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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Gabi Primary Database Resource Report Resource Website 10+ mentions |
Gabi Primary Database (RRID:SCR_002755) | GABI | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource |
Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload. |
molecular plant physiology, plant genome, genome, blast, sequence, snp, mapping, proteomics, image collection | has parent organization: Max Planck Institute of Molecular Plant Physiology; Golm; Germany | German Resource Center for Genome Research RZPD GmbH ; Max Planck Society ; BMBF 0312272; BMBF 0313112; BMBF 0315046 |
PMID:18812395 | Free, Freely available | nif-0000-02866, r3d100012432 | http://gabi.rzpd.de/, https://doi.org/10.17616/R3QB61 | SCR_002755 | SciCrunch Registry | GabiPD | 2026-10-31 12:13:11 | 13 | ||||
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DSS Resource Report Resource Website 1+ mentions |
DSS (RRID:SCR_002754) | software library, software resource, software toolkit | Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions. | standalone software, unix/linux, mac os x, windows, r, differential expression, rna-seq, chip-seq, dna methylation, differential expression, sequencing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24561809 | Free, Freely available, Available for download | OMICS_03273 | SCR_002754 | SciCrunch Registry | Dispersion Shrinakge for Sequencing data, DSS - Dispersion shrinakge for sequencing data | 2026-10-31 12:13:12 | 9 | |||||||
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SumsDB Resource Report Resource Website 10+ mentions |
SumsDB (RRID:SCR_002759) | SumsDB, WebCaret | analysis service resource, atlas, data analysis service, data or information resource, data repository, database, image repository, production service resource, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures | segmentation, volume, neuroimaging, brain, fmri, stereotaxic foci, stereotaxic coordinate, brain-mapping, foci, structural mri, mri, cerebral cortex, cerebellar cortex, afni brik, analyze, atlas, nifti, registration, rendering, spatial transformation, surface analysis, surface rendering, visualization, volume rendering, brain mapping, neuroanatomy |
is used by: NIF Data Federation is listed by: Biositemaps is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: re3data.org is related to: Computerized Anatomical Reconstruction and Editing Toolkit is related to: Integrated Manually Extracted Annotation has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
Mental disease, Neurological disorder, Normal | Human Brain Project ; NSF ; NCI ; NLM ; NASA ; National Partnership for Advanced Computational Infrastructure ; NIMH R01 MH60974-06 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00016, r3d100010169 | http://brainvis.wustl.edu/wiki/index.php/Sums:About http://www.nitrc.org/projects/sumsdb, https://doi.org/10.17616/R3JC76 | SCR_002759 | SciCrunch Registry | SumsDB WebCaret, SumsDB Database, Web Caret, WebCaret Online Visualization, Surface Management System Database and WebCaret Online Visualization, SumsDB and WebCaret, Sums database, SumsDB (Surface Management System Database) and WebCaret Online Visualization, Sums DB, SumsDB (Surface Management System Database) WebCaret Online Visualization, Surface Management System Database | 2026-10-31 12:13:12 | 14 | ||||
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Society for Research on Nicotine and Tobacco Resource Report Resource Website 1+ mentions |
Society for Research on Nicotine and Tobacco (RRID:SCR_002753) | SRNT | institution | With over a thousand members, including many of the top experts on nicotine and tobacco from over 20 countries around the world, the Society for Research on Nicotine and Tobacco's mission is to stimulate the generation of new knowledge concerning nicotine in all its manifestations - from molecular to societal. The Society has the following goals: 1. To sponsor scientific meetings and publications fostering the exchange of information on the biological, behavioral, social, and economic effects of nicotine; these activities shall include basic research and research on mechanisms of action and the use of nicotine as a probe for studying nervous systems function as well as applied research on the behavioral and pharmacological aspects of tobacco use, nicotine dependence, the therapeutic uses of nicotine, and related areas. 2. To encourage scientific research on public health efforts for the prevention and treatment of cigarette and tobacco use. 3. To provide the means by which various legislative, governmental, regulatory, and other public agencies and the ethical drug industry can obtain expert advice and consultation on critical issues concerning tobacco use, nicotine dependence, and the therapeutic uses of nicotine. Membership dues will be used to plan an annual meeting, to publish a newsletter, to compile a directory, to conduct advocacy and liaison activities for nicotine research, and to begin work on professional publications such as a journal. Though the Society will meet at least once per year in North America and will be incorporated in the United States, the intent is to be international in scope, with co-sponsorship of meetings in other countries and active recruitment of members outside the United States. By clicking on the various links on the website you can gain access to further information about the society, its publications, activities and membership. In 2004, the Society for Research on Nicotine and Tobacco celebrated the tenth anniversary of its founding. During its first decade, the Society grew from around 100 to over 900 members, sponsored well-attended annual meetings and highly-influential