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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 Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
COBrA
 
Resource Report
Resource Website
1000+ mentions
COBrA (RRID:SCR_005677) COBrA software resource COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. ontology, anatomy, browser, ontology or annotation browser is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: OBO
has parent organization: University of Edinburgh; Scotland; United Kingdom
BBSRC 15/BEP 17046 PMID:15513995 THIS RESOURCE IS NO LONGER IN SERVICE nlx_149117 SCR_005677 COBrA - An Ontology Browser for Anatomy, COBrA: a bio-ontology editor 2026-08-01 12:02:57 1396
Roth Laboratory
 
Resource Report
Resource Website
1+ mentions
Roth Laboratory (RRID:SCR_005711) Roth Lab data or information resource, laboratory portal, portal, software resource, organization portal The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein has parent organization: University of Toronto; Ontario; Canada
has parent organization: Harvard Medical School; Massachusetts; USA
is parent organization of: FuncAssociate: The Gene Set Functionator
nlx_149163 http://llama.med.harvard.edu SCR_005711 2026-08-01 12:02:57 5
netClass
 
Resource Report
Resource Website
netClass (RRID:SCR_005672) netClass software resource An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker is listed by: OMICtools
has parent organization: SourceForge
PMID:24443376 Free, Public OMICS_02241 SCR_005672 2026-08-01 12:03:01 0
University of Pacific; California; USA
 
Resource Report
Resource Website
University of Pacific; California; USA (RRID:SCR_005706) university Private Methodist affiliated university with its main campus in Stockton, California, and graduate campuses in San Francisco and Sacramento. is parent organization of: University of the Pacific School of Pharmacy and Health Sciences nlx_70007 SCR_005706 2026-08-01 12:02:57 0
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab
 
Resource Report
Resource Website
GUMC Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab (RRID:SCR_005708) GUMC Liu Lab portal, organization portal, data or information resource, laboratory portal THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. microarray, data mining, natural language processing, biomedical, ontology, biomedicine, data analysis, dna microarray, gene THIS RESOURCE IS NO LONGER IN SERVICE nlx_149157 SCR_005708 Georgetown University Medical Center Department of Biostatistics Bioinformatics and Biomathematics - Liu Lab, Georgetown University Medical Center Liu Lab, GUMC Department of Biostatistics Bioinformatics Biomathematics - Liu Lab 2026-08-01 12:02:58 0
GeneMANIA
 
Resource Report
Resource Website
1000+ mentions
GeneMANIA (RRID:SCR_005709) GeneMANIA data analysis service, data or information resource, database, service resource, production service resource, software resource, analysis service resource Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list is listed by: Gene Ontology Tools
is related to: Cytoscape
is related to: Gene Ontology
is related to: PSICQUIC Registry
has parent organization: University of Toronto; Ontario; Canada
Genome Canada ;
Ontario Ministry of Research and Innovation 2007-OGI-TD-05
PMID:20576703
PMID:18613948
PMID:20926419
Open unspecified license, Free for academic use nlx_149159, r3d100013978 https://doi.org/10.17616/R31NJNA2 SCR_005709 2026-08-01 12:03:01 3358
DMRforPairs
 
Resource Report
Resource Website
1+ mentions
DMRforPairs (RRID:SCR_005702) software resource Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
has parent organization: Bioconductor
PMID:24884391 GNU General Public License, v2 or greater biotools:dmrforpairs, OMICS_04059 https://bio.tools/dmrforpairs SCR_005702 DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles 2026-08-01 12:03:01 4
Research at Cincinnati Childrens
 
