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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 Authority Synonyms Record Last Update Mentions Count
ISPS Data Archive
 
Resource Report
Resource Website
1+ mentions
ISPS Data Archive (RRID:SCR_003127) ISPS Data Archive data or information resource, data repository, data set, service resource, storage service resource Data archive to assist in the sharing of research grade information pertaining to the social and economic sciences. The majority of digital content currently consists of social science research data from experiments, program files with the code for analyzing the data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only. When possible, Data is linked to Projects and Publications, via the ISPS KnowledgeBase. ISPS operates in accordance with the prevailing standards and practices of the digital preservation community including the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003) and the Data Documentation Initiative (DDI) standard. Accordingly, ISPS supports digital life-cycle management, interoperability, and preferred methods of preservation. The ISPS Data Archive is intended for use by social science researchers, policy-makers, and practitioners who are conducting or analyzing field (and other) experiments in various social science disciplines. Currently, Replication Files originate with ISPS-affiliated scholars. life-cycle management, interoperability, preservation, scholarly community, scholarship, data curation, social sciences, economics, political science, political science literature, political ethics, bioethics is listed by: re3data.org
has parent organization: Yale University; Connecticut; USA
Free, Freely available nlx_156779, r3d100010833 https://doi.org/10.17616/R3FP5M SCR_003127 SciCrunch Registry Yale University Institution for Social and Policy Studies Data Archive, Yale ISPS Data Archive 2026-09-26 02:13:23 1
PathGuide: the pathway resource list
 
Resource Report
Resource Website
10+ mentions
PathGuide: the pathway resource list (RRID:SCR_003248) Pathguide catalog, data or information resource, database Catalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated. gene interaction network, metabolic pathway, signaling pathway, pathway diagram, protein-compound interaction, protein-protein interaction, protein sequence focused, transcription factor, gene regulatory network, transcription factor target, genetic interaction, pathway, molecular interaction, FASEB list is listed by: OMICtools
is related to: PSI-MI
is related to: bioDBcore
is related to: Biological Pathways Exchange
is related to: CellML
is related to: SBML
is related to: Biological Pathways Exchange
PMID:16381921 Free, Freely available SciRes_000148, OMICS_01701, nif-0000-00640 SCR_003248 SciCrunch Registry 2026-09-26 02:13:26 47
Laura and John Arnold Foundation
 
Resource Report
Resource Website
1+ mentions
Laura and John Arnold Foundation (RRID:SCR_003240) LJAF institution Private foundation whose funding activities are primarily centered around improving life in the United States. Its mission is to produce big and lasting changes in society over the long term. Their four areas of focus (2014) are: criminal justice, K-12 education, public accountability, and research integrity. grant, criminal justice, k-12 education, public accountability, research integrity Free, Freely available Crossref funder ID: 100009827, ISNI: 0000 0004 0555 6315, nlx_157294, grid.480593.3, Wikidata: Q17088752 https://www.arnoldventures.org/people/laura-arnold-john-arnold SCR_003240 SciCrunch Registry Arnold Foundation 2026-09-26 02:13:26 4
Japanese Genotype-phenotype Archive (JGA)
 
Resource Report
Resource Website
10+ mentions
Japanese Genotype-phenotype Archive (JGA) (RRID:SCR_003118) JGA data or information resource, data repository, database, service resource, storage service resource 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 SciCrunch Registry JGA, Japanese Genotype-phenotype Archive (JGA), Japanese Genotype-phenotype Archive 2026-09-26 02:13:23 37
Open Science Framework
 
Resource Report
Resource Website
500+ mentions
Open Science Framework (RRID:SCR_003238) OSF data repository, service resource, storage service resource Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research. workflow, cloud, data management, provenance, network, collaboration, data sharing, interdisciplinary research, FASEB list is used by: NIH Heal Project
is listed by: re3data.org
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: DataCite
is listed by: FAIRsharing
has parent organization: Center for Open Science
Free, Freely available DOI:10.25504/FAIRsharing.g4z879, DOI:10.17605, nlx_157292, DOI:10.17616/R3N03T, r3d100011268, SCR_017419 http://openscienceframework.org, https://doi.org/10.17616/R3N03T, https://doi.org/10.17616/r3n03t, https://doi.org/10.17605/, https://dx.doi.org/10.17605/, https://fairsharing.org/10.25504/FAIRsharing.g4z879, https://doi.org/10.17616/R35G9K SCR_003238 SciCrunch Registry 2026-09-26 02:13:25 938
JCVI Primer Designer
 
Resource Report
Resource Website
1+ mentions
JCVI Primer Designer (RRID:SCR_003275) JCVI Primer Designer software resource High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. perl, command-line, pcr primer design, pcr, primer, high throughput sequencing is listed by: OMICtools
has parent organization: SourceForge
PMID:18405373 Free, Available for download, Freely available OMICS_02330 SCR_003275 SciCrunch Registry 2026-09-26 02:13:26 1
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 SciCrunch Registry tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions 2026-09-26 02:13:21 4
SaskPrimerFS
 
