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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
flytrap
 
Resource Report
Resource Website
10+ mentions
flytrap (RRID:SCR_003075) Flytrap data or information resource, database, image, video resource Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use. brain, genetics, 3d model, expression pattern, anatomy, anatomical structure, cell, gene expression, brain function, neuroimaging, FASEB list has parent organization: University of Edinburgh; Scotland; United Kingdom BBSRC ;
EPSRC
PMID:14681446 Free, Freely available nif-0000-00051, r3d100011203 https://doi.org/10.17616/R3VD0P SCR_003075 2026-02-14 02:00:39 48
Cancer Genome Anatomy Project
 
Resource Report
Resource Website
100+ mentions
Cancer Genome Anatomy Project (RRID:SCR_003072) CGAP data or information resource, portal, topical portal Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools gene, gene expression, normal cell, precancer cell, cancer cell, cell, genome, anatomy, gene expression profile, tissue, pathway, rnai, chromosome, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: National Cancer Institute
is parent organization of: CGAP GO Browser
Cancer, Normal, Precancer NCI Free, download Freely available biotools:cgap, nif-0000-30468 https://mitelmandatabase.isb-cgc.org/mb_search SCR_003072 Cancer Genome Anatomy Project (CGAP) 2026-02-14 02:00:22 107
MethDB
 
Resource Report
Resource Website
10+ mentions
MethDB (RRID:SCR_003108) MethDB data repository, storage service resource, data or information resource, service resource, database Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc.. methylation is listed by: OMICtools
has parent organization: University of Perpignan Via Domitia; Perpignan; France
has parent organization: French National Center for Scientific Research
PMID:11125109
PMID:17965614
PMID:12163707
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03119, OMICS_01840 http://www.methdb.net/ SCR_003108 DNA Methylation Database, MethDB - the database for DNA methylation and environmental epigenetic effects 2026-02-14 02:00:22 15
DnaSP
 
Resource Report
Resource Website
5000+ mentions
DnaSP (RRID:SCR_003067) DnaSP data analysis software, software resource, data processing software, software application A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form. genetics, dna, population genetics, sequence, polymorphism, nucleotide polymorphism, dna sequence, population, noncoding, synonymous, nonsynonymous is listed by: OMICtools
has parent organization: University of Barcelona; Barcelona; Spain
Spanish Direccion General de Investigacion Cientifica y Technica PB91-0245;
Spanish Direccion General de Investigacion Cientifica y Technica PB94-0923;
Spanish Direccion General de Investigacion Cientifica y Technica PB97-0918;
Spanish Direccion General de Investigacion Cientifica y Technica TXT98-1802;
Spanish Direccion General de Investigacion Cientifica y Technica BMC2001-2906;
Spanish Direccion General de Investigacion Cientifica y Technica BFU2004-02253;
Spanish Direccion General de Investigacion Cientifica y Technica BFU2007-6292
PMID:19346325
PMID:19378153
PMID:14668244
PMID:10089204
PMID:9183537
PMID:8808578
Free, Available for download, Freely available OMICS_01820, nif-0000-30461 SCR_003067 DNA Sequence Polymorphism 2026-02-14 02:00:22 5935
JuncBASE
 
Resource Report
Resource Website
10+ mentions
JuncBASE (RRID:SCR_003103) data analysis software, software resource, data processing software, software application Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples. splicing event, splicing events, alternative splicing event, rna seq is listed by: OMICtools
is hosted by: GitHub
Free, Available for download, Freely available OMICS_01335 https://github.com/anbrooks/juncBASE SCR_003103 2026-02-14 02:00:39 19
brainmap.org
 
Resource Report
Resource Website
100+ mentions
brainmap.org (RRID:SCR_003069) BrainMap data or information resource, software resource, database, software application A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results 3d model, atlas, data management, imaging, map, neuroinformatics, warping, neuroimaging, brain, talairach, mni, java, modeling, magnetic resonance, nifti-1, ontology, os independent, pet, spect, visualization, functional neuroimaging, fmri uses: Scribe
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Brede Database
has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA
is parent organization of: Sleuth
is parent organization of: GingerALE
Healthy, Diseased NIMH 2R01-MH074457 PMID:15897617
PMID:11967563
PMID:15846810
Free, Freely available nif-0000-00049 http://www.nitrc.org/projects/brainmap SCR_003069 BrainMap Database 2026-02-14 02:00:29 448
pFind
 
Resource Report
Resource Website
100+ mentions
pFind (RRID:SCR_003011) software resource A search engine system for automated peptide and protein identification from tandem mass spectra. mass spectrometry, proteomics is listed by: OMICtools
has parent organization: Chinese Academy of Sciences; Beijing; China
PMID:17702057 OMICS_02467 SCR_003011 2026-02-14 02:00:21 118
AlzSWAN Knowledge Base
 