Resource Report
Resource Website
Research at Cincinnati Childrens (RRID:SCR_005703) Research at Cincinnati Children's data or information resource, portal, service resource, training service resource, training resource, organization portal Foundation scientists and physicians conduct breakthrough research to improve care for children as well as train the next generation of investigators. Cincinnati Children's Research Foundation is dedicated to advancing basic, translational, clinical and outcomes-based research. Why choose our cores for your research? We can provide you with cutting-edge, cost-effective technology and data analysis that would be unattainable on an individual research basis. Our fee-for-service program also offers unique studies that you can't find anywhere else. Our faculty also has access to the research cores hosted at the University of Cincinnati College of Medicine. * Animal Behavioral Core * Cardiovascular Imaging Core * Cell Manipulations Laboratory * Cell Processing Core * Cincinnati Biobank * Cincinnati Center for Nutritional Research and Analysis * Comprehensive Mouse and Cancer Core * Gene Expression Microarray Core * Genetic Variation and Gene Discovery Core * Imaging Research Center * Laser Capture Microdissection Microscopy * Lenti-shRNA Library Core * Pathology Research Core * Pluripotent Stem Cell Facility * Research Flow Cytometry Core * Stem Cell Processing Core Lab * Transgenic and Gene Targeting Core * Translational Core Labs * Translational Trials Development and Support Laboratory (TTDSL) * Vector Production Facility * Veterinary Services * Viral Vector Core Support Services: We provide expert consultation, including grant proposal design, data management and regulatory compliance, to investigators at Cincinnati Children's. Research Education and Training: The Cincinnati Children's Research Foundation offers research-based education and training options for scientists, often in conjunction with the University of Cincinnati. High School Programs, Undergraduate Programs, Graduate Degree Programs, Medical Student Program, Postgraduate Programs, Postdoctoral Programs pediatric, child, young human nlx_149152 SCR_005703 Cincinnati Children's Research Foundation 2026-08-01 12:02:57 0
University of Barcelona Statistics and Bioinformatics Research Group
 
Resource Report
Resource Website
University of Barcelona Statistics and Bioinformatics Research Group (RRID:SCR_005704) UB Statistics and Bioinformatics Research Group data analysis service, data or information resource, portal, service resource, topical portal, production service resource, analysis service resource The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers. statistics, bioinformatics, next generation sequencing, dna microarray, dna, microarray, biology, biomedicine, data mining, modeling, analysis has parent organization: University of Barcelona; Barcelona; Spain nlx_149154 SCR_005704 University of Barcelona Statistics Bioinformatics Research Group 2026-08-01 12:02:58 0
University of Lorraine; Lorraine; France
 
Resource Report
Resource Website
University of Lorraine; Lorraine; France (RRID:SCR_005705) UL university French public university. is parent organization of: Suggested Ontology for Pharmacogenomics Wikidata:Q4173330, Crossref funder ID:100008990, nlx_158101, ISNI:0000 0001 2194 6418, grid.29172.3f https://ror.org/04vfs2w97 SCR_005705 Universit� de Lorraine, University of Lorraine, Universite de Lorraine 2026-08-01 12:03:01 0
go-moose
 
Resource Report
Resource Website
go-moose (RRID:SCR_005666) go-moose data processing software, data analysis software, software application, software resource go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible software library, slimmer-type tool, analysis, gene ontology, other analysis is listed by: Gene Ontology Tools
is related to: Gene Ontology
is related to: go-perl
is related to: go-db-perl
has parent organization: SourceForge
has parent organization: Berkeley Bioinformatics Open-Source Projects
has parent organization: Lawrence Berkeley National Laboratory
Free for academic use nlx_149189 SCR_005666 2026-08-01 12:03:01 0
MolGen
 
Resource Report
Resource Website
10+ mentions
MolGen (RRID:SCR_005700) MolGen topical portal, data or information resource, portal The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches. molecular biology, gram-positive bacteria, pathogen, transcript, protein, profile, high-throughput, dna microarray, proteomics, dna, microarray, functional genomics, bioinformatics, genetics, gene has parent organization: University of Groningen; Groningen; Netherlands
is parent organization of: FIVA - Functional Information Viewer and Analyzer
nlx_149166 http://molgen.biol.rug.nl/molgen/index.php SCR_005700 Molecular Genetics 2026-08-01 12:02:57 27
KI Biobank
 
Resource Report
Resource Website
KI Biobank (RRID:SCR_005664) KI Biobank - Gallstone biomaterial supply resource, material resource THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. KI Biobank - Gallstone aims at investigating genetics of gallstone disease on Swedish Twins. Types of samples * EDTA whole blood * DNA * Plasma Number of sample donors: 82 gene, genetics is listed by: One Mind Biospecimen Bank Listing
is related to: Swedish Twin Registry
has parent organization: Karolisnka Biobank
Gallstone disease, Twin THIS RESOURCE IS NO LONGER IN SERVICE nlx_151297, nlx_151300, SCR_005796 https://www.researchgate.net/publication/246710484_Gallstone_disease_in_Swedish_twins_is_linked_to_ABCG8_D19H_risk_genotype SCR_005664 KI Biobank - Gallstone, KI Biobank - KTS 2026-08-01 12:02:57 0
NIDA Podcasts
 
