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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Stanford Center for Narcolepsy Resource Report Resource Website |
Stanford Center for Narcolepsy (RRID:SCR_007021) | Stanford Center for Narcolepsy | material resource, brain bank, tissue bank, biomaterial supply resource | The Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy. | brain tissue, brain, tissue, hypocretin, orexin, narcolepsy, sleep disorder, cataplexy, idiopathic hypersomnia, normal control, kleine-levin syndrome, dog, zebrafish, research, therapy |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Stanford University School of Medicine; California; USA |
Narcolepsy, Sleep disorder, Cataplexy, Idiopathic hypersomnia, Normal control, Kleine-Levin Syndrome | Individual gifts ; NIH |
Private: not stated but looks that way | nlx_144254 | http://med.stanford.edu/school/Psychiatry/narcolepsy/ | SCR_007021 | Stanford University Center for Narcolepsy | 2026-08-13 09:27:37 | 0 | ||||
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ProDom Resource Report Resource Website 100+ mentions |
ProDom (RRID:SCR_006969) | ProDom | data or information resource, analysis service resource, production service resource, database, service resource, data analysis service | Comprehensive set of protein domain families automatically generated from UniProt Knowledge Database. Automated clustering of homologous domains generated from global comparison of all available protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | set, protein, domain, family, automatically, generated, UniProt, database, homologous, sequence, compare, FASEB list |
is listed by: OMICtools is related to: UniProt is related to: InterPro has parent organization: PRABI |
‘Programme de Bio-Informatique InterOrganismes ; Re´seau des Ge´nopoles ; European Union |
PMID:15608179 PMID:12230033 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01698, nif-0000-03342 | http://prodom.prabi.fr/prodom/current/html/home.php | SCR_006969 | 2026-08-13 09:27:37 | 354 | |||||
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WSsas - Web Service for the SAS tool Resource Report Resource Website |
WSsas - Web Service for the SAS tool (RRID:SCR_007051) | WSsas | data access protocol, software resource, web service | SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank and provides functional residue annotation based on data from the Catalytic Site Atlas and PDBsum. The web service is aimed to facilitate the use of the SAS tool when having a huge number of queries. Currently, the web service provides annotation for binding sites (to ligand, metal or nucleic acid), catalytic residues and amino acids related to protein-protein interactions. | gold standard, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: SAS - Sequence Annotated by Structure has parent organization: European Bioinformatics Institute |
nlx_18182, biotools:wssas | https://bio.tools/wssas | SCR_007051 | Web Service for the SAS tool | 2026-08-13 09:27:38 | 0 | |||||||
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The NeuroCommons Project Resource Report Resource Website |
The NeuroCommons Project (RRID:SCR_007171) | topical portal, data or information resource, software application, community building portal, systems interoperability software, software resource, software development tool, portal | The Neurocommons project is an Open Source knowledge management platform for biological research. It seeks to make all scientific research materials - research articles, annotations, data, physical materials - as available and as usable as they can be. We do this by both fostering practices that render information in a form that promotes uniform access by computational agents - sometimes called interoperability. We want knowledge sources to combine meaningfully, enabling semantically precise queries that span multiple information sources. Our work covers general data and knowledge sources used in computational biology as well as sources specific to neuroscience and neuromedicine. The practices that we develop and promote are designed to play well on the Semantic Web. We view our technical work not as creating a new service or content library, although we do both, but rather as helping to promote the growth of semantically linked scientific information. | analytic tools, bundles, common naming), documenting, installer, interoperation, ontologies, protocol, rdf, rdf distribution, semantic web, software repository, sparql - protocol for querying triple stores, text processing - automated text to rdf, triple store, uris (manifesto, user interface, ontology, owl | nif-0000-01644 | SCR_007171 | NeuroCommons | 2026-08-13 09:27:39 | 0 | ||||||||||
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Biowulf at the NIH Resource Report Resource Website 100+ mentions |
