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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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INVERTER Resource Report Resource Website 1+ mentions |
INVERTER (RRID:SCR_007956) | INVERTER | software resource | Software for a de novo exact match tandem repeat finder which main advantage is without the need to specify either the pattern or a particular pattern size, integrated with a data visualization tool and has a built-in user-friendly Graphical User Interface. | is listed by: OMICtools | OMICS_00108 | SCR_007956 | 2026-09-03 04:49:28 | 3 | ||||||||||
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ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulation Resource Report Resource Website 1+ mentions |
ARGONAUTE 2 - A database on mammalian microRNAs and their function in gene and pathway regulation (RRID:SCR_007553) | data computation service, data or information resource, database | A database is a of mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their co-expression and proteins known to be involved in miRNA processing. This database also contains three other navigation tools that can be used to find information relating to miRNA: 1.) Gene Annotations is an information retrieval system for miRNA target genes. It provides comprehensive information from sequence databases and allows to simultaneously search PubMed with all synonyms of a given gene. 2.) miRNA Motif Finder - Argonaute predicts miRNA motifs binding to the gene sequence of the user. The miRNA mature sequences are taken from Agronaute 2 database. miRNA Motif Finder - Custom predicts miRNA motifs binding to the gene sequence, both the gene sequence and miRNA mature sequences provided by the user. 3.) miRNA Statistics provides statistics for the mature miRNA sequences from Argonaute 2 as well as for the miRNA sequences uploaded by the user. It provides statitics on the individual nucleotide as well as pattern of nucleotides apperaing in the sequence. | gene, metabolic and signaling pathways, mirna, protein-protein interaction, rna sequence database | has parent organization: Heidelberg University; Baden-Wurttemberg; Germany | Deutsche Forschungsgemein ; Federal Ministry of Research and Education |
nif-0000-02567 | http://argonaute.uni-hd.de | SCR_007553 | ARGONAUTE | 2026-09-03 04:49:41 | 1 | |||||||
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BAMS Thesaurus Resource Report Resource Website |
BAMS Thesaurus (RRID:SCR_008003) | thesaurus | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19,2022. The BAMS Thesaurus is a part of the larger BAMS The Foundational Model of Connectivity (FMC). The principle of constructing the resource are: 1. Systematic attempts to produce internally consistent classifications and taxonomies require theoretical frameworks for deciding between alternatives. 2. Alternate classification and taxonomy schemes are always possible and must be accommodated. 3. The FMC is based on evidence, not authority. All components are justified by reference to the best observational or experimental evidence from the literature, combined with reference to priority when possible, not by undocumented statements from textbooks, the Web, or elsewhere. 4. The FMC is based on evolving evidence and concepts, revisions are based on enforced rules, and versioning is systematic and historical. The first version of FMC and the foundation of this online version was published in Swanson & Bota (2010). Please cite this reference whenever any part of the FMC is used in any way. This online version of FMC has the following main parts: 1. Thesaurus, which includes an alphabetical list of all concepts and terms used in FMC to date. The preferred terms are in bold. Clicking on each term of the Thesaurus will retrieve its definition, reference, list of synonyms, and a comment form that can be used by registered users. 2. References, which includes an alphabetical list of the literature used to construct FMC. Listed references are associated with the definitions included in the Thesaurus, and PubMed links. 3. Search form that can be used to search for terms defined in FMC, included in their definitions, their abbreviations, and references (search by authors). We strongly recommend to read FMC rules and notations before starting to use the online version. | brain, anatomy, connectivity, thesaurus, | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07739 | SCR_008003 | 2026-09-03 04:49:32 | 0 | ||||||||||
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Health Research Funding Resource Report Resource Website |
