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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
GeneNetwork
 
Resource Report
Resource Website
100+ mentions
GeneNetwork (RRID:SCR_002388) GeneNetwork, WebQTL database, service resource, storage service resource, data repository, data or information resource Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data. Variation, trait, vertebrate trait ontology, phenotype, systems genetics, quantitative trait, gene mapping, experimental precision medicinenetwork analysis, causal modeling, genomic location, genotype, inbred strain, sex, heterogeneous stock, phenome, phenotype, QTL, expression QTL, genetic reference population, single nucleotide polymorphism, RNA expression, protein expression, metabolite expression, metagenomics, epigenomics, gene-by-environmental interaction, epistasis, FAIR data standards, open source software, FASEB list is used by: NIF Data Federation
is used by: Hypothesis Center
is related to: NIH Data Sharing Repositories
has parent organization: University of Tennessee Health Science Center; Tennessee; USA
NIGMS R01 GM123489;
NIAAA U01 AA016662;
NIAAA U01 AA13499;
NIAAA U24 AA13513;
NIAAA U01 AA014425;
NIA R01 AG043930;
NIDA P20 DA21131;
NCI U01 CA105417;
NCRR U24 RR021760
PMID:8043953
PMID:11737945
PMID:15043217
PMID:15114364
PMID:15043220
PMID:15043219
PMID:15711545
PMID:18368372
PMID:27933521
Restricted nif-0000-00380 SCR_002388 GeneNetwork and WebQTL, GeneNetwork / WebQTL, www.genenetwork.org, GeneNetwork WebQTL, The GeneNetwork / WebQTL 2026-02-15 09:18:17 473
Michigan Molecular Interactions
 
Resource Report
Resource Website
1+ mentions
Michigan Molecular Interactions (RRID:SCR_003521) MiMI data analysis service, database, software resource, data access protocol, web service, service resource, production service resource, data or information resource, analysis service resource MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID, CCSB at Harvard, cPath, DIP, GO (Gene Ontology), HPRD, IntAct, InterPro, IPI, KEGG, Max Delbreuck Center, MiBLAST, NCBI Gene, Organelle DB, OrthoMCL DB, PFam, ProtoNet, PubMed, PubMed NLP Mining, Reactome, MINT, and Finley Lab. The data integration service is supplied under the conditions of the original data sources and the specific terms of use for MiMI. Access to this website is provided free of charge. The MiMI data is queryable through a web services api. The MiMI data is available in PSI-MITAB Format. These files represent a subset of the data available in MiMI. Only UniProt and RefSeq identifiers are included for each interactor, pathways and metabolomics data is not included, and provenance is not included for each interaction. If you need access to the full MiMI dataset please send an email to mimi-help (at) umich.edu. gene, interaction, molecule, protein, protein interaction, protein-protein interaction is related to: MiMI Plugin for Cytoscape
has parent organization: National Center for Integrative Biomedical Informatics
Michigan Center for Biological Information ;
National Center for Integrative Biomedical Informatics ;
Pfizer ;
Medical and Academic Partnerships ;
Howard Hughes Medical Institute ;
Microsoft Corporation ;
NLM R01 LM008106;
NIDA U54 DA021519;
NSF IIS 0219513
PMID:18978014
PMID:17130145
nif-0000-00214 SCR_003521 2026-02-15 09:18:32 5
Brain Architecture Project
 
Resource Report
Resource Website
10+ mentions
Brain Architecture Project (RRID:SCR_004283) topical portal, data or information resource, portal Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts central nervous system, connectivity, mapping, model, neuroanatomy, organism, post-mortem, structure, nervous system, structure, human, mouse, brain, zebra finch, addiction gene, addiction is used by: BICCN
lists: Allen Institute for Brain Science
lists: University of California at Los Angeles; California; USA
is related to: Mouse Brain Architecture Project
is related to: BICCN Anatomy and Morphology Project
is related to: Allen Institute for Brain Science
has parent organization: Cold Spring Harbor Laboratory
is parent organization of: Human Brain Connectivity Database
is parent organization of: OBART
is parent organization of: Zebrafinch Brain Architecture Project
is parent organization of: Mouse Brain Architecture Project
W. M. Keck Foundation ;
NIMH ;
NIDA ;
Crick-Clay Professorship in Biomathematics at CSHL ;
Mathers Foundation ;
Simons Foundation
Free, Public nlx_143664 SCR_004283 BrainArchitecture.org, BrainArchitecture 2026-02-15 09:18:40 14
Schistosoma mansoni Database
 
