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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

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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
IMEx - The International Molecular Exchange Consortium
 
Resource Report
Resource Website
100+ mentions
IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) IMEx data repository, storage service resource, community building portal, portal, consortium, data or information resource, organization portal, service resource, database Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data. protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interaction, bio.tools, FASEB list is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is affiliated with: MINT
is related to: MatrixDB
is related to: MPIDB
is related to: Database of Interacting Proteins (DIP)
is related to: Database of Interacting Proteins (DIP)
is related to: InnateDB
is related to: IntAct
is related to: Interaction Reference Index
is related to: MPIDB
is related to: UniProt
is related to: InnateDB
is related to: MatrixDB
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: I2D
is related to: Molecular Connections NetPro
is related to: SIB Swiss Institute of Bioinformatics
is related to: IntAct
is related to: PSI-MI
is related to: PSICQUIC Registry
is related to: mentha
is related to: Bioconductor
has parent organization: European Bioinformatics Institute
works with: CellPhoneDB
works with: Cytoscape
works with: IntAct
works with: MINT
works with: MPact: Representation of Interaction Data at MIPS
works with: Molecular Connections NetPro
works with: Biological General Repository for Interaction Datasets (BioGRID)
works with: InnateDB
works with: BIND
European Union PMID:22453911
PMID:17893861
Free, Freely available, Available for download nif-0000-00447, OMICS_01545, r3d100010669, biotools:imex http://imex.sourceforge.net/
https://bio.tools/imex
https://doi.org/10.17616/R3090W
SCR_002805 The International Molecular Exchange Consortium, International Molecular Exchange Consortium 2026-02-14 02:00:27 144
University of Southern California LONI Software
 
Resource Report
Resource Website
1+ mentions
University of Southern California LONI Software (RRID:SCR_002802) data or information resource, portal, topical portal Portal provides list of software resources. LONI is leader in development of advanced computational algorithms and software for comprehensive and quantitative mapping of brain structure and function. Aims to encourage communication between users and LONI software engineers in order to improve effectiveness. visualization, image processing, shape analysis, pre-processing, registration, segmentation, statistical analysis, surface modeling, data management NIH Roadmap for Medical Research ;
NCRR U54 RR021813
Free, Freely available, Available for download nif-0000-00445, nif-0000-00063, SCR_003323 http://www.loni.ucla.edu/Software/ SCR_002802 2026-02-14 02:00:32 2
ConTrack
 
Resource Report
Resource Website
10+ mentions
ConTrack (RRID:SCR_002681) ConTrack image processing software, software resource, data processing software, software application An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo. diffusion tensor imaging, tractography, brain connectivity, mri, software, source code, pathway, fiber tractography, tissue analysis is listed by: Biositemaps
has parent organization: Simtk.org
NIH Roadmap for Medical Research ;
NIGMS U54 GM072970;
NEI EY015000
PMID:18831651 Free, Available for download, Freely available nif-0000-23303 SCR_002681 Connectivity Tracking, Connectivity Tracking (ConTrack) 2026-02-14 02:00:18 13
CRE Driver Network
 
Resource Report
Resource Website
1+ mentions
CRE Driver Network (RRID:SCR_002720) CRE Driver Network biomaterial supply resource, organism supplier, material resource Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine. cre-recombinase, expression, neuroscience, mutant mouse strain, knock out mouse, phenotype, expression profile, image collection, microarray, electrophysiology, atlas, morphology, cell, annotation is related to: JAX Cre Repository
is related to: Recombinase (cre) Activity
has parent organization: NIH Blueprint for Neuroscience Research
is parent organization of: Mouse Neuronal Expression Database
NIH Blueprint for Neuroscience Research ;
NIH
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-23753 SCR_002720 Mouse Models for Neuroscience Research, CRE-driver Network, CRE-Driver Network, NIH Neuroscience Blueprint CRE Driver Network 2026-02-14 02:00:30 9
sapFinder
 