Resource Report
Resource Website
SaskPrimerFS (RRID:SCR_003159) SaskPrimerFS software resource Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism. gene family, pcr primer, pcr, primer, dna sequence, command-line, perl is listed by: OMICtools
has parent organization: SourceForge
Free, Available for download, Freely available OMICS_02335 SCR_003159 SciCrunch Registry 2026-09-26 02:13:24 0
NLSdb: a database of nuclear localization signals
 
Resource Report
Resource Website
1+ mentions
NLSdb: a database of nuclear localization signals (RRID:SCR_003273) NLSdb analysis service resource, data analysis service, data or information resource, database, production service resource, service resource A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree nuclear localization signal, nuclear protein, nucleus, motif, predict, protein has parent organization: Columbia University; New York; USA NIGMS 1-P50-GM62413-01;
NSF DBI-0131168
PMID:12520032 Free for academic use, Acknowledgement requested, All others should inquire about a commercial license nif-0000-03191 http://cubic.bioc.columbia.edu/db/NLSdb/ SCR_003273 SciCrunch Registry NLSdb - a database of nuclear localization signals 2026-09-26 02:13:27 4
MultiLoc
 
Resource Report
Resource Website
10+ mentions
MultiLoc (RRID:SCR_003151) MultiLoc analysis service resource, data analysis service, production service resource, service resource, software resource An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available. subcellular localization, protein, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Tubingen; Tubingen; Germany
PMID:19723330 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_01628, biotools:multiloc2 https://bio.tools/multiloc2 SCR_003151 SciCrunch Registry 2026-09-26 02:13:25 41
Jackson Laboratory Cytogenetic Models Resource
 
Resource Report
Resource Website
1+ mentions
Jackson Laboratory Cytogenetic Models Resource (RRID:SCR_003270) biomaterial supply resource, material resource, organism supplier Maintains and distributes chromosome aberration stocks that provide primarily mouse models for Down syndrome. The Resource currently provides models for Down syndrome research, including: Rb(6.16)24Lub x Rb(16.17)7Bnr F1 hybrids that are used to produce Chr 16 trisomy (Ts16) embryos, which have many of the fetal developmental features of DS, and; Ts(1716)65Dn, segmental trisomy mice that survive to adulthood and have many of the features of DS. The Resource also includes stocks with selected reciprocal translocations involving Chr 16 and some Chr 16 transgenic stocks. In addition, a large number of Robertsonian chromosome stocks are held as frozen embryos in the Cryopreservation Resource. Each mouse chromosome is present in at least two different Robertsonian chromosomes in these strains so that specific trisomies for each of the 19 mouse autosomes can be produced. Breeding pairs and individual mice are provided. chromosome mutation, mouse model, down syndrome model, transgenic mouse has parent organization: Jackson Laboratory Down syndrome NICHD contract N01-HD-73265 Free, Available for download, Freely available nif-0000-01258 https://www.jax.org/research-and-faculty/resources/cytogenetic-and-down-syndrome-models-resource SCR_003270 SciCrunch Registry Jackson Lab: Cytogenetic Models Resource, Cytogenetic Models Resource 2026-09-26 02:13:26 1
GeneCopoeia
 
Resource Report
Resource Website
5000+ mentions
GeneCopoeia (RRID:SCR_003145) commercial organization Commercial organization which provides reagents and services for molecular biology research. Its services include clone collections, microRNA solutions, genome editing, qPCR products, and fluorescent labeling and detection. reagent, pcr, clone, microrna, cell biology Free, Freely available nlx_152370 SCR_003145 SciCrunch Registry GeneCopoeia Inc 2026-09-26 02:13:24 6984
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 SciCrunch Registry MicroArray and Gene Expression Markup Language 2026-09-26 02:13:21 5
JAX Neuroscience Mutagenesis Facility Protocols
 