Resource Report
Resource Website
10+ mentions
Schistosoma mansoni Database (RRID:SCR_004341) SchistoDB database, service resource, storage service resource, data repository, data or information resource SchistoDB is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. Make your data available: If you''d like to have your updates and/or datasets integrated in SchistoDB, drop us an email. FASEB list has parent organization: Rene Rachou Research Center - FIOCRUZ; Belo Horizonte; Brazil NIDA 5D43TW007012-03 PMID:18842636 nif-0000-03438 SCR_004341 2026-02-15 09:18:45 36
Open Connectome Project
 
Resource Report
Resource Website
1+ mentions
Open Connectome Project (RRID:SCR_004232) Open Connectome Project source code, data analysis service, software resource, data set, data access protocol, web service, service resource, storage service resource, data repository, production service resource, data or information resource, image repository, analysis service resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or which neurons synapse onto this one. Create your own annotations or browse others. *Sample Downloads - In addition to being able to select arbitrary downloads from the datasets, they have also collected a few choice volumes of interest. * Volume Viewer - A web and GPU enabled stand-alone app for viewing volumes at arbitrary cutting planes and zoom levels. The code and program can be downloaded. * Machine Vision Pipeline - They are building a machine vision pipeline that pulls volumes from the 3ddb and outputs neural circuits. - a work in progress. As soon as we have a stable version, it will be released. * Mr. Cap - The Magnetic Resonance Connectome Automated Pipeline (Mr. Cap) is built on JIST/MIPAV for high-throughput estimation of connectomes from diffusion and structural imaging data. * Graph Invariant Computation - Upload your graphs or streamlines, and download some invariants. * iPad App - WholeSlide is an iPad app that accesses utilizes our open data and API to serve images on the go. human, primary visual cortex, data sharing, male, electron microscopy, mri, connectome, annotation, image collection, array tomography is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: CATMAID
is related to: neurodata
is parent organization of: Rambo3D
Johns Hopkins University; Maryland; USA ;
JHU Applied Research Laboratory IRAD ;
JHU Whiting School of Engineering ;
Dean's Award ;
NIBIB 1RO1EB016411-01 (CRCNS);
DARPA N66001-14-1-4028 (GRAPHS);
NSF ACI-1261715;
NSF OCI-1040114;
NIDA 1R01DA036400-01;
PMID:23707591 THIS RESOURCE IS NO LONGER IN SERVICE SciRes_000189, nlx_143645 http://openconnecto.me
http://www.nitrc.org/projects/ocp/
SCR_004232 openconnectomeproject, Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time., Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time 2026-02-15 09:18:39 7
Hippocampal Slice Wave Animations
 
Resource Report
Resource Website
Hippocampal Slice Wave Animations (RRID:SCR_008372) software application, data visualization software, portal, data processing software, software resource, animation software, simulation software, data or information resource, topical portal, resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 29, 2013. Supplemental data for the paper Changes in mitochondrial function resulting from synaptic activity in the rat hippocampal slice, by Vytautas P. Bindokas, Chong C. Lee, William F. Colmers, and Richard J. Miller that appears in the Journal of Neuroscience June 15, 1998. You can view digital movies of changes in fluorescence intensity by clicking on the title of interest. animation, hippocampal, hippocampus, mitochondrial, movie, neuroscience, rat, slice, wave MRC of Canada MT10520;
NIDA DA02575;
NIDA DA02121;
NIMH MH40165;
NIDDK DK42086;
NIDDK DK44840;
NINDS NS-33502;
NIGMS 5T32GM07151-22;
NICHD HD07009
PMID:9614233 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-25609 SCR_008372 GIF Animations 2026-02-15 09:19:30 0
iTools
 
Resource Report
Resource Website
10+ mentions
iTools (RRID:SCR_009626) iTools database, software resource, data access protocol, web service, service resource, storage service resource, data repository, data or information resource, software repository An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org). computational neuroscience, data, experiment control, hardware, imaging genomics, information specification, java, loni pipeline, model, ontology, os independent, metadata is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: National Centers for Biomedical Computing
has parent organization: Laboratory of Neuro Imaging
NIH Roadmap for Medical Research ;
NCRR U54-RR021813;
NIDA U54-DA021519;
NCI U54-CA121852;
NHGRI U54-HG004028;
NIGMS U54-GM072970;
NIBIB U54-EB005149;
NLM U54-LM008748
PMID:18509477 GNU Lesser General Public License nlx_155852 http://www.nitrc.org/projects/itools
http://www.loni.usc.edu/research/software
http://itools.loni.ucla.edu/ SCR_009626 ITools Resourceome, NCBC iTools 2026-02-15 09:20:13 45
USC Multimodal Connectivity Database
 