Resource Report
Resource Website
NIDA Podcasts (RRID:SCR_005660) NIDA Podcasts narrative resource, podcast, data or information resource Audio clips that highlight research efforts at the National Institute on Drug Abuse and include interviews with prominent NIDA scientists. To listen to these clips, just click Listen Now under the clip summary. You must have Real Media Player or Windows Media Player installed to download these clips. To view a printable transcript of a clip, click View Transcript under the clip summary. drug abuse, transcript has parent organization: National Institute on Drug Abuse NIDA All of these clips are free from copyright and can be used for broadcast or other use with acknowledgement of the National Institute on Drug Abuse. nlx_149377 SCR_005660 2026-08-01 12:03:01 0
Stanford Center for Biomedical Informatics Research
 
Resource Report
Resource Website
Stanford Center for Biomedical Informatics Research (RRID:SCR_005698) BMIR portal, organization portal, data or information resource, laboratory portal Mark Musen''s laboratory studies components for building knowledge-based systems, controlled terminologies and ontologies, and technology for the Semantic Web. For more than two decades, Musen''s group has worked to elucidate reusable building blocks of intelligent systems, and to develop scalable computational architectures for systems with significant applications in biomedicine. Informatics is the study of information: its structure, its communication, and its use. As society becomes increasingly information intensive, the need to understand, create, and apply new methods for modeling, managing, and acquiring information has never been greater especially in biomedicine. BMIR is home to world class scientists and trainees developing cutting-edge ways to acquire, represent, process, and manage knowledge and data related to health, health care, and the biomedical sciences. Our faculty, students, and staff are committed to ensuring the biomedical community is properly equipped for the information age, and believe our efforts will provide the structure for the burgeoning revolution of health care and the biomedical sciences. biomedicine, informatics has parent organization: Stanford University; Stanford; California
is parent organization of: CLENCH
is parent organization of: BioPortal
is parent organization of: Center for Expanded Data Annotation and Retrieval
is parent organization of: Protege
is parent organization of: WebProtege
nlx_149147 SCR_005698 Stanford Medical Informatics 2026-08-01 12:02:58 0
Science of Mental Illness: Grades 6- 8
 
Resource Report
Resource Website
Science of Mental Illness: Grades 6- 8 (RRID:SCR_005612) video resource, data or information resource, narrative resource, training material A set of lessons for students used to gain insight into the biological basis of mental illnesses and how scientific evidence and research can help us understand its causes and lead to treatments and, ultimately, cures. Both the Web version and the free supplement are available. It is a creative, inquiry-based instruction program designed to promote active learning and stimulate student interest in medical topics. This curriculum supplement aims to help students experience the process of scientific inquiry and develop an enhanced understanding of the nature and methods of science. mental disease, treatment, human, curriculum, student, adolescent, teacher, teacher's guide, lesson plan, k-12, training resource has parent organization: NIMH Educational Resources National Institute of Mental Health nlx_146230 http://science.education.nih.gov/customers.nsf/MSMental SCR_005612 Science of Mental Illness 2026-08-01 12:02:55 0
geneXplain
 
Resource Report
Resource Website
50+ mentions
geneXplain (RRID:SCR_005573) GeneXplain software toolkit, workflow software, software application, data processing software, software resource An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field. scientific workflow, bioinformatics, systems biology, network modeling, microarray, proteomics, mirna, chip-chip, sequence, biomarker, gene expression nlx_146199 SCR_005573 geneXplain GmbH 2026-08-01 12:02:54 66
Virtual Biology Lab
 