Biowulf at the NIH (RRID:SCR_007169) | data processing software, systems interoperability software, software resource, software application | The NIH Biowulf cluster is a GNU/Linux parallel processing system designed and built at the National Institutes of Health and managed by the Helix Systems Staff. The system is designed for large numbers of simultaneous jobs common in bioinformatics as well as large-scale distributed memory tasks such as molecular dynamics. Sponsor: This work was supported by the National Institutes of Health Intramural Research Program through the Center for Information Technology and the National Institute of Neurological Disorders and Stroke, and by the Internal National Institute of Standards and Technology Research Fund. Keywords: Software, Program, Processing, System, Simulatenous, Bioinformatics, Memory, Molecular, Dynamics, | has parent organization: National Institutes of Health | nif-0000-30204 | http://biowulf.nih.gov | SCR_007169 | NIH Biowulf | 2026-08-13 09:27:45 | 120 | |||||||||
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European Xenopus Resource Center Resource Report Resource Website 50+ mentions |
European Xenopus Resource Center (RRID:SCR_007164) | EXRC | biomaterial supply resource, material resource, organism supplier | Supports researchers using Xenopus models. Researchers are encouraged to deposit Xenopus transgenic and mutant lines, Xenopus in situ hybridization probes, Xenopus specific antibodies and Xenopus expression clones with the Centre. EXRC staff perform quality assurance testing on these reagents and then make them available to researchers at cost. Supplies wild-type Xenopus, embryos, oocytes and Xenopus tropicalis fosmids. | RIN, Resource Information Network, Xenopus, Resouce, Distributor, Supplier, Researcher, Research, Model, Hybridization, Probe, Antibody, Expression, Clone, Reagent, Embryo, Oocyte, Fosmid, Xenopus tropicalis, RRID Community Authority | is listed by: Resource Information Network | Wellcome Trust ; BBSRC ; NC3Rs |
nif-0000-38111 | SCR_007164 | 2026-08-13 09:27:44 | 54 | ||||||||
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Brandeis University Neuroscience Undergraduate Program Resource Report Resource Website |
Brandeis University Neuroscience Undergraduate Program (RRID:SCR_007166) | data or information resource, organization portal, department portal, undergraduate program resource, degree granting program, training resource, portal | Students entering Neuroscience Program at Brandeis have opportunities to work in range of fields, from cognitive neuroscience to structure and function of ion channels. Undergraduate concentration in neuroscience is designed to provide interdisciplinary program of study of neural mechanisms involved in control of human or animal behavior. Program is especially appropriate for students wishing to pursue further study in medicine, experimental psychology, or neuroscience. | has parent organization: Brandeis University; Massachusetts; USA | nif-0000-38224 | SCR_007166 | Undergraduate Neuroscience at Brandeis | 2026-08-13 09:27:39 | 0 | ||||||||||
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DART - Drug Adverse Reaction Targets Resource Report Resource Website 1+ mentions |
DART - Drug Adverse Reaction Targets (RRID:SCR_007041) | DART | data or information resource, database, service resource, data repository, storage service resource | Database that provides comprehensive information about adverse effect targets of drugs described in the literature, including information about known drug adverse reaction targets, functions and properties. Moreover, proteins involved in adverse effect targets of chemicals not yet confirmed as adverse drug reaction (ADR) targets are also included as potential targets. Associated references are also included. This database gives physiological function of each target, binding drugs / agonists / antagonists / activators / inhibitors, IC(50) values of the inhibitors, corresponding adverse effects, and type of ADR induced by drug binding to a target. Cross-links to other databases are also introduced to facilitate the access of information about the sequence, 3-dimensional structure, function, and nomenclature of each target along with drug/ligand binding properties, and related literature. Each entry can be retrieved through multiple search methods including target name, target physiological function, adverse effect, ligand name, and biological pathways. A special page is provided for contribution of new or additional information. Function for ADR-target prediction by SVMDART: Submit protein primary sequence for ADR-related protein prediction. | drug, drug target, evaluation, adverse drug reaction, adverse reaction, agonist, antagonist, binding, ic value, inhibitor, ligand binding property, ligand, physiological function, protein prediction, protein, protein target, target, type, toxicity, data analysis service, toxic | has parent organization: National University of Singapore; Singapore; Singapore | PMID:12862503 | Non-commercial use, The community can contribute to this resource | nif-0000-02720 | SCR_007041 | 2026-08-13 09:27:43 | 2 | |||||||
