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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OEI: fMRI compatible olfactometer Resource Report Resource Website 1+ mentions |
OEI: fMRI compatible olfactometer (RRID:SCR_002507) | OEI fMRI compatible olfactometer | instrument resource | A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory. | experiment control, hardware, magnetic resonance, stimulus presentation, odor, olfactory, instrument, equipment | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Commercial License | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_002507.pdf | nlx_155907 | http://www.nitrc.org/projects/oei, http://www.osmicenterprises.com/docs/OsmicFMRIOlfactomterManual%207-1-13.pdf | SCR_002507 | 2026-08-08 11:57:51 | 4 | ||||||
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BINOCh Resource Report Resource Website 1+ mentions |
BINOCh (RRID:SCR_002778) | BINOCh | software resource | Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | proximal nucleosome occupancy data, transcription factor determination, differentiation |
is listed by: OMICtools has parent organization: Dana-Farber Cancer Institute has parent organization: Harvard University; Cambridge; United States |
PMID:21551136 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00500 | SCR_002778 | Binding Inference from Nucleosome Occupancy Changes (BINOCh), BINOCh - Binding Inference from Nucleosome Occupancy Changes, Binding Inference from Nucleosome Occupancy Changes | 2026-08-08 11:57:46 | 3 | ||||||
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Circleator Resource Report Resource Website 1+ mentions |
Circleator (RRID:SCR_002801) | software resource, software application, data visualization software, data processing software | A Perl-based visualization software tool that generates circular figures of genome-associated data. Common uses of the tool include: * Displaying the sequence and/or genes in a GenBank flat file. * Highlighting differences and/or similarities in gene content between related organisms. * Comparing SNPs and indels between closely-related strains or serovars. * Comparing gene expression values across multiple samples or timepoints. * Visualizing coverage plots of RNA-Seq read alignments. | standalone software, perl |
is listed by: OMICtools has parent organization: University of Maryland School of Medicine; Maryland; USA |
PMID:25075113 | Free, Freely available, Available for download | OMICS_05206 | https://github.com/jonathancrabtree/Circleator/ | SCR_002801 | Charm City Circleator | 2026-08-08 11:57:55 | 9 | ||||||
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sapFinder Resource Report Resource Website |
sapFinder (RRID:SCR_002685) | software resource | An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. | standalone software, r, mass spectrometry, proteomics, rna-seq, report writing, snp, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:25053745 | Free, Available for download, Freely available | biotools:sapfinder, OMICS_05285 | https://bio.tools/sapfinder | SCR_002685 | sapFinder - A package for variant peptides detection and visualization in shotgun proteomics. | 2026-08-08 11:57:45 | 0 | ||||||
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CNSforum: Image Bank Resource Report Resource Website |
CNSforum: Image Bank (RRID:SCR_002718) | data or information resource, image collection | A collection of downloadable central nervous system (CNS) images for teaching, presentations, articles, and other purposes. The following major categories of images are as follows: Brain anatomy, Brain physiology, Anxiety, Depression, Schizophrenia, Dementia, Parkinson's disease, Stroke, and Others. | image collection, human brain, brain anatomy, brain physiology, anxiety, depression, schizophrenia, dementia, parkinson's disease, stroke, brain | has parent organization: CNS Forum | Anxiety, Depressive Disorder, Schizophrenia, Dementia, Parkinson's disease, Stroke, Normal | Free, Freely available | nif-0000-23576 | SCR_002718 | CNS Forum Image Bank, Lundbeck Institute CNSforum Image Bank | 2026-08-08 11:57:54 | 0 | |||||||
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leeHom Resource Report Resource Website 50+ mentions |
leeHom (RRID:SCR_002710) | software resource | Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. | standalone software, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25100869 | Free, Available for download, Freely available | biotools:leehom, OMICS_05254 | https://bio.tools/leehom | SCR_002710 | 2026-08-08 11:57:53 | 59 | |||||||
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Neuroscience Berlin Resource Report Resource Website |
Neuroscience Berlin (RRID:SCR_002741) | group | THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 10, 2017. In the last few years the Berlin neuroscience community has been highly successful in creating new research projects. Not the least of these is the cluster of excellence, NeuroCure, which has brought nine new professors and their research groups to Berlin. Along with the increasing levels of research, a number of new neuroscience training programs have recently been established. In 2002 the International Graduate Program Medical Neurosciences was the only structured Masters and PhD program: as of 2009 Berlin hosts four neuroscience schools and several DFG funded research training groups. The purpose of this website to highlight the many projects and people involved in the Berlin neuroscience community. We hope that you, the reader, can benefit from this summary., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-24042 | SCR_002741 | 2026-08-08 11:57:54 | 0 | |||||||||||
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University of Basel; Basel; Switzerland Resource Report Resource Website 1+ mentions |
