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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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COMPARE Resource Report Resource Website 1+ mentions |
COMPARE (RRID:SCR_000855) | COMPARE | data processing software, software application, image processing software, software resource | Generic classification tool for 3D images | magnetic resonance | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free, Available for download, Freely available | nlx_155598 | SCR_000855 | 2026-08-15 11:21:48 | 1 | ||||||||
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Massachusetts Institute of Technology; Massachusetts; USA; Resource Report Resource Website 1+ mentions |
Massachusetts Institute of Technology; Massachusetts; USA; (RRID:SCR_000977) | MIT | institution | Independent, coeducational, privately endowed university, organized into five schools: architecture and planning; engineering; humanities, arts, and social sciences; management; and science. | university, architecture, planning, engineering, humanities, arts, social sciences, management, science school, massachusetts institute, coeducation, independent |
uses: ShareLaTeX uses: Overleaf uses: ReadCube uses: Scizzle uses: Paperpile uses: GenomeCompiler is affiliated with: Broad Institute is related to: Charles Stark Draper Laboratory is related to: Beta Cell Biology Consortium is related to: ShareLaTeX is parent organization of: Laser Biomedical Research Center is parent organization of: GISTIC is parent organization of: MIT/ Harvard Center for Magnetic Resonance is parent organization of: BioMEMS Resource Center is parent organization of: Hollywood is parent organization of: MISO is parent organization of: Massachusetts Institute of Technology; Department of Brain and Cognitive Sciences is parent organization of: Center for Integration of Medicine and Innovative Technology is parent organization of: MIT Center for Biomedical Innovation is parent organization of: Wikigenes is parent organization of: TPEHG DB is parent organization of: GEM is parent organization of: MIT OpenCourseWare is parent organization of: SIMILE is parent organization of: Edgerton Center High Speed Imaging is parent organization of: Edgerton Digital Collections is parent organization of: Artifact Detection Tools is parent organization of: ProPortal is parent organization of: Noise Enhancement of Sensorimotor Function is parent organization of: A Whole Genome Admixture Scan for Type 2 Diabetes in African Americans is parent organization of: Center for Biological and Compulational Learning Face Database is parent organization of: PhysioNet is parent organization of: International Stroke Database is parent organization of: International Stroke Database/Software is parent organization of: CoC Central is parent organization of: MSY Breakpoint Mapper is parent organization of: lobSTR is parent organization of: Protein Knots is parent organization of: BLAST Similarity Search is parent organization of: RESCUE-ESE is parent organization of: EyeWire is parent organization of: Channelrhodopsin-2 enables optical activation of neurons is parent organization of: Zebrafish RNAi Database is parent organization of: Neural Decoding Toolbox is parent organization of: Non-rigid groupwise registration method is parent organization of: CONN is parent organization of: SPM SS - fMRI functional localizers is parent organization of: St. Vincents University Hospital / University College Dublin Sleep Apnea Database is parent organization of: SHHS is parent organization of: MGH/MF Waveform Database is parent organization of: TargetScan is parent organization of: miRNAminer is parent organization of: MIT-BIH polysomnographic is parent organization of: MIMIC II is parent organization of: Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking is parent organization of: Effect of Deep Brain Stimulation on Parkinsonian Tremor is parent organization of: Apnea-ECG Database is parent organization of: GENSCAN is parent organization of: edX is parent organization of: Magnaporthe comparative Database is parent organization of: ChemBank is parent organization of: JIP Analysis Toolkit is parent organization of: Neuroimaging in Python is parent organization of: Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) is parent organization of: CummeRbund is parent organization of: METAFLUIDICS is parent organization of: FFTW is parent organization of: MAxEntScan is parent organization of: seqNMF is parent organization of: Massachusetts Institute of Technology Koch Institute Bioinformatics and Computing Core Facility is parent organization of: Massachusetts Institute of Technology Koch Institute Histology Core Facility is parent organization of: Online Animal Tracker project is parent organization of: Hybrid-drive combining Optogenetics, Pharmacology, and Electrophysiology project is parent organization of: Koch Institute at MIT Data Science and Multimodal Integration Core Facility is parent organization of: Massachusetts Institute of Technology Swanson Biotechnology Center Nanotechnology Materials Core Facility is parent organization of: Massachusetts Institute of Technology Koch Institute High Throughput Sciences Core Facility is parent organization of: Massachusetts Institute of Technology MIT BioMicro Center Core Facility |