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Gene Ontology Tools Resource Report Resource Website 10+ mentions |
Gene Ontology Tools (RRID:SCR_006941) | GO Tools | data or information resource, database, software repository, catalog, software resource | Collection of tools developed by GO Consortium and by third parties. Tools are listed by category or alphabetically and continue to be improved and expanded. | registry, annotation browser, annotation search engine, annotation visualization, ontology, annotation editor, database, data warehouse, software library, statistical analysis, slimmer-type tool, term enrichment, text mining, protein interaction, functional similarity, semantic similarity, analysis, annotation, visualization, editor |
lists: GOALIE lists: GenNav lists: High-Throughput GoMiner lists: Onto-Design lists: Avadis lists: GONUTS lists: PiNGO lists: TM4 Microarray Software Suite - TIGR MultiExperiment Viewer lists: FunSimMat lists: BioPerl lists: Database for Annotation Visualization and Integrated Discovery lists: GOToolBox Functional Investigation of Gene Datasets lists: StRAnGER lists: Short Time-series Expression Miner (STEM) lists: GORetriever lists: Gene Ontology Browsing Utility (GOBU) lists: GeneTools lists: GOSlimViewer lists: go-moose lists: Network Ontology Analysis lists: OBO-Edit lists: Onto-Compare lists: Onto-Express lists: OntoVisT lists: STRAP lists: CGAP GO Browser lists: COBrA lists: Gene Class Expression lists: GeneInfoViz lists: GOfetcher lists: GoFish lists: GOProfiler lists: GOanna lists: Manatee lists: Pandora - Protein ANnotation Diagram ORiented Analysis lists: TAIR Keyword Browser lists: Wandora lists: GeneMANIA lists: GOTaxExplorer lists: go-db-perl lists: Onto-Miner lists: Onto-Translate lists: ToppGene Suite lists: DBD - Slim Gene Ontology lists: go-perl lists: ONTO-PERL lists: OWLTools lists: Blip: Biomedical Logic Programming lists: OWL API lists: CLENCH lists: BiNGO: A Biological Networks Gene Ontology tool lists: CateGOrizer lists: FuSSiMeG: Functional Semantic Similarity Measure between Gene-Products lists: ProteInOn lists: GeneMerge lists: GraphWeb lists: ClueGO lists: CLASSIFI - Cluster Assignment for Biological Inference lists: GOHyperGAll lists: FuncAssociate: The Gene Set Functionator lists: GOdist lists: FuncExpression lists: FunCluster lists: FIVA - Functional Information Viewer and Analyzer lists: GARBAN lists: GOEx - Gene Ontology Explorer lists: SGD Gene Ontology Slim Mapper lists: GOArray lists: GoSurfer lists: GOtcha lists: MAPPFinder lists: GoAnnotator lists: MetaGeneProfiler lists: OntoGate lists: ProfCom - Profiling of complex functionality lists: SerbGO lists: SOURCE lists: Ontologizer lists: THEA - Tools for High-throughput Experiments Analysis lists: Generic GO Term Mapper lists: GREAT: Genomic Regions Enrichment of Annotations Tool lists: GoBean - a Java application for Gene Ontology enrichment analysis lists: TXTGate lists: GO-Module lists: IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures lists: G-SESAME - Gene Semantic Similarity Analysis and Measurement Tools lists: Expression Profiler lists: GOChase lists: Whatizit lists: REViGO lists: WEGO - Web Gene Ontology Annotation Plot lists: Blast2GO lists: InterProScan lists: PubSearch lists: GO Online SQL Environment (GOOSE) lists: Gene Ontology For Functional Analysis (GOFFA) lists: MGI GO Browser lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: Ontology Lookup Service lists: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit lists: g:Profiler lists: OwlSim lists: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool lists: FastSemSim lists: RamiGO lists: GeneCodis lists: FunSpec lists: FunNet - Transcriptional Networks Analysis lists: agriGO lists: GOblet lists: DynGO lists: SeqExpress lists: ProbeExplorer lists: GOstat lists: Onto-Express To Go (OE2GO) lists: Tk-GO lists: Spotfire lists: GOMO - Gene Ontology for Motifs lists: GFINDer: Genome Function INtegrated Discoverer lists: Agile Protein Interactomes DataServer lists: elk-reasoner lists: Flash Gviewer lists: L2L Microarray Analysis Tool lists: OnEx - Ontology Evolution Explorer lists: Semantic Measures Library lists: AmiGO lists: Babelomics lists: T-profiler lists: QuickGO lists: FSST - Functional Similarity Search Tool lists: GoPubMed lists: Bioconductor lists: ErmineJ lists: Comparative Toxicogenomics Database (CTD) lists: LexGrid lists: Candidate Genes to Inherited Diseases lists: EGAN: Exploratory Gene Association Networks lists: Generic GO Term Finder lists: Integrated Manually Extracted Annotation lists: EASE: the Expression Analysis Systematic Explorer is listed by: NIF Data Federation has parent organization: Gene Ontology |
Free, Freely available | nlx_146273 | https://neuinfo.org/mynif/search.php?q=*&t=indexable&nif=nlx_146273-1 | http://www.geneontology.org/GO.tools.shtml | SCR_006941 | 2026-08-13 09:27:40 | 27 | ||||||
