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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site Resource Report Resource Website 1+ mentions |
HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) | HAMSTeRS, HADB, HADB/HAMSTeRS, HADB / HAMSTeRS | data repository, service resource, storage service resource, database, data or information resource |
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019. Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines) |
function, gene, genetic, analysis, bioinformatic, biological, biostatistic, caeruloplasmiin, crystal, haemophilia a, human, murine, porcine, canine, level, molecular, molecule, mutation, nucleic acid, or disease- specific databases, pathology, structural, structure, system-, vitromutagenesis, fviii genetic variation, dna, protein, factor viii, blood-clotting protein, point mutation, deletion, insertion | has parent organization: Imperial College London; London; United Kingdom | Pfizer UK ; MRC |
PMID:9399839 PMID:9016520 PMID:8594555 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21184 | http://europium.csc.mrc.ac.uk/WebPages/Main/main.htm, http://hadb.org.uk/ | SCR_006883 | HAMSTeRS - The Haemophilia A Mutation Structure Test Resource Site, Haemophilia A Mutation Database, Haemophilia A Mutation Structure Test and Resource Site, Haemophilia A Mutation Structure Test Resource Site | 2026-02-12 09:44:28 | 9 | ||||
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PhysioToolkit Resource Report Resource Website 1+ mentions |
PhysioToolkit (RRID:SCR_006868) | PhysioToolkit | source code, software resource, time-series analysis software, software repository, software application, data analysis software, data processing software, signal processing software | Growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of the research projects that contribute software to PhysioToolkit is the extraction of hidden information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. Contributions of software to PhysioToolkit are welcome, http://physionet.org/guidelines.shtml#software-contributions | signal processing, analysis, matlab, wfcb, data visualization, data mining, model, simulation, deidentification, data import, data export | is related to: Physiobank | PMID:10851218 | GNU General Public License, The community can contribute to this resource | nlx_152537 | SCR_006868 | 2026-02-12 09:44:25 | 5 | |||||||
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Gene Ontology Tools Resource Report Resource Website 10+ mentions |
Gene Ontology Tools (RRID:SCR_006941) | GO Tools | software resource, database, software repository, data or information resource, catalog | 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 | 2026-02-12 09:44:20 | 27 | ||||||
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Cambridge Brain Activation Resource Report Resource Website 10+ mentions |
Cambridge Brain Activation (RRID:SCR_007109) | CamBA | software toolkit, workflow software, software resource, software application, data processing software, image analysis software | 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 | 2026-02-12 09:44:28 | 11 | ||||||
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CD-HIT Resource Report Resource Website 1000+ mentions |
CD-HIT (RRID:SCR_007105) | CD-HIT | source code, software application, software resource, data processing software | 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 | 2026-02-12 09:44:28 | 3203 | |||
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Brain Architecture Management System Resource Report Resource Website 1+ mentions |
Brain Architecture Management System (RRID:SCR_007251) | BAMS | data repository, service resource, storage service resource, database, data or information resource, ontology, controlled vocabulary | Knowledge management system designed to handle neurobiological information at different levels of organization of vertebrate nervous system. Database and repository for information about neural circuitry, storing and analyzing data concerned with nomenclature, taxonomy, axonal connections, and neuronal cell types. Handles data and metadata collated from original literature, or inserted by scientists that is associated to four levels of organization of vertebrate nervous system. Data about expressed molecules, neuron types and classes, brain regions, and networks of brain regions. | neurobiology, vertebrate, nervous, system, database, repository, neural, circuitry, analysis, data, nomenclature, taxonomy, axonal, connection, cell, |
is used by: NIF Data Federation is used by: Integrated Nervous System Connectivity is related to: Integrated Manually Extracted Annotation has parent organization: University of Southern California; Los Angeles; USA is parent organization of: BAMS Nested Regions is parent organization of: BAMS Connectivity is parent organization of: BAMS Cells is parent organization of: BAMS Neuroanatomical Ontology |
NIBIB ; Human Brain Project ; NIMH MH61223; NINDS NS16686; NINDS NS50792 |
Restricted | nif-0000-00018 | http://brancusi.usc.edu/bkms/ | SCR_007251 | Brain Architecture Management System, The Brain Architecture Management System | 2026-02-12 09:44:39 | 6 | |||||
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Internet Analysis Tools Registry Resource Report Resource Website 1+ mentions |
Internet Analysis Tools Registry (RRID:SCR_005638) | IATR | software resource, software repository, software application, data processing software, image analysis software | A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web. | database, tool, neuroimaging, image, analysis |