Resource Report
Resource Website
10+ mentions
USC Multimodal Connectivity Database (RRID:SCR_012809) UMCD database, service resource, storage service resource, data repository, data or information resource Web-based repository and analysis site for connectivity matrices that have been derived from neuroimaging data including different imaging modalities, subject groups, and studies. Users can analyze connectivity matrices that have been shared publicly and upload their own matrices to share or analyze privately. fmri, dti, dsi, mri, eeg, meg, data set, image, computational hosting, connectivity, neuroimaging, data sharing, brain, rendering, diffusion-weighted mri, functional connectivity, graph theory, resting-state fmri, structural connectivity, image display, magnetic resonance, python, rendering, visualization, connectivity matrix, network, brain network, matrix, de-identified, male, female, apoe, child, adult is used by: NIF Data Federation
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: MGH-USC Human Connectome Project
Normal, Lesioned, Attention deficit-hyperactivity disorder, Autism Spectrum Disorder, Obsessive-Compulsive Disorder, BDD, APOE 4/4, APOE 3/4, APOE 3/3, Alzheimer's disease NRSA ;
NIH Blueprint for Neuroscience Research ;
NIA F31AG035438-01;
NIDA HHSN271200800035C
PMID:23226127
PMID:20850551
The community can contribute to this resource, Some features require an account nlx_83091 http://www.nitrc.org/projects/umcd http://jessebrown.webfactional.com/welcome/default/index SCR_012809 UCLA Connectivity Database, UCLA Multimodal Connectivity Database: Web-based brain network analysis and data sharing, UCLA Multimodal Connectivity Database 2026-02-15 09:20:21 25
EpiModel
 
Resource Report
Resource Website
1+ mentions
EpiModel (RRID:SCR_018539) software application, data processing software, software resource, software toolkit, data analysis software Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools is listed by: Debian
is listed by: bio.tools
NICHD R01 HD068395;
NIMH R21 MH112449;
NICHD R21 HD075662;
NIDA P30 DA027828;
NIAID P30 AI050409;
NIAID P30 AI027757;
NICHD T32 HD007543
PMID:29731699 Free, Available for download, Freely available biotools:epimodel https://bio.tools/epimodel SCR_018539 2026-02-15 09:22:22 7
RatsPub
 
Resource Report
Resource Website
RatsPub (RRID:SCR_018905) software application, software resource, data access protocol, web service, text-mining software Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords. Literature mining, addiction gene, PubMed abstract, gene, addiction, addiction relationship, neurogenetics NIDA P30 DA044223;
NIDA U01 DA047638
Free, Freely available https://github.com/chen42/ratspub SCR_018905 rats.pub, Rats.pub, Relationship with Addiction Through Searches of PubMed 2026-02-15 09:22:17 0
exRNA Atlas
 
Resource Report
Resource Website
10+ mentions
exRNA Atlas (RRID:SCR_017221) organization portal, portal, expression atlas, data analysis service, software resource, database, ontology, data access protocol, atlas, service resource, storage service resource, consortium, production service resource, data repository, data or information resource, controlled vocabulary, analysis service resource, application programming interface Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data. Differential, expression, RNA, sequencing, qPCR, data, visualization, extracellular, exRNA, atlas, repository, dataset is recommended by: National Library of Medicine
has parent organization: Baylor College of Medicine; Houston; Texas
has parent organization: exRNA
gastric cancer, colon carcinoma, colorectal cancer, prostate carcinoma, pancreatic carcinoma, multiple sclerosis, glioblastoma multiforme, ulcerative colitis, Alzheimer's disease, ischemic stroke, intraparenchymal hemorrhage of brain, asthma, cardiovascular disorder, myocardial infarction, lupus, nephrotic syndrome, transplanted kidney present, liver disease, transplanted liver present, pre-eclampsia, Parkinson disease, intraventricular brain hemorrhage, subarachnoid hemorrhage NIDA U54 DA036134;
NCI R01 CA163849;
NIGMS R25 GM056929;
NCATS UH3 TR000906;
NCI U19 CA179512;
NIDDK P30 DK63720;
NHLBI K23 HL127099;
NHLBI R01 HL136685;
NIA R01 AG059729;
NCATS UH3 TR000943;
NCI R35 CA209904;
NCI CA217685;
NHLBI R01 HL122547;
American Cancer Society ResearchProfessor Award ;
Frank McGraw Memorial Chair in CancerResearch
PMID:30951672 Restricted SCR_017221 2026-02-15 09:21:59 24
redcap-importer
 
Resource Report
Resource Website
redcap-importer (RRID:SCR_016032) software application, data processing software, data acquisition software, software resource Software that automates the process of retrieving and converting data to the format of a RedCap table and allows selection of directories and files for import. automate, process, retrvinig, converting, data, format, research, electronic, data, capture, table, selection, directory, import is related to: University of California at San Diego; California; USA NIDA U24 DA041123 Free, Available for download SCR_016032 2026-02-15 09:21:01 0
ABCDreport
 