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EcoliHub Resource Report Resource Website |
EcoliHub (RRID:SCR_007114) | topical portal, data or information resource, portal | Sixty years of study have made Escherichia coli K-12 the most deeply understood organism at the molecular level. Much of what we know about cellular processes can be traced to fundamental discoveries in E. coli. In spite of its great importance as a model organism, information about E. coli is distributed among many online resources. EcoliHub uses web services that are being developed to make seamless bidirectional connections between E. coli resources, thereby enabling the full use of existing knowledge and supporting cutting-edge research into the molecular basis of life. :topical portal; | is parent organization of: GONUTS | nif-0000-00367 | SCR_007114 | EcoliHub | 2026-08-13 09:27:39 | 0 | ||||||||||
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Tetraodon Genome Browser Resource Report Resource Website 1+ mentions |
Tetraodon Genome Browser (RRID:SCR_007079) | topical portal, data or information resource, database, portal | The initial objective of Genoscope was to compare the genomic sequences of this fish to that of humans to help in the annotation of human genes and to estimate their number. This strategy is based on the common genetic heritage of the vertebrates: from one species of vertebrate to another, even for those as far apart as a fish and a mammal, the same genes are present for the most part. In the case of the compact genome of Tetraodon, this common complement of genes is contained in a genome eight times smaller than that of humans. Although the length of the exons is similar in these two species, the size of the introns and the intergenic sequences is greatly reduced in this fish. Furthermore, these regions, in contrast to the exons, have diverged completely since the separation of the lineages leading to humans and Tetraodon. The Exofish method, developed at Genoscope, exploits this contrast such that the conserved regions which can be identified by comparing genomic sequences of the two species, correspond only to coding regions. Using preliminary sequencing results of the genome of Tetraodon in the year 2000, Genoscope evaluated the number of human genes at about 30,000, whereas much higher estimations were current. The progress of the annotation of the human genome has since supported the Genoscope hypothesis, with values as low as 22,000 genes and a consensus of around 25,000 genes. The sequencing of the Tetraodon genome at a depth of about 8X, carried out as a collaboration between Genoscope and the Whitehead Institute Center for Genome Research (now the Broad Institute), was finished in 2002, with the production of an assembly covering 90 of the euchromatic region of the genome of the fish. This has permitted the application of Exofish at a larger scale in comparisons with the genome of humans, but also with those of the two other vertebrates sequenced at the time (Takifugu, a fish closely related to Tetraodon, and the mouse). The conserved regions detected in this way have been integrated into the annotation procedure, along with other resources (cDNA sequences from Tetraodon and ab initio predictions). Of the 28,000 genes annotated, some families were examined in detail: selenoproteins, and Type 1 cytokines and their receptors. The comparison of the proteome of Tetraodon with those of mammals has revealed some interesting differences, such as a major diversification of some hormone systems and of the collagen molecules in the fish. A search for transposable elements in the genomic sequences of Tetraodon has also revealed a high diversity (75 types), which contrasts with their scarcity; the small size of the Tetraodon genome is due to the low abundance of these elements, of which some appear to still be active. Another factor in the compactness of the Tetraodon genome, which has been confirmed by annotation, is the reduction in intron size, which approaches a lower limit of 50-60 bp, and which preferentially affects certain genes. The availability of the sequences from the genomes of humans and mice on one hand, and Takifugu and Tetraodon on the other, provide new opportunities for the study of vertebrate evolution. We have shown that the level of neutral evolution is higher in fish than in mammals. The protein sequences of fish also diverge more quickly than those of mammals. A key mechanism in evolution is gene duplication, which we have studied by taking advantage of the anchoring of the majority of the sequences from the assembly on the chromosomes. The result of this study speaks strongly in favor of a whole genome duplication event, very early in the line of ray-finned fish (Actinopterygians). An even stronger evidence came from synteny studies between the genomes of humans and Tetraodon. Using a high-resolution synteny map, we have reconstituted the genome of the vertebrate which predates this duplication - that is, the last