lists: Extensible MATLAB Medical image Analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
Human Brain Project | Public Domain | nlx_146252 | SCR_005638 | IATR - Internet Analysis Tools Registry | 2026-02-12 09:44:05 | 1 | ||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | analysis service resource, software resource, data access protocol, service resource, web service, production service resource, software application, data analysis service, data analysis software, data processing software | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html https://bio.tools/interproscan_4 |
SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-02-12 09:44:07 | 6936 | |||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | analysis service resource, software resource, service resource, production service resource, database, data analysis service, data or information resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-02-12 09:44:13 | 3358 | |||||
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University of Barcelona Statistics and Bioinformatics Research Group Resource Report Resource Website |
University of Barcelona Statistics and Bioinformatics Research Group (RRID:SCR_005704) | UB Statistics and Bioinformatics Research Group | analysis service resource, service resource, production service resource, topical portal, data analysis service, data or information resource, portal | The Statistics and Bioinformatics research group has as its main objectives the development of methods and tools to deal with problems appearing in the interface between Statistics and Bioinformatics. We started focusing in DNA microarrays but we are also interested in statistical methods for ''omics'' data integration and next generation sequencing (NGS). Our group collaborates with different research groups in the fields of biology and biomedicine, to whom it offers statistical support for problems which are specifically statistic in nature, such as experimental design or microarray data analysis, and also in more general aspects, such as modeling, analysis or data mining. After a first period of collaboration agreements with the Fundaci�� Vall d''Hebr��n Institut de Recerca we contributed to the creation of the Statistics and Bioinformatics Unit (UEB) which provides statistical and bioinformatical support to VHIR researchers. | statistics, bioinformatics, next generation sequencing, dna microarray, dna, microarray, biology, biomedicine, data mining, modeling, analysis | has parent organization: University of Barcelona; Barcelona; Spain | nlx_149154 | SCR_005704 | University of Barcelona Statistics Bioinformatics Research Group | 2026-02-12 09:44:06 | 0 | ||||||||
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go-moose Resource Report Resource Website |
go-moose (RRID:SCR_005666) | go-moose | software resource, software application, data analysis software, data processing software | go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | software library, slimmer-type tool, analysis, gene ontology, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: go-perl is related to: go-db-perl has parent organization: SourceForge has parent organization: Berkeley Bioinformatics Open-Source Projects has parent organization: Lawrence Berkeley National Laboratory |
Free for academic use | nlx_149189 | SCR_005666 | 2026-02-12 09:44:12 | 0 | ||||||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool | annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | Free for academic use | nlx_149182 | SCR_005725 | 2026-02-12 09:44:09 | 3 | |||||||
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GOTaxExplorer Resource Report Resource Website |
GOTaxExplorer (RRID:SCR_005720) | GOTaxExplorer | analysis service resource, software resource, service resource, production service resource, database, data analysis service, data or information resource | GOTaxExplorer presents a new approach to comparative genomics that integrates functional information and families with the taxonomic classification. It integrates UniProt, Gene Ontology, NCBI Taxonomy, Pfam and SMART in one database. GOTaxExplorer provides four different query types: selection of entity sets, comparison of sets of Pfam families, semantic comparison of sets of GO terms, functional comparison of sets of gene products. This permits to select custom sets of GO terms, families or taxonomic groups. For example, it is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes. Furthermore, it enables to determine the distribution of specific molecular functions or protein families in the taxonomy. The comparison of sets of GO terms allows to assess the semantic similarity of two different GO terms. The functional comparison of gene products makes it possible to identify functionally equivalent and functionally related gene products from two organisms on the basis of GO annotations and a semantic similarity measure for GO. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, molecular function, protein family, taxonomy, visualization, functional similarity, semantic similarity, analysis, comparative genomics analysis, comparative genomics, search engine, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, function, other analysis |
is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: UniProt is related to: NCBI Taxonomy is related to: Pfam is related to: SMART is related to: FSST - Functional Similarity Search Tool has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
German National Genome Research Network ; BMBF 016R0453; DFG KFO 129/1-1; European Union contract LSHG-CT-2003-503265 |