satellite conferences to promote research, provided timely electronic and print services to increase the flow of information, and founded a new peer-reviewed journal (Nicotine and Tobacco Research: The Journal of SRNT) to facilitate communication of scientific advances. The record documents considerable progress in meeting the objective of the Society to stimulate new knowledge about nicotine in all its manifestations. As part of SRNT's Decade One celebration, two projects were developed to commemorate its achievements and help preserve its collective memory. The first is an article by two past presidents, Ovide Pomerleau and John Hughes, entitled With a little help from its friends: A brief history of the Society for Research on Nicotine and Tobacco, published in the Societys journal, Nicotine and Tobacco Research. The second is a series of e-interviews with each of SRNTs first ten presidents. A brief structured interview was designed, and the former presidents were invited to respond in writing to each question in as little or as much detail as desired. An open-ended question was provided at the end to allow for more free-form commentary. The results of this effort can be accessed via the links below. | behavioral effects, biological effects, cigarette, newsletter, nicotine, nicotine use disorder, prevention, public health, research, social effects, tobacco, treatment | Free | grid.430369.b, nif-0000-24137, Wikidata: Q23583082, ISNI: 0000 0004 0370 3617 | https://ror.org/04q0te651 | SCR_002753 | SciCrunch Registry | SRNT | 2026-10-31 12:13:11 | 4 | |||||||
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rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser, https://bio.tools/rbiopaxparser | SCR_002744 | SciCrunch Registry | rBiopaxParser - Parses BioPax files and represents them in R | 2026-10-31 12:13:12 | 4 | ||||||
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Stanley Neuropathology Consortium Integrative Database Resource Report Resource Website 10+ mentions |
Stanley Neuropathology Consortium Integrative Database (RRID:SCR_002749) | SNCID | analysis service resource, data analysis service, data or information resource, data set, database, production service resource, service resource | A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access. | schizophrenia, bipolar disorder, depressive disorder, brain, blinded study, microarray, single-nucleotide polymorphism, mental disorder, biomarker | has parent organization: Stanley Medical Research Institute | Schizophrenia, Bipolar Disorder, Depressive Disorder, Mental disorder | PMID:19829293 | Free | nif-0000-24103 | SCR_002749 | SciCrunch Registry | Stanley Neuropathology Consortium Integrative Database | 2026-10-31 12:13:12 | 20 | |||||
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Charles University; Prague; Czech Republic Resource Report Resource Website 10+ mentions |
Charles University; Prague; Czech Republic (RRID:SCR_002931) | CU | university | Research university located in Prague, Czech Republic. | university, research university, degree |
is parent organization of: IRESite is parent organization of: Database of Germline p53 Mutations is parent organization of: Culture Collection of Fungi is parent organization of: IRESite is parent organization of: Charles University Vinicna Microscopy Core Facility |
ISNI 0000 0004 1937 116X, nlx_87455, Crossref Funder ID 100007397, Wikidata Q31519, GRID grid.4491.8 | https://ror.org/024d6js02 | SCR_002931 | SciCrunch Registry | Charles University, Charles University in Prague, Univerzita Karlova | 2026-10-31 12:13:14 | 11 | |||||||
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Genox Corpooration Resource Report Resource Website |
Genox Corpooration (RRID:SCR_002930) | commercial organization | Biotechnological company that produces and supplies materials to oxidative stress and aging researchers. | oxidative stress, biomarker, antibody | nlx_152373 | SCR_002930 | SciCrunch Registry | 2026-10-31 12:13:14 | 0 | |||||||||||
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Time-series RNA-seq Analysis Package Resource Report Resource Website 1+ mentions |
Time-series RNA-seq Analysis Package (RRID:SCR_002935) | TRAP | software resource | A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment. | time-series, rna-seq, analysis |
is listed by: OMICtools has parent organization: Seoul National University; Seoul; South Korea |
PMID:24518221 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02590 | SCR_002935 | SciCrunch Registry | 2026-10-31 12:13:15 | 3 | |||||||
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Wasserman Lab Online Software Tools Resource Report Resource Website 1+ mentions |
Wasserman Lab Online Software Tools (RRID:SCR_002892) | software library, software resource, software toolkit | This portal leads to the numerous Wasserman Lab online software tools available for use. The following are list of active Software tools available: - ConSite: Transcription factor binding site detection using phylogenetic footprinting - dbMTN: Multiple Tissue Northern Blot Comparison Tool - Gene Set Builder: A tool for collation, curation and distribution of sets of genes - The Gene Characterization Index: a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described - JASPAR: Transcription Factor Binding Profile Database - MSCAN: Algorithm that detects clusters of transcription factor binding sites in genomic sequences - NHRscan: A computational predictor of nuclear hormone receptor binding sites - oPOSSUM: Web-based analysis of over-represented transcription factor binding sites - ORCA: Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite) - OrthoSeq: Alignment of DNA sequences - PAZAR: An open-access system for the collection and dissemination of regulatory sequence annotation - Phylofoot: Tools for phylogenetic footprinting - RAVEN: Regulatory analysis of Variation in ENhancers - SAGE2Splice: A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome - TFBS: Perl modules for transcription factor binding site detection and analysis - TFCat: TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. - TFe: An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes - Ulysses: Protein Interactions Conserved Across Evolution | lab, library, online, software, tool | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-25613 | SCR_002892 | SciCrunch Registry | Wasserman Software | 2026-10-31 12:13:14 | 9 | |||||||||