Resource Report
Resource Website
ABCDreport (RRID:SCR_016030) software application, data processing software, data analysis software, software resource Software application as a simple system to review study progress. Used in ABCD study. system, simple, review, study, progress, development, adolescence, brain, cognitive, report is related to: University of California at San Diego; California; USA NIDA U24 DA041123 Free, Available for download SCR_016030 2026-02-15 09:21:29 0
FIONASITE
 
Resource Report
Resource Website
FIONASITE (RRID:SCR_016012) data management software, software application, data processing software, software resource, data transfer software, data acquisition software Software for uploading data to FIONA and capturing MR images and k-space data from medical image systems. It provides a web-interface to automate the data review (image viewer), integrate with the centralized electronic data record for assigning anonymized id's, and forward the data to the central archive. automate, data, upload, collection, network, appliance, abcd, study is related to: University of California at San Diego; California; USA NIDA U24 DA041123 Free, Available for download SCR_016014, SCR_016013 http://qi.ucsd.edu/news-article.php?id=2342&go=newer SCR_016012 2026-02-15 09:21:29 0
Minimally-Processed-Image-Sharing
 
Resource Report
Resource Website
Minimally-Processed-Image-Sharing (RRID:SCR_016016) data management software, software application, data processing software, software resource, data transfer software, data distribution software Software to share ABCD minimally processed data. It uploads minimally-processed MRI data to the NDA ( Non-Disclosure Agreement) ABCD (Adolescent Brain Cognitive Development) repository. share, data, minimally processed, image, files, fast-track, non-processed, link, store, upload is related to: University of California at San Diego; California; USA
works with: ABCD Study
NIDA U24 DA041123 SCR_016016 2026-02-15 09:21:00 0
enroll
 
Resource Report
Resource Website
10+ mentions
enroll (RRID:SCR_016011) data management software, software application, data processing software, software resource, data storage software Software which provides a framework for the secure storage of Personal Identifyable Information (PII) for a multi-site longitudinal project centrally. Used in Adolescent Brain Cognitive Development (ABCD) Study. database, secure, framework, multisite, personal, identifiable, information, adolescence, abcd has parent organization: University of California at San Diego; California; USA
works with: ABCD Study
NIDA U24 DA041123 Free, Available for download SCR_016011 2026-02-15 09:21:30 13
tick-tock
 
Resource Report
Resource Website
tick-tock (RRID:SCR_016023) software application, data visualization software, data processing software, software resource, web application Software for research study observation that visualizes study related events per day. Any event generating function sends a 'tick' event to this application which will be visible on this applications web-interface. application, research, study, visualization, event, web, interface, observation, abcd is related to: University of California at San Diego; California; USA
works with: ABCD Study
NIDA U24 DA041123 Free, Available for download SCR_016023 2026-02-15 09:21:44 0
FIONA-protocol-compliance
 
Resource Report
Resource Website
FIONA-protocol-compliance (RRID:SCR_016027) software application, data processing software, data analysis software, software resource Software that contains multiple sequential lines of MATLAB commands and function calls for numerical computing for ABCD study protocol compliance. application, multiple, sequential, lines, commands, function, numerical, computing, protocol, compliance is related to: University of California at San Diego; California; USA NIDA U24 DA041123 Free, Available for download SCR_016027 2026-02-15 09:21:45 0
Fast-Track-Image-Sharing
 
Resource Report
Resource Website
Fast-Track-Image-Sharing (RRID:SCR_016021) data management software, software application, data processing software, software resource, data transfer software Software for sharing the ABCD (Adolescent Brain Cognitive Development) study data on the National Data Archive (NDA). sharing, tool, study, data, national, archive, abcd, nda, adolescent is related to: University of California at San Diego; California; USA NIDA U24 DA041123 Free, Available for download SCR_016021 2026-02-15 09:21:30 0
eprime-data-clean
 
Resource Report
Resource Website
eprime-data-clean (RRID:SCR_016020) data management software, software application, data processing software, software resource Software to convert E-Prime (software tool for psychology computerized experiment design, data collection, and analysis) generated files to CSV files without errors during conversion. The ABCD project is using E-Prime to run behavioral tests. convert, data, psychology, computerized, experiment, design, collection, analysis, generate, file, errors, conversion, abcd is related to: University of California at San Diego; California; USA
works with: ABCD Study
NIDA U24 DA041123 Free, Available for download SCR_016020 2026-02-15 09:21:00 0

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