Resource Report
Resource Website
1+ mentions
AlzSWAN Knowledge Base (RRID:SCR_003017) AlzSWAN community building portal, portal, knowledge environment, data or information resource, knowledgebase THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers. hypothesis, claim, research paper, relationship, semantics, annotation is listed by: FORCE11
is related to: Semantic Web Applications in Neuromedicine (SWAN) Ontology
has parent organization: Alzheimer's Research Forum
Alzheimer's disease Ellison Medical Foundation ;
alz.org
PMID:17510163 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00524 SCR_003017 2026-02-14 02:00:37 1
GenePaint
 
Resource Report
Resource Website
100+ mentions
GenePaint (RRID:SCR_003015) GenePaint.org reference atlas, expression atlas, data or information resource, atlas, database Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution. gene expression, adult mouse, annotated, c57bl6, mouse, mouse embryo, mrna, non radioactive in situ hybridization, light microscopy, molecular neuroanatomy resource, in situ hybridization, embryonic, postnatal, adult, brain, head, annotation, rna probe, sequence, anatomical structure, FASEB list has parent organization: Max Planck Institute for Biophysical Chemistry; Gottingen; Germany
is parent organization of: GenePaint E15 Atlas
is parent organization of: GenePaint P7 Atlas
is parent organization of: GenePaint P56 Mouse Atlas
is parent organization of: GenePaint Interactive Anatomy Atlas
Burroughs Wellcome Fund ;
European Union ;
Max Planck Society ;
Merck Genome Research Institute ;
Romansky Endowment ;
NINDS ;
BMBF
PMID:14681479
PMID:22936000
nif-0000-00009, SCR_017526 SCR_003015 Atlas of Gene Expression Patterns in Mouse Embryo 2026-02-14 02:00:28 161
EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis
 
Resource Report
Resource Website
10+ mentions
EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis (RRID:SCR_003093) EUROSCARF biomaterial supply resource, organism supplier, material resource Archive of yeast strains and plasmids that were generated during various yeast functional analysis projects. plasmid, strain, wild type, deletion, tap fusion, degron, orf, functional analysis, yeast is listed by: One Mind Biospecimen Bank Listing
has parent organization: Goethe University Frankfurt am Main; Hessen; Germany
BMBF ;
European UnionROFAN I and II ;
European yeast industrial platform ;
federal state of Hessen
Free, Freely available nif-0000-30504 http://www.uni-frankfurt.de/fb15/mikro/EUROSCARF/indexhtml SCR_003093 2026-02-14 02:00:22 40
JETTA
 
Resource Report
Resource Website
1+ mentions
JETTA (RRID:SCR_003091) JETTA data analysis software, software resource, data processing software, software application THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study. exon, exon splicing is listed by: OMICtools
has parent organization: Stanford University; Stanford; California
PMID:22433281 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01334 SCR_003091 2026-02-14 02:00:39 3
Effect Size Calculator
 
Resource Report
Resource Website
1+ mentions
Effect Size Calculator (RRID:SCR_003094) Effect Size Calculators web application, data analysis service, analysis service resource, production service resource, service resource, software resource Calculator for a variety of functions, including Cohen's d and the effect-size correlation, rYl, using means and standard deviations or independent groups t test values and df. calculator, cohen, cohen d, ryi, effect size correlation has parent organization: University of Colorado; Colorado Springs; USA Free, Freely available nif-0000-30507 https://lbecker.uccs.edu/ SCR_003094 2026-02-14 02:00:39 8
Biomedical Information Science and Technology Initiative
 
Resource Report
Resource Website
1+ mentions
Biomedical Information Science and Technology Initiative (RRID:SCR_003123) BISTI training resource, portal, data or information resource, organization portal, funding resource, meeting resource A consortium of representatives from each of the NIH institutes and centers. BISTI was established in May 2000 to serve as the focus of biomedical computing issues at the NIH. The mission of BISTI is to make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and transdisciplinary initiatives between the computational and biomedical sciences. In support of this mission, the BISTI coordinates research grants, training opportunities, and scientific symposia associated with biomedical computing. Regular monthly meetings are conducted to discuss program status, future needs and directions, and topics of interest to the bioinformatics community. grant, funding opportunity, computer science, technology, biology, medicine, collaboration, transdisciplinary initiative, computation, biomedical sciences, bioinformatics, informatics has parent organization: National Institutes of Health NIH Blueprint for Neuroscience Research Free, Freely available nif-0000-00560 https://stip.oecd.org/stip/interactive-dashboards/policy-initiatives/2021%2Fdata%2FpolicyInitiatives%2F25417 SCR_003123 Biomedical Information Science Technology Initiative, BITSI - Biomedical Information Science and Technology Initiative, Biomedical Information Science & Technology Initiative 2026-02-14 02:00:22 1
Genetic Analysis Package
 