Resource Report
Resource Website
Virtual Biology Lab (RRID:SCR_005694) Virtual Biology data or information resource, laboratory portal, portal, software resource, organization portal Virtual Biology Lab portal from the University of Nice Sophia Antipolis; Nice; France. Offered are a variety of software including: * GenBank2Treedyn: Extract annotations from GenBank files for: ** More convenient alignments and phylogeny (replace def line of fasta file by GI number) ** Extremely powerful annotations of phylogenetic trees with TreeDyn. * THEA: Analyses of DNA chip data with ontologies * Blast2Tree: Blast server for the identification of procaryotes * Dashboard: e-Tool for data exchanges among partners, DNA chips design and developement * Oligo Heat Map: Check thermodynamical parameters for PCR primers and compute graphical representation to show specificity of target sequences * EmblEx: A cgi tool to parse and extract data from EMBL entries to various formats * Miscellaneous software ** Jane plugin: Add a small panel to Jane server to retrieve PMID of publications ** EtBlast plugin: Add a small panel to EtBlast server to retrieve PMID of publications ** Oligo Builder: Get the oligomers from a set of target sequences by avoiding non-target sequences biodiversity, ontology, bioinformatics, thea, ontology has parent organization: University of Nice Sophia Antipolis; Nice; France
is parent organization of: THEA - Tools for High-throughput Experiments Analysis
nlx_149144 SCR_005694 Virtual Biology Laboratory 2026-08-01 12:02:58 0
BIIT - Bioinformatics Algorithmics and Data Mining Group
 
Resource Report
Resource Website
1+ mentions
BIIT - Bioinformatics Algorithmics and Data Mining Group (RRID:SCR_005690) BIIT Research group data or information resource, text-mining software, portal, software application, software resource, organization portal, department portal The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools gene regulation, gene expression, data analysis, biological, data mining, systems biology, combinatorial pattern matching, software, biomedical research, stem cell, cancer has parent organization: University of Tartu; Tartu; Estonia
is parent organization of: GraphWeb
is parent organization of: g:Profiler
nlx_149141 http://biit.cs.ut.ee/about/main SCR_005690 BIIT - Bioinformatics Algorithmics Data Mining Group, BIIT Group - Institute of Computer Science 2026-08-01 12:02:57 7
Principe Felipe Research Centre; Valencia; Spain
 
Resource Report
Resource Website
1+ mentions
Principe Felipe Research Centre; Valencia; Spain (RRID:SCR_005691) CIPF institution The Pr��ncipe Felipe Research Centre (CIPF), which was inaugurated by their Royal Highnesses the Prince and Princess of Asturias on 17th March 2005, is a centre dedicated to biomedical research, with the aim of taking on new challenges in the field of basic research and encouraging scientific works of excellence. The construction of the Centre was carried out thanks to the Regional Development Funds from the European Union, and from the Regional Government (Generalitat Valenciana) through its Ministry of Health. The current financing of the CIPF comes mainly from the investment made by the Generalitat Valenciana through the Ministry of Health, as well as the Regenerative Medicine Programme, the fruit of an agreement between the Institute of Health Carlos III and the Ministry of Health for basic and translation research in this field. The CIPF takes the research tradition from the then Valencian Cytological Research Institute and the Valencian Biomedical Research Foundation, with the aim of consolidating and expanding this research. Therefore the activity in the CIPF can be divided into three main strategic work areas: The Regenerative Medicine area focuses its research on cellular therapy and interdisciplinary research in human embryonic and adult stem cells, with the aim of regenerating damaged organs to improve human health. The Chemical and Quantative Biology area aims to understand, through the application of (bio) chemical, genetic, and bioinformatic methods, to understand the molecular mechanisms that control the biological processes and alterations that lead to pathological conditions. The Biomedicine area focuses on understanding the molecular bases of human pathologies that require new diagnostic and clinical procedures for their identification and treatment, pathologies such as cancer, neurological pathologies and rare illnesses. is parent organization of: QualiMap
is parent organization of: VARIANT
is parent organization of: CIPF Bioinformatics and Genomics Department
is parent organization of: Blast2GO
is parent organization of: Gene Expression Profile Analysis Suite
nlx_149142, grid.418274.c, ISNI: 0000 0004 0399 600X https://ror.org/05xr2yq54 SCR_005691 Centro de Investigaci��n Pr��ncipe Felipe, Centro de Investigacion Principe Felipe, Principe Felipe Research Center, Pr��ncipe Felipe Research Centre 2026-08-01 12:02:58 2

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