||||||
|
ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | data or information resource, organization portal, portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-07-28 09:44:02 | 12 | ||||||
|
PopMedNet Resource Report Resource Website 1+ mentions |
PopMedNet (RRID:SCR_016456) | PopMedNet | data or information resource, portal | Software as an open source informatics platform to facilitate the implementation and operation of distributed health data networks. Consists of a web-based portal for distributing requests and administering the network, and the DataMart Client. Designed by the Therapeutics Research and Infectious Disease Epidemiology (TIDE) group at the Department of Population Medicine (DPM) of the Harvard Pilgrim Health Care Institute (HPHCI) to enable creation, operation, and governance of distributed health data networks. | implement, distribute, health, data, network, research, coordinate, center, governance, | has parent organization: Harvard Medical School; Massachusetts; USA | The National Institutes of Health ; the HHS Assistant Secretary for Planning and Evaluation ; NIH DRN |
PMID:27141522 | Free, Available for download, Freely available | https://github.com/PopMedNet-Team/popmednet | SCR_016456 | Population Medicine Network | 2026-07-28 09:44:19 | 3 | |||||
|
wavethresh Resource Report Resource Website 1+ mentions |
wavethresh (RRID:SCR_024311) | software toolkit, software resource | Software R package to perform 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation. | perform 1D, 2D and 3D real and complex valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage, data, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-wavethresh/ | SCR_024311 | 2026-07-28 09:46:05 | 3 | |||||||||
|
redcap-completion Resource Report Resource Website |
redcap-completion (RRID:SCR_016019) | software application, software resource, data management software | Software to measure item level completion in a large REDCap project. It provides a web-interface to review data and it is used in the ABCD project to assess data collection sites for the reached level of completion. | measure, item, level, completion, large, electronic, data, capture, research, review, data, collection |
is related to: University of California at San Diego; California; USA works with: REDCap |
NIDA U24 DA041123 | Free, Available for download | SCR_016019 | 2026-07-28 09:44:03 | 0 | |||||||||
|
cOMet Resource Report Resource Website 1+ mentions |
cOMet (RRID:SCR_016276) | software application, software resource, data management software | Software for error correction of optical mapping data. | optical, mapping, error, correction, data, visual, image | Free, Available for download | SCR_016276 | 2026-07-28 09:44:16 | 3 | |||||||||||
|
bioSyntax Resource Report Resource Website 1+ mentions |
bioSyntax (RRID:SCR_016207) | software application, software resource, data management software | Software for syntax highlighting for computational biology. | computation, syntax, language, code, scientific, data, workflow, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1186/s12859-018-2315-y | Free, Available for download | biotools:biosyntax, OMICS_25594 | https://github.com/bioSyntax/bioSyntax, https://bio.tools/biosyntax, https://sources.debian.org/src/biosyntax/ | SCR_016207 | 2026-07-28 09:44:12 | 2 | |||||||
|
Allen Mouse Brain Reference Atlas Resource Report Resource Website 100+ mentions |
Allen Mouse Brain Reference Atlas (RRID:SCR_002978) | ABA, ARA, ABA Mouse Brain | data or information resource, atlas, reference atlas | Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer. | 3D, map, gene, expression, data, adult, mouse, brain, interactive, image |
is used by: NIF Data Federation is used by: BICCN is related to: BrainStars is related to: PubAnatomy is related to: Integrated Brain Gene Expression is related to: Allen Brain Atlas API is related to: 3DBar is related to: aGEM is related to: CellTax vignette is related to: Blue Brain Cell Atlas is related to: Allen Mouse Brain Common Coordinate Framework is related to: SHARCQ is related to: Enhancer Trap Line Browser is related to: Linked Neuron Data has parent organization: Allen Institute for Brain Science has parent organization: Allen Brain Atlas works with: MeshView works with: Brain Gene Expression Analysis toolbox works with: VisuAlign works with: MIRACL |
Free, Freely available | SCR_013286, nlx_21010, nif-0000-00508 | http://mouse.brain-map.org/atlas/index.html, http://mouse.brain-map.org/ | SCR_002978 | Allen Mouse Brain Reference Atlas, Allen Reference Atlases, ABA Adult Mouse Brain, ARA ontology | 2026-07-28 09:40:34 | 444 | ||||||
|
National Sleep Research Resource (NSRR) Resource Report Resource Website 50+ mentions |
National Sleep Research Resource (NSRR) (RRID:SCR_016576) | NSRR | data or information resource, organization portal, portal | System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community. | sleep, clinical, data, cohort, study, trial, dataset, visualization, exploration |