Resource Report
Resource Website
sapFinder (RRID:SCR_002685) software resource An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. standalone software, r, mass spectrometry, proteomics, rna-seq, report writing, snp, visualization, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:25053745 Free, Available for download, Freely available biotools:sapfinder, OMICS_05285 https://bio.tools/sapfinder SCR_002685 sapFinder - A package for variant peptides detection and visualization in shotgun proteomics. 2026-02-14 02:00:26 0
Simbody(tm): SimTK Multibody Dynamics Toolset
 
Resource Report
Resource Website
1+ mentions
Simbody(tm): SimTK Multibody Dynamics Toolset (RRID:SCR_002684) software resource, simulation software, software application This project is a SimTK Core toolset providing general multibody dynamics capability, i.e., the capability to solve Newton's 2nd law F=ma in any set of coordinates. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results. Binaries of this software are bundled with other SimTK Core modules. articulated body, coarse-grained molecule modeling, constrained motion, internal coordinates, mechanical simulation, mechanics, molecular dynamics, multibody dynamics, rigid body, simtk core, skeletal mechanics, torsion coordinates is used by: CPODES numerical integrator
is related to: Simtk.org
PMID:25866705 Free, Available for download, Freely available nif-0000-23309 SCR_002684 Simbody 2026-02-14 02:00:29 1
CNSforum: Image Bank
 
Resource Report
Resource Website
CNSforum: Image Bank (RRID:SCR_002718) data or information resource, image collection A collection of downloadable central nervous system (CNS) images for teaching, presentations, articles, and other purposes. The following major categories of images are as follows: Brain anatomy, Brain physiology, Anxiety, Depression, Schizophrenia, Dementia, Parkinson's disease, Stroke, and Others. image collection, human brain, brain anatomy, brain physiology, anxiety, depression, schizophrenia, dementia, parkinson's disease, stroke, brain has parent organization: CNS Forum Anxiety, Depressive Disorder, Schizophrenia, Dementia, Parkinson's disease, Stroke, Normal Free, Freely available nif-0000-23576 SCR_002718 CNS Forum Image Bank, Lundbeck Institute CNSforum Image Bank 2026-02-14 02:00:18 0
leeHom
 
Resource Report
Resource Website
50+ mentions
leeHom (RRID:SCR_002710) software resource Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. standalone software, illumina, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:25100869 Free, Available for download, Freely available biotools:leehom, OMICS_05254 https://bio.tools/leehom SCR_002710 2026-02-14 02:00:26 53
Cognitive Atlas
 
Resource Report
Resource Website
10+ mentions
Cognitive Atlas (RRID:SCR_002793) Cognitive Atlas data or information resource, ontology, controlled vocabulary Knowledge base (or ontology) that characterizes the state of current thought in cognitive science that captures knowledge from users with expertise in psychology, cognitive science, and neuroscience. There are two basic kinds of knowledge in the knowledge base. Terms provide definitions and properties for individual concepts and tasks. Assertions describe relations between terms in the same way that a sentence describes relations between parts of speech. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers. A fundamental feature of the knowledge base is the desire and ability to capture not just agreement but also disagreement regarding definitions and assertions. Thus, if you see a definition or assertion that you disagree with, then you can assert and describe your disagreement. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). Most tasks used in cognitive psychology research are not identical across different laboratories or even within the same laboratory over time. A major advantage of anchoring cognitive ontologies to the measurement level is that the strategy for determining changes in task properties is easier than tracking changes in concept definitions and usage. The process is easier because task parameters are usually (if not always) operationalized objectively, offering a clear basis to judge divergence in methods. The process is also easier because most tasks are based on prior tasks, and thus can more readily be considered descendants in a phylogenetic sense. cognitive function, cognitive phenotype, cognitive process, cognitive science, cognitive state, human, cognitive ontology, cognitive task, experimental task, mental construct, concept, task, eeg, meg, electrocorticography, magnetic resonance, ontology, pet, spect, knowledge environment is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Speech Perception
is related to: Brainspell
has parent organization: University of Texas at Austin; Texas; USA
is parent organization of: Cognitive Atlas Ontology
NIMH RO1MH082795 PMID:21922006
PMID:19634038
Free, Freely Available nif-0000-24591 http://www.nitrc.org/projects/cogatlas SCR_002793 cognitive atlas - a collaboratively developed cognitive science ontology 2026-02-14 02:00:32 32
Diseasome
 