University of Basel; Basel; Switzerland (RRID:SCR_002699) | university | Public university in Basel, Switzerland that offers degree programs in theology, law, medicine, humanities and social sciences, science, psychology, and business and economics. | public university, switzerland, degree program |
is related to: EU-AIMS is related to: Bsoft is parent organization of: DogMap is parent organization of: PredictHaplo is parent organization of: TSSer is parent organization of: Ashbya Genome Database is parent organization of: DINO is parent organization of: CLIPZ is parent organization of: SWISS-MODEL Repository is parent organization of: SWISS-MODEL is parent organization of: 4 Port Nose Poke |
Free | nlx_24036 | SCR_002699 | University of Basel, Universitat Basel | 2026-08-08 11:57:45 | 3 | ||||||||
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Pathview Resource Report Resource Website 500+ mentions |
Pathview (RRID:SCR_002732) | software resource | A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. | software package, r, differential expression, gene expression, gene set enrichment, genetics, graph, network, metabolomics, microarray, pathway, proteomics, rna-seq, sequencing, systems biology, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23740750 | Free, Freely available, Available for download | biotools:pathview, OMICS_05212 | http://pathview.r-forge.r-project.org/, https://bio.tools/pathview | SCR_002732 | path view | 2026-08-08 11:57:46 | 569 | ||||||
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GLProbs Resource Report Resource Website 1+ mentions |
GLProbs (RRID:SCR_002739) | software resource | Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:26357079 | Free, Freely available, Available for download | OMICS_03732 | SCR_002739 | 2026-08-08 11:57:45 | 1 | ||||||||
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Erasmus MC Department of Neuroscience Resource Report Resource Website 1000+ mentions |
Erasmus MC Department of Neuroscience (RRID:SCR_002737) | university | The department of Neuroscience was founded in 2001, resulting from a merger between the Physiology and Anatomy department. In 2008, the BNT department joined forces. At present we consist of about 150 people. Our research is dedicated to Plasticity and Dynamics of Sensori-Motor Systems, which we investigate at the physiological, anatomical end molecular level in 18 different research groups. We have teaching responsibilities within the whole bachelor's phase of the medical curriculum at the Erasmus MC, teaching both basic anatomy and physiology, as well as neuroscience. The department hosts its own Master of Neuroscience program. The department of Neuroscience is embedded in the ONWAR, Helmholtz, and MGC research school | anatomical, anatomy, department, molecular, neuroscience, physiology | Free | nif-0000-24051 | SCR_002737 | Neuroscience | 2026-08-08 11:57:54 | 1057 | |||||||||
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FlyMine Resource Report Resource Website 100+ mentions |
FlyMine (RRID:SCR_002694) | FlyMine | database, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API | anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list |
is related to: FlyBase is related to: UniProt is related to: Ensembl is related to: InterPro is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Tree families database is related to: IntAct is related to: Gene Ontology is related to: GOA is related to: ArrayExpress is related to: REDfly Regulatory Element Database for Drosophilia is related to: KEGG is related to: Reactome has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust 067205; NHGRI |
PMID:17615057 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02845 | SCR_002694 | 2026-08-08 11:57:45 | 107 | ||||||
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LONI ShapeViewer Resource Report Resource Website |
LONI ShapeViewer (RRID:SCR_002695) | software resource, software application, data visualization software, data processing software | Java-based geometry viewer that supports file formats used by Center for Computational Biology (CCB) researchers and provides necessary viewing functions. ShapeViewer uses ShapeTools library support to read and display LONI Ucf, VTX XML, FreeSurfer, Minc Obj (both binary and ascii), Open Dx, Gifti, and OFF format data files. | ccb license, manifold viewer, computed tomography, magnetic resonance, pet, java |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: LONI ShapeTools has parent organization: Laboratory of Neuro Imaging |
NCRR U54 RR021813 | Free, Available for download, Freely available | nif-0000-23321 | SCR_002695 | ShapeViewer, LONI Shape Viewer | 2026-08-08 11:57:45 | 0 | |||||||
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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 | Dispersion Shrinakge for Sequencing data, DSS - Dispersion shrinakge for sequencing data | 2026-08-08 11:57:46 | 9 | |||||||
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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 | SRNT | 2026-08-08 11:57:54 | 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 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-08-08 11:57:46 | 4 | ||||||
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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 |
nlx_87455, ISNI 0000 0004 1937 116X, Crossref Funder ID 100007397, Wikidata Q31519, GRID grid.4491.8 | https://ror.org/024d6js02 | SCR_002931 | Charles University, Charles University in Prague, Univerzita Karlova | 2026-08-08 11:57:48 | 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 | 2026-08-08 11:57:57 | 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 | 2026-08-08 11:57:49 | 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 | Wasserman Software | 2026-08-08 11:57:49 | 9 |
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