SCR_016675, nlx_32884, grid.116068.8, ISNI: 0000 0001 2341 2786, Crossref funder ID: 100006919, Wikidata: Q49108 | https://ror.org/042nb2s44 | SCR_000977 | Massachusetts Institute of Technology (MIT), MIT; Cambridge; Massachusetts; United States, Massachusetts Institute of Technology; Cambridge; USA; | 2026-08-15 11:22:01 | 2 | |||||||
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SIMM Resource Report Resource Website 1+ mentions |
SIMM (RRID:SCR_000849) | software application, simulation software, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Gene dropping simulation software. The program is a gzip'ed tar archive and is designed to run under UNIX/Linux operating system. | gene, genetic, genomic, software | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154626 | http://mlemire.freeshell.org/software.html | SCR_000849 | SimM | 2026-08-15 11:21:49 | 2 | |||||||
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Genome Canada Resource Report Resource Website 10+ mentions |
Genome Canada (RRID:SCR_000966) | Genome Canada | nonprofit organization | Genome Canada is a non-profit organization that is funded by the Government of Canada. The organization funds large-scale science and technology to fuel innovation regarding genomics in multiple sectors such as health, agriculture and agri-food, forestry, fisheries and aquaculture, environment, energy and mining. They create partnerships at the program and research project levels. | genome, genomics, funding, non profit, non-profit, innovation, health, agriculture, agri-food, agri food, forestry, fisheries, aquaculture, environment, energy, mining | is related to: Structural Genomics Consortium | Available to the research community | Crossref funder ID: 100008762, nlx_151964, Wikidata: Q3123000, ISNI: 0000 0001 0352 8618, grid.440163.4 | https://ror.org/029s29983 | SCR_000966 | 2026-08-15 11:21:49 | 11 | |||||||
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EZ BioResearch Resource Report Resource Website 1+ mentions |
EZ BioResearch (RRID:SCR_001050) | reagent manufacture, material service resource, service resource, production service resource | A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control. | molecular biology, tool kit, dna, rna, microarray, pcr, transgenic, genotyping, analysis, biotechnology | is listed by: ScienceExchange | Commercial | SciEx_571 | http://www.scienceexchange.com/facilities/ez-bioresearch | SCR_001050 | EZ BioResearch LLC | 2026-08-15 11:21:51 | 3 | |||||||
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University of Hawaii; Hawaii; USA Resource Report Resource Website 1+ mentions |
University of Hawaii; Hawaii; USA (RRID:SCR_000998) | UH | university | University in Hawaii that provides undergraduate, master's, doctorate, and professional degree programs. Campuses are located in Manoa and in Hilo. | hawaii, undergraduate, graduate, doctorate, master's, university | is related to: lilikoi | Crossref funder ID:100008782, Wikidata:Q217439, nlx_88254, grid.162346.4, ISNI:0000 0001 1482 1895 | https://ror.org/03tzaeb71 | SCR_000998 | University of Hawaii | 2026-08-15 11:21:50 | 1 | |||||||
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University of Melbourne; Victoria; Australia Resource Report Resource Website 1+ mentions |
University of Melbourne; Victoria; Australia (RRID:SCR_000999) | university | University in Victoria, Australia that provides undergraduate and graduate degree programs. | melbourne undergraduate, melbourne graduate, melbourne university, melbourne institute, melbourne study |
uses: Writefull is related to: International AMD Genetics Consortium is related to: Bionitio is parent organization of: is-rSNP is parent organization of: Network Based Statistic Toolbox is parent organization of: Australian Sheep Gene Mapping is parent organization of: mixOmics is parent organization of: Twins Research Australia is parent organization of: University of Melbourne Biological Optical Microscopy Platform (BOMP) Core Facility is parent organization of: Subread is parent organization of: epiR is parent organization of: DynaMut |
ISNI:0000 0001 2179 088X, nlx_20770, grid.1008.9, Wikidata:Q319078, Crossref funder ID:501100001782 | https://ror.org/01ej9dk98 | SCR_000999 | University of Melbourne | 2026-08-15 11:22:01 | 5 | ||||||||
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BSDPF Resource Report Resource Website 1+ mentions |
BSDPF (RRID:SCR_001162) | BSDPF | funding resource, topical portal, data or information resource, portal | A nonprofit organization whose goal is to find better treatments and cures for the movement disorders dystonia and Parkinson's disease. Funding opportunities are available through the collaborative research program between BSDPF and the Michael J. Fox Foundation. | parkinson's disease, parkinson's disease online community, funding resource, organization portal, dystonia, treatment | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-11645 | https://www.michaeljfox.org/research/apply-for-grant.html | SCR_001162 | Bachmann-Strauss Dystonia & Parkinson Foundation, The Bachmann-Strauss Dystonia and Parkinson Foundation, The Bachmann-Strauss Dystonia and Parkinson Foundation Inc. | 2026-08-15 11:22:03 | 2 | |||||||