common ancestor to all bony vertebrates (most of the vertebrates apart from cartilaginous fish and agnaths like lamprey). This ancestral karyotype contains 12 chromosomes, and the 21 Tetraodon chromosomes derive from it by the whole genome duplication and a surprisingly small number of interchromosomal rearrangements. On the contrary, exchanges between chromosomes have been much more frequent in the lineage that leads to humans. Sponsors: The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute. | duplication, element, euchromatic, evolution, exon, fish, gene, genetic, actinopterygians, aganth, ancestor, cartilaginous, cdna, chromosome, coding, collagen, cytokine, diversity, genome, genomic, heritage, hormone, human, interchromossomal, intergenic, intron, karyotype, lineage, mammal, molecule, mouse, nigroviridis, protein, proteome, pufferfish, receptor, region, selenoprotein, sequence, size, specie, synteny, system, takifugu, tetraodon, transposable, vertebrate | nif-0000-20997 | SCR_007079 | TGB | 2026-08-13 09:27:38 | 8 | ||||||||||
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University of Texas Health Science Center at San Antonio Department of Pharmacology Resource Report Resource Website |
University of Texas Health Science Center at San Antonio Department of Pharmacology (RRID:SCR_007078) | data or information resource, organization portal, department portal, portal | The Department of Pharmacology at the Health Science Center at San Antonio is uniquely positioned to carry out research into the most relevant areas in pharmacology as well as to deliver superior training in pharmacology. Our faculty use approaches that range from the molecular and cellular through electrophysiology and systems to behavior. The Department of Pharmacology at the University of Texas Health Science Center at San Antonio (UTHSCSA) has 18 tenure-track or tenured faculty, 11 research-track faculty, 15 graduate students, and 15 postdoctoral fellows. We are very excited about recent developments in pharmacology that allow new and challenging means of exploring the biological effects of drugs. Graduate studies leading to a Doctor of Philosophy degree in the basic biomedical sciences at UTHSCSA are offered in the Integrated Multidisciplinary Graduate Program (IMGP). The Department of Pharmacology administers two tracks within the IMGP: the pharmacology track and the neuroscience track. The Department of Pharmacology has a ten-week summer research program that offers participants a variety of experiences that will help prepare them for success in research-intensive doctoral programs. Participants will have research responsibilities, attend seminars, actively participate in a student journal club and take part in formal course work. Prior research experience is not necessary, and students of all undergraduate levels are encouraged to apply. | has parent organization: University of Texas Health Science Center at San Antonio; Texas; USA | nif-0000-02269 | SCR_007078 | UTHSCSA Department of Pharmacology | 2026-08-13 09:27:44 | 0 | ||||||||||
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American Journal of Psychiatry Podcasts Resource Report Resource Website 1+ mentions |
American Journal of Psychiatry Podcasts (RRID:SCR_007070) | AJP Podcasts | data or information resource, narrative resource, podcast | An audio summary of highlights and key articles from each issue of The American Journal of Psychiatry. Users may subscribe to the podcast to get automatic updates with each issue or download each issue''s audio file individually. | audio, psychiatry |
is used by: NIF Data Federation is related to: Integrated Podcasts |
nlx_39039 | http://ajp.psychiatryonline.org/misc/audio.dtl | SCR_007070 | AJP Audio podcast, The American Journal of Psychiatry Podcast, AJP Podcast, AJP Audio, American Journal of Psychiatry Podcast, American Journal of Psychiatry Audio Downloads | 2026-08-13 09:27:38 | 1 | |||||||
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RTPrimerDB- The Real-Time PCR and Probe Database Resource Report Resource Website 10+ mentions |
RTPrimerDB- The Real-Time PCR and Probe Database (RRID:SCR_007106) | RTPrimerDB | data or information resource, database, service resource, data repository, storage service resource | Database for primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridization Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimization, and to introduce a certain level of uniformity and standardization among different laboratories. Researchers are encouraged to submit their validated primer and probe sequence, so that other users can benefit from their expertise. The database can be queried using the official gene name or symbol, Entrez or Ensembl Gene identifier, SNP identifier, or oligonucleotide sequence. Different options make it possible to restrict a query to a particular application (Gene Expression Quantification/Detection, DNA Copy Number Quantification/Detection, SNP Detection, Mutation Analysis, Fusion Gene Quantification/Detection, Chromatin immunoprecipitation (ChIP)), organism (Human, Mouse, Rat, and others) or detection chemistry. | primer, probe, sequence, real-time pcr, gene, assay, real-time pcr assay, FASEB list |