Health Research Funding (RRID:SCR_007790) | funding resource | Health Research Funding is designed to bring researchers with peer-reviewed, worthwhile, unfunded projects together with patient advocacy organizations and other funding sources. Working together, we hope to foster the funding of new research that will provide hope to millions of people in this country with chronic diseases and disabilities. * We invite researchers with promising projects that have been scored but not funded by the NIH to submit their abstracts. By registering, you will be able to search for information about organizations that fund research and their requests for abstracts. * Researchers with proposals that have been peer-reviewed but not funded by a NHC member patient advocacy organization may also register. The National Health Council (NHC) developed this site with input from the National Institutes of Health (NIH), the nation''s medical research agency. | has parent organization: National Institutes of Health | nif-0000-03130 | SCR_007790 | 2026-09-03 04:49:16 | 0 | |||||||||||
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BigWig and BigBed Resource Report Resource Website 10+ mentions |
BigWig and BigBed (RRID:SCR_007708) | BigWig and BigBed | software resource | Allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. |
is listed by: OMICtools is related to: UCSC Genome Browser is related to: bedGraphToBigWig has parent organization: University of California at Santa Cruz; California; USA |
OMICS_00626 | SCR_007708 | 2026-09-03 04:49:26 | 43 | ||||||||||
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HighSSR Resource Report Resource Website 1+ mentions |
HighSSR (RRID:SCR_007949) | HighSSR | software resource | Software that predicts microsatellites with Tandem Repeats Finder (TRF). |
is listed by: OMICtools has parent organization: Google Code |
PMID:22954626 | OMICS_00107 | SCR_007949 | highssr - Microsatellites prediction and analysis with next generation sequencing data | 2026-09-03 04:49:30 | 1 | ||||||||
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ADDA - Automatic Domain Decomposition Algorithm Resource Report Resource Website 10+ mentions |
ADDA - Automatic Domain Decomposition Algorithm (RRID:SCR_007546) | ADDA | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | This is a web interface for ADDA, an automatic algorithm for domain decomposition and clustering of all protein domain families. We use alignments derived from an all-on-all sequence comparison to define domains within protein sequences based on a global maximum likelihood model. ADDA is downloadable. There are three ways in which you can retrieve a protein sequence and its domains from ADDA. Sequences can be located using sequence identifiers and/or accession numbers, using a identical fragment lookup, or by running BLAST against all sequences in ADDA. ADDA is a protein sequence clustering algorithm. It takes a set of sequences and returns domain families. ADDA has two steps corresponding to the two aspects of the protein sequence clustering domain. First, ADDA splits protein sequences into domains. The idea behind ADDA is in principle the application of Occam''s razor; the goal is to describe the diversity of protein sequences with a minimal set of protein domains. The algorithm behind ADDA approximates this minimal set. In practice ADDA works by looking at where BLAST alignments are located on the sequence and splits the sequences, so that as few as possible alignments are cut by domain boundaries and that as many alignments as possible stretch over complete domains. Secondly, ADDA takes all the domains and then arranges them in a minimum spanning tree, where the similarity between two domains is determined by their relative overlap given a BLAST alignment. Each link in the tree is then checked by a pairwise profile-profile comparison and links below a threshold are removed. The remaining connected components are then taken to represent protein domain families. | has parent organization: University of Helsinki; Helsinki; Finland | PMID:12706730 | nif-0000-02535 | SCR_007546 | Automatic Domain Decomposition Algorithm | 2026-09-03 04:49:27 | 10 | ||||||||
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NMPDR Resource Report Resource Website 1+ mentions |
NMPDR (RRID:SCR_007821) | NMPDR | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The National Microbial Pathogen Data Resource provides curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio; as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma. This edition of the NMPDR includes 47 archaeal, 725 bacterial, and 29 eukaryal genomes with 3,257,100 genetic features, of which 1,338,895 are in FIGfams curated using 616 active subsystems. ''''''Notice to NMPDR Users'''''' - The NMPDR BRC contract ended in December 2009. At that time we ceased maintenance of the NMPDR web resource and data. Bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. | has parent organization: University of Chicago; Illinois; USA | NIAID contract HHSN266200400042C | PMID:17145713 | nif-0000-03193 | http://www.nmpdr.org | SCR_007821 | NMPDR - National Microbial Pathogen Data Resource, National Microbial Pathogen Data Resource, NMPDR BRC, NMPDR Bioinformatics Resource Center | 2026-09-03 04:49:42 | 3 | ||||||
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Washington State University Pullman WA. Pharmacology and Toxicology Resource Report Resource Website |
Washington State University Pullman WA. Pharmacology and Toxicology (RRID:SCR_007543) | data or information resource, department portal, organization portal, portal |