Resource Report
Resource Website
1+ mentions
Diseasome (RRID:SCR_002792) Diseasome map, data set, data or information resource, book, service resource, image, narrative resource A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems. disease, disorder, genotype, phenotype, poster, network is related to: Allen Institute Neurowiki
has parent organization: Gephi
Dana-Farber Cancer Institute ;
W. M. Keck Foundation ;
NHGRI ;
NIGMS
PMID:17502601 Free, Freely Available nif-0000-24580 SCR_002792 Diseaseome 2026-02-14 02:00:27 1
ANDES
 
Resource Report
Resource Website
10+ mentions
ANDES (RRID:SCR_002791) data processing software, data analysis software, software toolkit, software application, software resource Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. deep sequencing, biomarker detection, statistical analysis, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: SourceForge
PMID:20633290 Free, Freely available, Available for download biotools:andes, OMICS_01119 https://bio.tools/andes SCR_002791 Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing 2026-02-14 02:00:32 25
BLOCK-iT RNAi Designer
 
Resource Report
Resource Website
10+ mentions
BLOCK-iT RNAi Designer (RRID:SCR_002794) BLOCK-iT RNAi Designer commercial organization, data analysis service, analysis service resource, production service resource, service resource A free tool to design effective RNAi molecules that includes the following target design options: Stealth RNAi siRNA, siRNA, miR RNAi, shRNA, siRNA to Stealth RNAi siRNA, and siRNA to shRNA. rnai, design, sirna, blast, molecule, rnai design has parent organization: Life Technologies Free, Freely Available rid_000099 SCR_002794 2026-02-14 02:00:19 10
NCBI database of Genotypes and Phenotypes (dbGap)
 
Resource Report
Resource Website
500+ mentions
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) dbGaP data repository, storage service resource, data or information resource, service resource, database Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools is used by: International Genomics of Alzheimers Project
is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium
is used by: NIH Heal Project
is used by: Genomic Data Commons Data Portal (GDC Data Portal)
is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is listed by: OMICtools
is listed by: re3data.org
is listed by: NIDDK Information Network (dkNET)
is listed by: bio.tools
is listed by: Debian
is related to: NIDDK Central Repository
is related to: eMERGE Network: electronic Medical Records and Genomics
is related to: Framingham Heart Study
is related to: PhenoExplorer
is related to: Chronic Renal Insufficiency Cohort Study
is related to: DbGaP Cleaner
is related to: Psychiatric Genomics Consortium
is related to: ISCA Consortium
is related to: Allen Institute for Brain Science
has parent organization: NCBI
is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging
NLM PMID:24297256
PMID:17898773
Restricted nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap
https://bio.tools/dbgap
https://doi.org/10.17616/R3GS4K
SCR_002709 database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes 2026-02-14 02:00:30 683
Volocity 3D Image Analysis Software
 
Resource Report
Resource Website
1000+ mentions
Volocity 3D Image Analysis Software (RRID:SCR_002668) Volocity Imaging software data processing software, commercial organization, software application, software resource, image analysis software THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. 3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience. 3d, confocal microscopy, visualization, analyze THIS RESOURCE IS NO LONGER IN SERVICE. SciRes_000112 SCR_002668 2026-02-14 02:00:18 3998
Aging Genes and Interventions Database
 