is listed by: OMICtools has parent organization: Ghent University; Ghent; Belgium |
PMID:18948285 PMID:16381959 PMID:12519963 |
Public, The community can contribute to this resource | nif-0000-03431, OMICS_02322 | SCR_007106 | 2026-08-13 09:27:44 | 49 | |||||||
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Cambridge Brain Activation Resource Report Resource Website 10+ mentions |
Cambridge Brain Activation (RRID:SCR_007109) | CamBA | data processing software, software application, software toolkit, image analysis software, workflow software, software resource | Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution. | analysis, brain, anova, resampling, statistical, wavelet, fmri, pipeline, affine warp, algorithm or reusable library, application, c, image-to-template, java, linux, macos, magnetic resonance, nifti-1, posix/unix-like, registration, regression, spatial transformation, spectral analysis, statistical operation, temporal transformation, time domain analysis, unix shell, warping, wavelet transformation, web environment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps has parent organization: University of Cambridge; Cambridge; United Kingdom |
GlaxoSmithKline ; Human Brain Project ; NIMH ; NIBIB |
GNU General Public License | nif-0000-00267 | http://www-bmu.psychiatry.cam.ac.uk/software/ | SCR_007109 | 2026-08-13 09:27:43 | 11 | ||||||
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CD-HIT Resource Report Resource Website 1000+ mentions |
CD-HIT (RRID:SCR_007105) | CD-HIT | data processing software, software resource, source code, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cluster, protein, sequence, classification, domain, analysis, nucleotide sequence, dna, protein sequence, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: University of California at San Diego; California; USA has parent organization: Google Code is parent organization of: CD-HIT-OTU |
NCRR 1R01RR025030 | PMID:20053844 PMID:16731699 DOI:10.1093/bioinformatics/btl158 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05157, biotools:cd-hit, nif-0000-30240 | http://cd-hit.org, https://code.google.com/p/cdhit/, https://bio.tools/cd-hit, https://sources.debian.org/src/cd-hit/ | http://bioinformatics.ljcrf.edu/cd-hi/ |
SCR_007105 | CD-HIT Program | 2026-08-13 09:27:43 | 3223 | |||
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Combine RTS2000 Resource Report Resource Website 1+ mentions |
Combine RTS2000 (RRID:SCR_007104) | image processing software, data processing software, software resource, software application | Software program that performs the auto-alignment and the composition of images to create the mosaic. | program, auto, alignment, composition, image, create, mosaic | has parent organization: National Center for Microscopy and Imaging Research | NCRR P41 RR04050 | Free, no longer available | nif-0000-10511 | SCR_007104 | 2026-08-13 09:27:38 | 1 | ||||||||
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Expression Database in 4D Resource Report Resource Website 1+ mentions |
Expression Database in 4D (RRID:SCR_007066) | 4DXpress | data or information resource, database, service resource, data repository, storage service resource | This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data. | genes, anatomical structures, developmental stage, microarray data, species, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
European Molecular Biology Laboratory; Heidelberg; Germany | PMID:17916571 | nif-0000-02524, biotools:4dxpress | https://bio.tools/4dxpress | SCR_007066 | 4DXpress Database | 2026-08-13 09:27:42 | 1 | |||||
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Cardiac Electrophysiology Ontology Resource Report Resource Website |
Cardiac Electrophysiology Ontology (RRID:SCR_007065) | EP | ontology, data or information resource, controlled vocabulary | Ontology that contains terms describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels. | owl |
is listed by: BioPortal has parent organization: CardioVascular Research Grid (CVRG) |
nlx_157352 | SCR_007065 | 2026-08-13 09:27:38 | 0 | |||||||||
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Cereal Plant Gross Anatomy Ontology Resource Report Resource Website |
Cereal Plant Gross Anatomy Ontology (RRID:SCR_007061) | GRO-CPGA | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary for the anatomy of Gramineae. Please note that this ontology has now been superseded by the Plant Ontology, http://bioportal.bioontology.org/ontologies/1587. | obo |
is listed by: BioPortal is related to: Plant Ontology has parent organization: Gramene |
nlx_157359 | http://www.gramene.org/plant_ontology/ | SCR_007061 | 2026-08-13 09:27:38 | 0 |
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