Resource Report
Resource Website
1+ mentions
Genetic Analysis Package (RRID:SCR_003006) software resource GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates. genetic, analysis, package, data, population, family, calculation, family, disease, aggregation, kinship, environmental, covariate, haplotype, marker nif-0000-30271 SCR_003006 GAP 2026-02-14 02:00:28 1
Primer3Plus
 
Resource Report
Resource Website
1000+ mentions
Primer3Plus (RRID:SCR_003081) Primer3Plus data analysis service, analysis service resource, production service resource, source code, service resource, software resource A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. primer, dna sequence, primer design, perl, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: Primer3
has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands
Howard Hughes Medical Institute ;
NHGRI R01-HG00257;
NHGRI P50-HG00098
PMID:17485472 Free, Freely available biotools:primer3plus, OMICS_02347 https://bio.tools/primer3plus SCR_003081 Primer3Plus - pick primers from a DNA sequence 2026-02-14 02:00:29 1673
NeuroML
 
Resource Report
Resource Website
10+ mentions
NeuroML (RRID:SCR_003083) NeuroML data or information resource, interchange format, markup language, narrative resource, standard specification A XML-based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models. It facilitates the exchange of complex neural models, allows for greater transparency and accessibility of models, enhances interoperability between simulators and other tools, and supports the development of new software and databases. Exchange of network models will aid the investigation of structure-function relationships in neuroscience including theoretical studies relating connectivity patterns to normal and neurodegenerative network states. NeuroML is a free and open community effort developed with input from many contributors. They will need your help as the standards and tools continue to evolve. cell, network, neuron, model, computation tool, neuronal cell, network model is used by: Open Source Brain
is used by: CNrun
is related to: GENESIS Neural Database and Modelers Workspace
is related to: Neural Open Simulation
is related to: ChannelDB
is related to: neuroConstruct
has parent organization: University College London; London; United Kingdom
has parent organization: Arizona State University; Arizona; USA
is parent organization of: Tools in NeuroML
Free, Freely available nif-0000-00542 SCR_003083 Neuro-Markup Language 2026-02-14 02:00:39 34
Japanese Genotype-phenotype Archive (JGA)
 
Resource Report
Resource Website
10+ mentions
Japanese Genotype-phenotype Archive (JGA) (RRID:SCR_003118) JGA data repository, storage service resource, data or information resource, service resource, database A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee. biomedical, genetic, phenotype, gene, data sharing, genotype is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
has parent organization: DNA DataBank of Japan (DDBJ)
has parent organization: NBDC - National Bioscience Database Center
Free, Freely available nlx_156741, r3d100010818 https://doi.org/10.17616/R3861Q http://trace.ddbj.nig.ac.jp/jga/, http://trace.ddbj.nig.ac.jp/jga/index_e.html SCR_003118 JGA, Japanese Genotype-phenotype Archive (JGA), Japanese Genotype-phenotype Archive 2026-02-14 02:00:22 35
tweeDEseq
 
Resource Report
Resource Website
1+ mentions
tweeDEseq (RRID:SCR_003038) software resource Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. standalone software, unix/linux, mac os x, windows, c, r, rna-seq, differential expression, sequencing, statistical method, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:23965047 Free, Available for download, Freely available OMICS_02406, biotools:tweedeseq https://bio.tools/tweedeseq SCR_003038 tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions 2026-02-14 02:00:29 4
MicroArray and Gene Expression Markup Language
 
Resource Report
Resource Website
1+ mentions
MicroArray and Gene Expression Markup Language (RRID:SCR_003023) MAGE-ML data or information resource, interchange format, markup language, narrative resource, standard specification A language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms. microarray, gene expression, bioinformatics is listed by: 3DVC
is related to: MADAM
is related to: MIAME
is related to: RNA Abundance Database
has parent organization: European Bioinformatics Institute
has parent organization: MAGE
European Union ;
TEMBLOR project
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-30390 SCR_003023 MicroArray and Gene Expression Markup Language 2026-02-14 02:00:37 5
BRAIN
 
Resource Report
Resource Website
10+ mentions
BRAIN (RRID:SCR_003018) software resource Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). standalone software, mac os x, unix/linux, windows, r, mass spectrometry, proteomics, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:23350948 GNU General Public License, v2 biotools:brain, OMICS_02410 https://bio.tools/brain SCR_003018 Baffling Recursive Algorithm for Isotopic distributioN calculations, Baffling Recursive Algorithm for Isotope distributioN 2026-02-14 02:00:21 44

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