Resource Report
Resource Website
JAX Neuroscience Mutagenesis Facility Protocols (RRID:SCR_003021) NMF Protocols data or information resource, experimental protocol, narrative resource THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Neuroscience Mutagenesis Facility of the Jackson Laboratory (NMF) was established to produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The protocols are available. The impetus for the program resulted from the recognition that * the value of genomic data would remain limited unless more information about the functionality of its individual components became available, and * the task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e. N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. Protocols: * Genetics ** Production of Mice for a Genome-Wide ENU Mutagenesis Screen ** Production of Mice using Chemical Mutagenesis of Mouse ES Cells * Protocols ** Step by step procedures-- Mouse mutagenesis with ENU ** Step by step procedures-- ES Cell mutagenesis with EMS * Phenotyping: Overview * Protocols:(currently only screens marked * are in use) ** Acoustic startle response (ASR) ** Auditory brainstem response (ABR) ** CLAMSTM(former CCMS) ** Creatine kinase ** Developmental Screen * ** Eye and Vision * ** Gait Analysis ** Gustation ** Observation * ** Seizure threshold * ** Additional Background Information mutant mouse strain, genetically-modified mouse, motor system function, impairment of function, eye disease, eye disorder, ophthalmological disorder, ophthalmic disorder, ocular disease, disease of eye, epilepsy, epileptic seizure, seizure disorder, gustatory system function, taste system function, bioinformatics, acoustic startle response, auditory brainstem response, creatine kinase, development, eye, vision, gait, gustation, observation, seizure, mutagenesis, n-ethyl-n-nitrosourea, es cell mutagenesis, ems, genetics, phenotyping has parent organization: JAX Neuroscience Mutagenesis Facility THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-00527 SCR_003021 SciCrunch Registry JAX Protocols, Protocols of the NMF, Protocols of the Neuroscience Mutagenesis Facility, JAX NMF Protocols 2026-09-26 02:13:21 0
BrainInfo
 
Resource Report
Resource Website
10+ mentions
BrainInfo (RRID:SCR_003142) atlas, data or information resource, database, narrative resource, portal, standard specification, topical portal Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures. brain, neuroanatomy is used by: NIF Data Federation
is listed by: Biositemaps
is related to: INIA19 Primate Brain Atlas
has parent organization: University of Washington; Seattle; USA
has parent organization: University of California at San Diego; California; USA
The Human Brain Project ;
NIBIB ;
NLM LM/OD-06243;
NIH Office of the Director LM/OD-06243;
NIMH MHO69259;
NCRR RR-00166
PMID:21789500
PMID:21163300
PMID:18368361
PMID:15055392
Free, Freely available nif-0000-00019 SCR_003142 SciCrunch Registry Brain Info 2026-09-26 02:13:24 16
R-pbh5
 
Resource Report
Resource Website
R-pbh5 (RRID:SCR_003026) software library, software resource, software toolkit Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5. software package, r is listed by: OMICtools Free, Available for download, Freely available OMICS_05139 https://github.com/extemporaneousb/R-pbh5 SCR_003026 SciCrunch Registry 2026-09-26 02:13:22 0
Isopat
 
Resource Report
Resource Website
Isopat (RRID:SCR_003025) software resource Software function that calculates the isotopic pattern (fine structures) for a given chemical formula. standalone software, mac os x, unix/linux, windows, r is listed by: OMICtools
has parent organization: CRAN
Free, Available for download, Freely available OMICS_02409 https://isopat.sourceforge.net/ SCR_003025 SciCrunch Registry isopat: Calculation of isotopic pattern for a given molecular formula 2026-09-26 02:13:21 0
GeneScissors
 
Resource Report
Resource Website
1+ mentions
GeneScissors (RRID:SCR_003146) data analysis software, data processing software, sequence analysis software, software application, software resource Software for detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment. transcriptome inference, read misalignment, rna seq is listed by: OMICtools
has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA
works with: Cufflinks
works with: TopHat
PMID:23812996 Free, Available for download, Freely available OMICS_01232 SCR_003146 SciCrunch Registry Gene Scissors 2026-09-26 02:13:24 2
nematodes.org
 
Resource Report
Resource Website
10+ mentions
nematodes.org (RRID:SCR_003267) nematodes.org data or information resource, organism-related portal, portal, topical portal Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes nematode, genomics, genome, gene, database, transcriptome, analysis tool, bioinformatics, genomics databases, software, expressed sequence tag, analysis, dna barcode, phylogenomics, FASEB list has parent organization: University of Edinburgh; Scotland; United Kingdom
is parent organization of: 959 Nematode Genomes
is parent organization of: MolluscDB PartiGene database
is parent organization of: NEMBASE
is parent organization of: PartiGene ARTHROPODA Database
is parent organization of: Bombus terrestris PartiGene Database
THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-03187 SCR_003267 SciCrunch Registry Nematode & Neglected Genomics (at) The Blaxter Lab, Blaxter Lab, Nematode and Neglected Genomics, nematodes.org Nematode & Neglected Genomics (at) The Blaxter Lab, Nematode & Neglected Genomics 2026-09-26 02:13:26 31
Biological Collections Ontology
 
Resource Report
Resource Website
Biological Collections Ontology (RRID:SCR_003262) BCO controlled vocabulary, data or information resource, ontology Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers. owl, interoperability, biodiversity, museum collection, environmental sample, metagenomic sample, ecological survey is listed by: BioPortal
is listed by: OBO
is listed by: Google Code
is related to: Information Artifact Ontology
PMID:24595056 Free, Available for download, Freely available nlx_157333 http://purl.obolibrary.org/obo/bco.owl, http://purl.bioontology.org/ontology/BCO SCR_003262 SciCrunch Registry 2026-09-26 02:13:26 0

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