is recommended by: National Library of Medicine lists: Apnea, Bariatric surgery, and CPAP study lists: Sleep Heart Health Study lists: Honolulu-Asia Aging Study of Sleep Apnea lists: Cleveland Family Study lists: Cleveland Children's Sleep and Health Study lists: Best Apnea Interventions for Research (BestAIR) sleep study |
sleep apnea | NHLBI | PMID:29860441 | Free, Freely available, Registration required for membership | https://sleepdata.org/share, https://sleepdata.org/datasets | SCR_016576 | National Sleep Research Resource | 2026-07-28 09:44:21 | 68 | ||||
|
tidyr Resource Report Resource Website 50+ mentions |
tidyr (RRID:SCR_017102) | software application, software resource, data management software | Software R package for easily tidy data with spread and gather functions. Used for simplifying process of creating tidy data. | tidy, data, spread, gather, function |
is used by: PlotsOfData is used by: tidyverse is listed by: CRAN is related to: R Project for Statistical Computing works with: dplyr |
Free, Available for download, Freely available | https://github.com/tidyverse/tidyr, https://tidyr.tidyverse.org/ | SCR_017102 | 2026-07-28 09:44:27 | 62 | |||||||||
|
Kinetic Models of Biological Systems (KiMoSys) Resource Report Resource Website 1+ mentions |
Kinetic Models of Biological Systems (KiMoSys) (RRID:SCR_017423) | service resource, data repository, data access protocol, software resource, web service, storage service resource | Web application for quantitative KInetic MOdels of biological SYStems. Platform includes public data repository of relevant published measurements, including metabolite concentrations, flux data, and enzyme measurements and tools in order to build ODE-based kinetic model. Designed to search, exchange and disseminate experimental data and associated kinetic models for systems modeling community. | Quantitative, kinetic, model, biological, system, data, storage, search, exchange, experiment |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases |
EU ; Portuguese national funding agency for science ; research and technology. |
Restricted | r3d100011562 | https://doi.org/10.17616/R3864V | https://fairsharing.org/FAIRsharing.6erywc | SCR_017423 | , Kinetic Models of Biological Systems (KiMoSys), KInetic MOdels of biological SYStems, KiMoSys | 2026-07-28 09:44:30 | 1 | |||||
|
Batch Data and Analysis Tool Resource Report Resource Website 1+ mentions |
Batch Data and Analysis Tool (RRID:SCR_017515) | data or information resource, service resource | Software tool to access various mouse genome information in batch format. Batch data and analysis tools. | Mouse, genome, information, batch, format, data, analysis, tool | has parent organization: Mouse Genome Informatics (MGI) | Free, Freely available | SCR_017515 | 2026-07-28 09:44:37 | 3 | ||||||||||
|
AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | service resource, data or information resource, database, production service resource, analysis service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
NIDA ; Department of Health and Human Services ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb, https://doi.org/10.17616/R3PX9Q | SCR_017592 | 2026-07-28 09:44:38 | 7 | ||||||
|
Transcriptional Regulatory Element Database Resource Report Resource Website 50+ mentions |
Transcriptional Regulatory Element Database (RRID:SCR_005661) | TRED | data or information resource, database | Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated. | Mammalian, cis, trans, regulatory, element, mapped, genome, gene, regulation, function, data, FASEB list |
uses: GenBank uses: Eukaryotic Promoter Database uses: DBTSS: Database of Transcriptional Start Sites has parent organization: Cold Spring Harbor Laboratory |
NCI ; NHGRI HG001696 |
PMID:17202159 | Free, Freely available | nif-0000-03585 | SCR_005661 | Transcriptional Regulatory Element Database | 2026-07-28 09:41:18 | 78 | |||||
|
Cancer Gene Index Resource Report Resource Website 1+ mentions |
Cancer Gene Index (RRID:SCR_001117) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data. | gene, cancer, genetics, pharmacology, disease, database, data |
is listed by: OMICtools has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
Cancer | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01575 | SCR_001117 | 2026-07-28 09:40:08 | 2 | ||||||||
|
PMAP Resource Report Resource Website |
PMAP (RRID:SCR_000740) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers. | proteolytic pathway, proteolysis, database, data | has parent organization: Sanford Burnham Prebys Medical Discovery Institute | PMID:18842634 PMID:16448029 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03318 | SCR_000740 | 2026-07-28 09:40:03 | 0 |
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