The research-oriented program in pharmacology and toxicology prepares students for careers in independent research and teaching in pharmacology, toxicology and related areas.The research interests of the faculty are very broad and active areas of research include cancer biology, pharmacogenomics, pharmacokinetics, immuno-pharmacology and -toxicology and neuroscience. The diversity in faculty research interests provides students with a solid foundation in many areas of molecular and cellular pharmacology and toxicology and gives them a wide variety of research programs from which a dissertation proposal may be selected. The curriculum provides exposure of students to virtually all areas of current research in molecular and cellular biochemistry, immunology, molecular biology, pharmacology and toxicology and formal course requirements are flexible to tailor programs to individual needs.Our graduates have been successfully placed in careers in universities and colleges, the pharmaceutical and biotech industries, and in federal and state agencies. The program awards Ph.D. and M.S. degrees. |
nif-0000-02299 | http://www.pharmacy.wsu.edu/PharmTox/ | SCR_007543 | WSU | 2026-09-03 04:49:14 | 0 | ||||||||||
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Gene Regulation Programs Resource Report Resource Website 50+ mentions |
Gene Regulation Programs (RRID:SCR_007787) | Gene Regulation Programs | data or information resource, portal, software resource, topical portal | In an effort to strongly support the collaborative nature of scientific research, BIOBASE offers access to their tools. Programs that are available through this portal are: * AliBaba 2.1: AliBaba2 is a program for predicting binding sites of transcription factor binding sites in an unknown DNA sequence. Therefore it uses the binding sites collected in TRANSFAC. AliBaba2 is currently the most specific tool for predicting sites. * Boxshade 3.3.1: Pretty Printing and Shading of Multiple-Alignment files. * ClustalW 1.8: ClustalW Multiple Sequence Alignment Program. * Dialign2.0: Multiple Sequence Alignment Program. * F-Match 1.0: F-MATCH is a program for identifying statistically overrepresented Transcription Factor Binding Sites (TFBS) in a set of sequences compared against a control set, assuming a binomial distribution of TFBS frequency. The program reads MATCH output files for the query and control sets. F-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * Match 1.0 Public: Match is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. MatchTM uses a library of mononucleotide weight matrices from TRANSFAC 6.0 * molwSearch 1.0: Search for transcription factors with a certain molecular weight. * P-Match 1.0: P-Match is a new tool for identifying transcription factor binding sites (TF binding sites) in DNA sequences. It combines pattern matching and weight matrix approaches thus providing higher accuracy of recognition than each of the methods alone. P-Match uses a library of mononucleotide weight matrices from TRANSFAC 6.0 along with the site alignments associated with these matrices. * Patch 1.0: Search for potential transcription factor binding sites in your own sequences with the pattern search program using TRANSFAC 6.0 public sites. * m2transfac 1.0: m2transfac is a PWM-PWM alignment interface for the TRANSFAC(R) database. For given user motifs, m2transfac reports all non-overlapping pairwise alignments to a TRANSFAC(R) matrix which satisfy a specified threshold. * MatrixCatch 2.7: The MatrixCatch tool is designed for searching potential composite elements (CEs) for transcription factors (TFs) in any DNA sequence, which may be of interest. MatrixCatch uses a library of CE matrix models, which were compiled on a basis of experimentally identified CEs collected in TRANSCOMPEL database and mononucleotide weight matrices for single TF-binding sites collected in TRANSFAC 6.0 public database. * Composite Module Analyst (CMA) 1.0: CMA reads output of Match program and applies a genetic algorithm in order to define promoter models based on the composition of transcription factor binding sites and their pairs. * PolyA Scan 0.000707: Scanning a Sequence for potential Polyadenylation Sites. * ReadSeq 2.0: ReadSeq reads and writes nucleic/protein sequences in various formats. * SignalScan: Analysis of DNA Sequences for known Eukaryotic Signals * SbBlast 1.0: Search Tool for Sequence Search in the S/MARt Binder Database. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). * SnpFind 0.3: SNPFIND is a tool for searches in the Database of Single Nucleotide Polymorphisms. The search algorithm used for the database search is the BLAST algorithm. * TfBlast 0.1: Search Tool for Sequence Search in the TRANSFAC Factor Table. SbBlast makes use of the BLAST Sequence Similarity Search Tool - Version 2.0.13 (May-26-2000). | has parent organization: BIOBASE Corporation | BIOBASE | nlx_143607 | SCR_007787 | gene-regulation.com: Programs | 2026-09-03 04:49:26 | 73 | ||||||||
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University of Western Ontario London Ontario Canada Physiology and Pharmacology Resource Report Resource Website |