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GenScript Resource Report Resource Website 5000+ mentions |
GenScript (RRID:SCR_002891) | commercial organization | Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service. | gene synthesis service, drug development, reagent provider | nlx_152374 | http://www.dddmag.com/company-profiles/genscript-usa-inc | SCR_002891 | SciCrunch Registry | GenScript USA, GenScript USA Inc | 2026-10-31 12:13:15 | 7134 | |||||||||
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pBuild Resource Report Resource Website 1+ mentions |
pBuild (RRID:SCR_002929) | software resource | A software tool that can compare several search engines' results and combine them together. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
OMICS_02468 | SCR_002929 | SciCrunch Registry | 2026-10-31 12:13:15 | 8 | ||||||||||
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National Postdoctoral Association Resource Report Resource Website 1+ mentions |
National Postdoctoral Association (RRID:SCR_002928) | NPA | institution | Representative organization for postdoctoral scholars in the United States. It is member-driven and non-profit. | representation, post doc, postdoctoral scholar | Restricted | nif-0000-00476, grid.436397.c | https://ror.org/01gsm0s82 | SCR_002928 | SciCrunch Registry | National Postdoctoral Association | 2026-10-31 12:13:14 | 7 | |||||||
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aCGH.Spline Resource Report Resource Website |
aCGH.Spline (RRID:SCR_002927) | software resource | An R package for array comparative genomic hybridization (aCGH) dye bias normalization. | standalone software, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:21357574 | Free, Available for download, Freely available | OMICS_02607 | http://cran.r-project.org/web/packages/aCGH.Spline/ | SCR_002927 | SciCrunch Registry | 2026-10-31 12:13:14 | 0 | |||||||
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StreamingTrim Resource Report Resource Website 1+ mentions |
StreamingTrim (RRID:SCR_002922) | software resource | A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. | standalone software, java, 16s rrna, sequence | is listed by: OMICtools | PMID:24128146 | Free, Available for download, Freely available | OMICS_05196 | SCR_002922 | SciCrunch Registry | 2026-10-31 12:13:14 | 8 | ||||||||
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Mind Research Network Resource Report Resource Website 10+ mentions |
Mind Research Network (RRID:SCR_002925) | MRN | nonprofit organization | Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility. | imaging, neuroimaging, magnetic resonance imaging, magnetoencephalogram, brain, forensics, medical image analysis, neurodevelopment, neuroinformatics, data sharing, clinical, cognitive, service resource, instrument manufacture, imaging technology, neuroscience, genetics |
has parent organization: University of New Mexico; New Mexico; USA is parent organization of: Mind Research Network - COINS is parent organization of: MEGSIM is parent organization of: MIALAB - Medical Image Analysis Lab is parent organization of: COBRE is parent organization of: Cognitive Paradigm Ontology |
Mental illness, Brain injury, Traumatic brain injury, Addiction, Autism, Psychosis, Behavioral disorder | nif-0000-00474, grid.280503.c, Wikidata: Q7751519, ISNI: 0000 0004 0409 4614 | https://ror.org/032cjfs80 | SCR_002925 | SciCrunch Registry | Mind Research Network for Neuroscience Discovery | 2026-10-31 12:13:14 | 10 | ||||||
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pLabel Resource Report Resource Website 10+ mentions |
pLabel (RRID:SCR_002923) | software resource | Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | mass spectrometry, proteomics |
is listed by: OMICtools has parent organization: Chinese Academy of Sciences; Beijing; China |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02469 | SCR_002923 | SciCrunch Registry | 2026-10-31 12:13:15 | 28 | |||||||||
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hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | Free, Freely available, Available for download | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | SciCrunch Registry | hot_scan | 2026-10-31 12:13:13 | 6 | ||||||
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centerline Resource Report Resource Website 1+ mentions |
centerline (RRID:SCR_002961) | data processing software, image analysis software, segmentation software, software application, software resource | An application for the automatic segmentation and tracing of three-dimensional neuronal images. | neuron, tracing | has parent organization: University of Houston; Texas; USA | THIS RESOURCE IS NO LONGER IN SERVICE | SciRes_000186 | SCR_002961 | SciCrunch Registry | 2026-10-31 12:13:15 | 7 | |||||||||
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GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr, http://www.greenphyl.org/v3/, https://bio.tools/greenphyldb | SCR_002834 | SciCrunch Registry | 2026-10-31 12:13:13 | 20 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