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DiMO Resource Report Resource Website 1+ mentions |
DiMO (RRID:SCR_001168) | DiMO | software resource | Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. | r, motif, perceptron |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:24369152 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02190 | SCR_001168 | Discriminative Motif Optimizer, DiMO: Discriminative Motif Optimizer | 2026-08-15 11:21:53 | 1 | ||||||
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LONI Pipeline Processing Environment Resource Report Resource Website 10+ mentions |
LONI Pipeline Processing Environment (RRID:SCR_001161) | LONI Pipeline | data processing software, software application, software resource, workflow software | A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely. | workflow, neuroscience, afni brik, analyze, bshort, bfloat, computational neuroscience, dicom, imaging genomics, java, linux, macos, microsoft, minc, minc2, nifti, pet, spect, posix/unix-like, sunos/solaris, windows, windows nt/2000, atlas, birn, ccb, functional, na-mic, registration, segmentation, statistical, surface analysis, visual processing environment, volume, warping, image processing |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of California at Los Angeles; California; USA |
NCRR P41 RR013642; NIMH R01 MH71940; NCRR U54 RR021813 |
PMID:12880830 | Free, Available for download, Freely available | nif-0000-00322 | http://www.nitrc.org/projects/pipeline | http://www.loni.ucla.edu/NCRR/Software/Pipeline.html | SCR_001161 | LONI Pipeline Environment | 2026-08-15 11:21:53 | 11 | |||
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ExomePeak Resource Report Resource Website 1+ mentions |
ExomePeak (RRID:SCR_001076) | exomePeak | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. | r, matlab |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Texas at San Antonio; Texas; USA |
PMID:23589649 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00570 | SCR_001076 | 2026-08-15 11:22:02 | 5 | |||||||
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National Center for Health Statistics Resource Report Resource Website 10+ mentions |
National Center for Health Statistics (RRID:SCR_001078) | NCHS | institution | Center dedicated to providing statistical information to guide policies to improve the health of the American people. An affiliate of the Center for Disease Control and Prevention. | statistics, public health, policy, cdc |
is affiliated with: Centers for Disease Control and Prevention is parent organization of: National Nursing Home Survey Follow-Up |
ISNI: 0000 0001 1958 5959, Wikidata: Q3336854, Crossref funder ID: 100005262, nlx_151844, grid.416789.5 | https://ror.org/03p15s250 | SCR_001078 | National Center for Health Statistics | 2026-08-15 11:21:51 | 21 | |||||||
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Mouse Brain Library Resource Report Resource Website 10+ mentions |
Mouse Brain Library (RRID:SCR_001112) | MBL | database, topical portal, video resource, portal, data or information resource, image collection, atlas | Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies. | brain, gene, genome, strain, c57bl/6j, dba/2j, a/j, genetic variant, phenotype, hippocampus, cerebellum, striatum, olfactory bulb, thalamus, neocortex, dorsal nucleus of lateral geniculate body, central nervous system |
is related to: Videoscribbler has parent organization: University of Tennessee Health Science Center; Tennessee; USA is parent organization of: MBL Pivot Collection is parent organization of: Mouse Brain Atlases |
NIMH P20 MH62009 | PMID:10857184 PMID:15043219 |
Restricted | nif-0000-00030 | SCR_001112 | MBL - Mouse Brain Library, Mouse Brain Library, The Mouse Brain Library | 2026-08-15 11:21:52 | 24 | |||||
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SynView Resource Report Resource Website 1+ mentions |
SynView (RRID:SCR_001106) | data processing software, software application, data analysis software, software resource, sequence analysis software | A software tool for comparative visualization of genomes. It is based in the GBrowse frameworks and integrates with the annotation features. | visualization, genome, comparison, gbrowse, sequence analysis software |
is used by: PlasmoDB is used by: ApiDB CryptoDB is listed by: OMICtools has parent organization: Generic Model Organism Database Project has parent organization: University of Georgia; Georgia; USA |
PMID:16844709 DOI:10.1093/bioinformatics/btl389 |
OMICS_00947 | SCR_001106 | 2026-08-15 11:22:02 | 1 | |||||||||
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ShortFuse Resource Report Resource Website 1+ mentions |
ShortFuse (RRID:SCR_001107) | data processing software, software application, data analysis software, software resource, sequence analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2. | fusion transcripts, rna, sequence data, python 2, c++, sequence analysis software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21330288 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:shortfuse, OMICS_01355 | https://bio.tools/shortfuse | SCR_001107 | 2026-08-15 11:21:51 | 1 | |||||||