University of Western Ontario London Ontario Canada Physiology and Pharmacology (RRID:SCR_007541) | UWO Department of Physiology and Pharmacology | data or information resource, department portal, organization portal, portal | Research-based medical science department of physiology and pharmacology in the Schulich School of Medicine and Dentistry at the University of Western Ontario that focus on biological processes from the cellular-molecular level to the integrative-systemic level, and on the effects of drugs and environmental agents on these processes. Their areas of research excellence include the physiology and pharmacology of the cardiovascular, neural, reproductive, endocrine and musculoskeletal systems. Several faculty work in the area of developmental biology related to these organ systems. Faculty members in this Department are leaders in nationally-funded collaborative research programs studying skeletal / bone development and biology, heart and vascular biology, cell communication and gap junctions, neural control of vision and movement, and osteoarthritis and pain. Funding from several large infrastructure grants from both national and provincial governments has facilitated the development of state-of-the-art research laboratories and core facilities. | physiology, pharmacology, toxicology | has parent organization: Western University; Ontario; Canada | nif-0000-02287 | http://www.physpharm.med.uwo.ca/, http://www.uwo.ca/physpharm/ | SCR_007541 | 2026-09-03 04:49:40 | 0 | ||||||||
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Computer-Based Patient Record Ontology Resource Report Resource Website |
Computer-Based Patient Record Ontology (RRID:SCR_007540) | CPRO | controlled vocabulary, data or information resource, ontology | A uniform core set of data elements (whose formal semantics are captured in OWL) for use in a Computer-Based Patient Record (CPR) | owl | is listed by: BioPortal | nlx_157375 | https://code.google.com/p/cpr-ontology/ | SCR_007540 | 2026-09-03 04:49:19 | 0 | ||||||||
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GenoTan Resource Report Resource Website 1+ mentions |
GenoTan (RRID:SCR_007935) | GenoTan | software resource | A free software tool to identify length variation of microsatellites from short sequence reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24135263 | GNU General Public License, v3 | biotools:genotan | https://bio.tools/genotan | SCR_007935 | GenoTan - Genotyping of microsatellite loci | 2026-09-03 04:49:28 | 1 | |||||
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University of Pennsylvania Medical Center Neuroscience Resource Report Resource Website |
University of Pennsylvania Medical Center Neuroscience (RRID:SCR_007978) | data or information resource, department portal, organization portal, portal | The Department of Neuroscience is located in the School of Medicine at the University of Pennsylvania. Founded in 1992 to recognize the growing importance of neuroscience as a scientific discipline, the Department laboratories pursue a wide variety of research interests reflecting the entire range of modern neuroscience. The Department lies at the heart of the campus-wide Mahoney Institute of Neurological Sciences, the first research organization to receive NIH funding for training in the neurosciences. | nif-0000-03991 | SCR_007978 | U Penn | 2026-09-03 04:49:23 | 0 | |||||||||||
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VISTA Enhancer Browser Resource Report Resource Website 100+ mentions |
VISTA Enhancer Browser (RRID:SCR_007973) | VISTA Enhancer Browser | data or information resource, data repository, database, service resource, storage service resource | Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth. | human, noncoding fragment, mutant mouse strain, molecular neuroanatomy resource, image, telencephalon, development, genome, enhancer, dna fragment, embryo, embryonic mouse, brain, neural tube, eye, ear, heart, tail, limb, nose, cranial nerve, trigeminal, dorsal root ganglia, face, branchial arch, gene expression, annotation, vector, transgenic embryo, lacz reporter vector, lacz, biomaterial supply resource, in vivo, image collection, transcriptional enhancer, chip-seq, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: NIF Data Federation is related to: One Mind Biospecimen Bank Listing is related to: OMICtools has parent organization: Lawrence Berkeley National Laboratory |
American Heart Association ; DOE contract DE-AC02-05CH11231; DOE DE020060; NHGRI HG003988; NHLBI HL066681; NIDCR ; NINDS NS062859 |
PMID:17130149 | Free, Freely available | nif-0000-03637, OMICS_01568, biotools:vista_enhancer_browser | https://bio.tools/vista_enhancer_browser | SCR_007973 | 2026-09-03 04:49:31 | 249 | |||||
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RSEG Resource Report Resource Website 10+ mentions |
RSEG (RRID:SCR_007695) | RSEG | software resource | Software package aimed to analyze ChIP-Seq data, especially for identifying genomic regions and their boundaries marked by diffusive histone modification markers, such as H3K36me3 and H3K27me3. |
is listed by: OMICtools has parent organization: University of Southern California; Los Angeles; USA |