Resource Report
Resource Website
1+ mentions
Aging Genes and Interventions Database (RRID:SCR_002701) AGEID data repository, storage service resource, data or information resource, service resource, database THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link. allele, strain, gene function, phenotype, mutant, homolog, mutation, degeneration, gene, intervention, life-span is used by: Aging Portal
is used by: NIF Data Federation
has parent organization: University of Washington; Seattle; USA
Aging, Age-related neurological disease, Neurological disease Ellison Medical Foundation PMID:12044961 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-23326 http://sageke.sciencemag.org/highlights/gidb/ SCR_002701 Aging Genes DB, Aging Genes Database, Genes/Interventions Database 2026-02-14 02:00:26 2
Dana Foundation
 
Resource Report
Resource Website
10+ mentions
Dana Foundation (RRID:SCR_002789) training service resource, podcast, training resource, outreach program, blog, funding resource, data or information resource, journal article, book, service resource, narrative resource, training material A private philanthropy with principal interests in brain science, immunology, and education. The portal provides general information about the brain and current brain research, links to validated sites related brain disorders, education resources and lesson plans, and support for the training of in-school arts specialists. The Dana Foundation science and health grants support brain research in neuroscience and immunology and their interrelationship in human health and disease. The grant sections include brain and immuno-imaging, clinical neuroscience research, human immunology and neuroimmunology. The Foundation also occasionally sponsors workshops and forums for working scientists, as well as offering funding for selected young researchers to continue their education or to attend seminars and workshops elsewhere. education, foundation, funding resource, human brain, clinical, development, disease, disorder, grant, neruroimmunology, neuroethics, neuroscience, philanthropy, podcast, research is parent organization of: Dana Foundation: BrainWeb Free nif-0000-24463 SCR_002789 The Dana Foundation 2026-02-14 02:00:19 21
Neuroscience Berlin
 
Resource Report
Resource Website
Neuroscience Berlin (RRID:SCR_002741) group THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 10, 2017. In the last few years the Berlin neuroscience community has been highly successful in creating new research projects. Not the least of these is the cluster of excellence, NeuroCure, which has brought nine new professors and their research groups to Berlin. Along with the increasing levels of research, a number of new neuroscience training programs have recently been established. In 2002 the International Graduate Program Medical Neurosciences was the only structured Masters and PhD program: as of 2009 Berlin hosts four neuroscience schools and several DFG funded research training groups. The purpose of this website to highlight the many projects and people involved in the Berlin neuroscience community. We hope that you, the reader, can benefit from this summary., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-24042 SCR_002741 2026-02-14 02:00:26 0
University of Basel; Basel; Switzerland
 
Resource Report
Resource Website
1+ mentions
University of Basel; Basel; Switzerland (RRID:SCR_002699) university Public university in Basel, Switzerland that offers degree programs in theology, law, medicine, humanities and social sciences, science, psychology, and business and economics. public university, switzerland, degree program is related to: EU-AIMS
is related to: Bsoft
is parent organization of: DogMap
is parent organization of: PredictHaplo
is parent organization of: TSSer
is parent organization of: Ashbya Genome Database
is parent organization of: DINO
is parent organization of: CLIPZ
is parent organization of: SWISS-MODEL Repository
is parent organization of: SWISS-MODEL
is parent organization of: 4 Port Nose Poke
Free nlx_24036 SCR_002699 University of Basel, Universitat Basel 2026-02-14 02:00:30 2
Pathview
 
Resource Report
Resource Website
500+ mentions
Pathview (RRID:SCR_002732) software resource A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. software package, r, differential expression, gene expression, gene set enrichment, genetics, graph, network, metabolomics, microarray, pathway, proteomics, rna-seq, sequencing, systems biology, visualization, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:23740750 Free, Freely available, Available for download biotools:pathview, OMICS_05212 http://pathview.r-forge.r-project.org/
https://bio.tools/pathview
SCR_002732 path view 2026-02-14 02:00:30 520
GLProbs
 
Resource Report
Resource Website
1+ mentions
GLProbs (RRID:SCR_002739) software resource Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. standalone software is listed by: OMICtools
has parent organization: SourceForge
PMID:26357079 Free, Freely available, Available for download OMICS_03732 SCR_002739 2026-02-14 02:00:19 1

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