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RIKEN Resource Report Resource Website 1+ mentions |
RIKEN (RRID:SCR_001065) | RIKEN | institution | An independent administrative institution dedicated to comprehensive research in science and technology and the dissemination of scientific research and technological developments to the public. RIKEN works in a range of fields, including physics, chemistry, medical science, biology, and engineering, covering the entire range from basic research to practical application. | research, science, technology, dissemination, public |
uses: ReadCube is used by: EMBRYS has parent organization: Japanese Ministry of Education Culture Sports Science and Technology (MEXT) is parent organization of: CAGE Basic Viewer for Mus musculus is parent organization of: RIKEN Brain Science Institute is parent organization of: BrainStars is parent organization of: CAGE is parent organization of: RIKEN Yokohama Institute; Kanagawa; Japan is parent organization of: RIKEN Tsukuba Institute; Kansai; Japan is parent organization of: CYANA is parent organization of: Digital Brain Atlas of the Common Marmoset is parent organization of: ReSpect for Phytochemicals |
THIS RESOURCE IS NO LONGER IN SERVICE | Crossref funder ID: 501100006264, grid.7597.c, nlx_143906, Wikidata: Q50295658, ISNI: 94465255 | https://ror.org/01sjwvz98 | SCR_001065 | 2026-08-15 11:22:02 | 7 | |||||||
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SparseAssembler Resource Report Resource Website 1+ mentions |
SparseAssembler (RRID:SCR_001100) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software for memory-efficient genome assembly. It utilizes sparse k-mer. | genome, genomics, genome assembly, k-mer, sequence analysis software, memory |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22537038 | Free, Available for download, Freely available | OMICS_00032 | SCR_001100 | 2026-08-15 11:21:51 | 1 | ||||||||
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University of Kentucky; Kentucky; USA Resource Report Resource Website 1+ mentions |
University of Kentucky; Kentucky; USA (RRID:SCR_001062) | UKY | university | A public co-educational university in Lexington, Kentucky that offers undergraduate, graduate and postgraduate degree programs in a variety of fields such as nursing, the arts, law and medicine. | university, kentucky, graduate program, undergraduate program, postgraduate, degree, public university |
is related to: Alzheimers Disease Genetics Consortium is parent organization of: Distributed Computing Engine is parent organization of: Sal-Site is parent organization of: rOGED: Rat Ovarian Gene Expression Database is parent organization of: Ambystoma Genetic Stock Center is parent organization of: Sanders Brown Center on Aging is parent organization of: MapSplice is parent organization of: DiffSplice is parent organization of: University of Kentucky Alzheimer's Disease Center is parent organization of: Kentucky University, Lexington, Energy Balance and Body Composition Core Facility is parent organization of: University of Kentucky College of Medicine, Lexington, Pathology Research Core Facility is parent organization of: University of Kentucky College of Medicine Protein Core Facility is parent organization of: University of Kentucky College of Medicine Genetic Technologies Core Facility is parent organization of: University of Kentucky Flow Cytometry and Immune Monitoring Core Facility is parent organization of: University of Kentucky Research Mass Spectrometry and Proteomics Core Facility is parent organization of: University of Kentucky Magnetic Resonance Imaging and Spectroscopy Center Core Facility is parent organization of: University of Kentucky Light Microscopy Core Facility is parent organization of: University of Kentucky Animal Behavior and Energy Balance Core Facility |
nlx_89604, Crossref funder ID:100007472, ISNI:0000 0004 1936 8438, grid.266539.d, Wikidata:Q1360303 | https://ror.org/02k3smh20 | SCR_001062 | University of Kentucky | 2026-08-15 11:21:51 | 1 | |||||||
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IBL-America Resource Report Resource Website 1+ mentions |
IBL-America (RRID:SCR_001131) | commercial organization | A commercial biomaterial supply resource for laboratory reagent assays. IBL-American provides resources to further research and clinical testing in various areas including autoimmunity, endocrinology, infectious disease, oncology and neuroscience among others. | reagents, assay, antibody, autoimmunity, endocrinology, infectious disease, endocrinology, neuroscience | nlx_152380 | SCR_001131 | IBL - America (Immuno-Biological Laboratories), IBL - America, IBL International GmbH, IBL, IBL America | 2026-08-15 11:21:52 | 3 | ||||||||||
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Google Compute Engine Resource Report Resource Website 1+ mentions |
Google Compute Engine (RRID:SCR_001011) | Compute Engine | service resource | An infrastructure as a service that lets you run your large-scale computing workloads on Linux virtual machines hosted on Google's infrastructure. | cloud | is listed by: OMICtools | OMICS_01204 | SCR_001011 | 2026-08-15 11:21:51 | 3 |
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