PMID:21325299 | Free | OMICS_00459 | SCR_007695 | 2026-09-03 04:49:20 | 14 | ||||||||
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Buzsaki Lab Resource Report Resource Website 10+ mentions |
Buzsaki Lab (RRID:SCR_008020) | Buzsaki Lab | data analysis software, data or information resource, data processing software, laboratory portal, organization portal, portal, software application, software resource | Lab interested in understanding how neuronal circuitries of the brain support its cognitive capacities. Its goal is to provide rational, mechanistic explanations of cognitive functions at a descriptive level. In the lab''s view, the most promising area of cognitive faculties for scientific inquiry is memory, since it is a well-circumscribed term, can be studied in animals and substantial knowledge has accumulated on the molecular mechanisms of synaptic plasticity. Available software: * NeuroScope: NeuroScope can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities. * Klusters: Klusters is a powerful and easy-to-use cluster cutting application designed to help neurophysiologists sort action potentials from multiple neurons on groups of electrodes (e.g., tetrodes or multisite silicon probes). * KlustaKwik: KlustaKwik is a program for automatic cluster analysis, specifically designed to run fast on large data sets. * MATLAB m-files: A selection of MATLAB files developed in the lab., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | eeg, electrode, environment, funtion, animal, application, behavioral, brain, capacity, circuit, cluster, cognitive, hippocampal, hippocampus, laboratory, local field potential, mechanism, memory, molecular, neuron, neuronal, plasticity, research, scientific, spike, synaptic, tetrode |
has parent organization: Rutgers University; New Jersey; USA is parent organization of: NeuroScope |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10182 | http://osiris.rutgers.edu/frontmid/indexmid.html | SCR_008020 | Buzsaki''s Lab | 2026-09-03 04:49:19 | 15 | ||||||
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ConSurf-DB Resource Report Resource Website 10+ mentions |
ConSurf-DB (RRID:SCR_007609) | data or information resource, service resource, database | Collection of pre-calculated evolutionary conservation profiles for proteins of known structure in the Protein DataBase (PDB). | evolution, conservation, protein, structure, pre-calculated, profile |
is affiliated with: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Free, Acknowledgement requested | BioTools:consurf-db, nif-0000-02685 | http://bental.tau.ac.il/new_ConSurfDB/, https://bio.tools/consurf-db | SCR_007609 | consurf-db, ConSurf-DataBase, ConSurf-DB, ConSurf- Data Base | 2026-09-03 04:49:25 | 17 | |||||||
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Soy Ontology Resource Report Resource Website |
Soy Ontology (RRID:SCR_007847) | SOY | controlled vocabulary, data or information resource, ontology | Growth, trait and development ontology for soybean | obo |
is listed by: BioPortal has parent organization: SoyBase |
nlx_157593 | SCR_007847 | 2026-09-03 04:49:43 | 0 | |||||||||
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Brain Resource Company Resource Report Resource Website 10+ mentions |
Brain Resource Company (RRID:SCR_008019) | Brain Resource | standard specification, service resource, organization portal, database, material resource, portal, data or information resource, assessment test provider, training service resource, production service resource, narrative resource | Commercial provider of cognitive assessments, including their proprietary database, the Brain Resource International Database (BRID). The BRID is a database that allows users to quantify individual differences in brain function, compare individual performance against peers, and provide a robust frame of reference for clinical assessment and treatment decisions. The Brain Resource International Database provides evidence for the brain-behavior connection so important to reliably enabling optimal solutions for mental health and wellbeing. It powers all Brain Resource products. The database has collected over 50,000 datasets. There are over 4,000 healthy controls from the age of 6-100 in our normative database as well as large and growing clinical databases in Depression, Schizophrenia, Mild Cognitive Impairment, PTSD, ADHD and Brain Injury. Test standardization ensures total quality control and robust representative profiles in each disorder. | emotion, adhs, anxiety, behavior, brain, clinician, health, mild cognitive impairment, psychological, post-traumatic stress disorder, schizophrenia, cognition, brain training, healthy control, neuroplasticity, clinical, personalized medicine, adhd, brain assessment, biomarker, presenteeism, stress, assessment, neurocognition, questionnaire, FASEB list | Depressive Disorder, Attention deficit-hyperactivity disorder, Post-Traumatic Stress Disorder, Healthy control, Schizophrenia, Mild Cognitive Impairment, :Category:Traumatic Brain Injury | nif-0000-10179 | SCR_008019 | 2026-09-03 04:49:30 | 31 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