PMID:17346342 | Free for academic use | nlx_149179 | SCR_005720 | 2026-02-12 09:44:15 | 0 | ||||||
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Onto-Miner Resource Report Resource Website |
Onto-Miner (RRID:SCR_005722) | OM | analysis service resource, service resource, production service resource, database, data analysis service, data or information resource | Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool | gene, annotation, search engine, database, analysis, ontology or annotation search engine, database or data warehouse, other analysis, scripted search of the onto-tools database for gene annotations |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 PMID:17584796 |
Free for academic use | nlx_149181 | SCR_005722 | Onto-Miner (OM) | 2026-02-12 09:44:13 | 0 | ||||||
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Brede Toolbox Resource Report Resource Website 1+ mentions |
Brede Toolbox (RRID:SCR_006204) | Brede Toolbox | software resource, software application, data processing software, image processing software, image analysis software | A package for neuroinformatics and neuroimaging analysis mostly programmed in Matlab with a few additional programs in Python and Perl. It allows coordinate-based meta-analysis and visualization, neuroimaging analysis of voxel or regional data - not the original data but rather the summary images (e.g., statistical parametric images) and location data in stereotactic space. Among the algorithms implemented are kernel density estimation (for coordinate-based meta-analysis), independent component analysis, non-negative matrix factorization, k-means clustering, singular value decomposition, partial correlation analysis with permutation testing and partial canonical correlation analysis. Visualization of coordinate, surfaces and volumes are possible in 2D and 3D. Generation of HTML for results are possible and algorithms can be accessed from the command line or via a flexible graphical interface. With the Brede Toolbox comes the Brede Database with a small coordinate database from published neuroimaging studies, and ontologies for, e.g., brain function and brain regions. | ontology, database application, independent component analysis, principal component analysis, regression, neuroinformatics, neuroimaging, analysis, matlab, python, perl, coordinate, kernel density estimation, brain function, brain region, visualization, voxel, region |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is related to: Brede Database is related to: Brede Database is related to: Brede Wiki has parent organization: THOR Center for Neuroinformatics |
Free for academic use, Acknowledgement requested | nif-0000-00275 | SCR_006204 | 2026-02-12 09:44:18 | 1 | ||||||||
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Knime Resource Report Resource Website 500+ mentions |
Knime (RRID:SCR_006164) | KNIME | software toolkit, text-mining software, workflow software, software resource, software application, data processing software | KNIME (Konstanz Information Miner) is a user-friendly and comprehensive Open-Source data integration, processing, analysis, and exploration platform. KNIME (naim) is a user-friendly graphical workbench for the entire analysis process: data access, data transformation, initial investigation, powerful predictive analytics, visualization and reporting. The open integration platform provides over 1000 modules (nodes), including those of the KNIME community and its extensive partner network. KNIME can be downloaded onto the desktop and used free of charge. KNIME products include additional functionalities such as shared repositories, authentication, remote execution, scheduling, SOA integration and a web user interface as well as world-class support. Robust big data extensions are available for distributed frameworks such as Hadoop. KNIME is used by over 3000 organizations in more than 60 countries. The modular data exploration platform, initially developed at the University of Konstanz, Germany, enables the user to visually create data flows, execute selected analysis steps, and later investigate the results through interactive views on data and models. KNIME is a proven integration platform for tools of numerous vendors due to its open and modular API. The KNIME.com product pipeline includes an Enterprise Server, Cluster Execution, Reporting solutions, and professional KNIME support subscriptions. KNIME.com also offer services such as data analysis, hands-on training and the development of customized components for KNIME. | platform, next-generation sequencing, data analysis, visualization, selection, analysis, high-throughput screening, data mining, drug discovery | has parent organization: University of Konstanz; Baden-Wurttemberg; Germany | PMID:23110532 PMID:22644661 PMID:22607449 PMID:21984761 PMID:21873641 |
nlx_151666 | SCR_006164 | Konstanz Information Miner | 2026-02-12 09:44:18 | 717 | |||||||
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LeadDiscovery: Providing Information to the Drug Discovery Sector Resource Report Resource Website |
LeadDiscovery: Providing Information to the Drug Discovery Sector (RRID:SCR_006464) | data or information resource, portal, topical portal | LeadDiscovery was founded by life scientists to expedite drug discovery and pharmaceutical development. Based on a solid background of experience from within the pharmaceutical research and development sector, the aim of this resource is to help companies optimize drug discovery and product pipelines through the identification of breaking research and the in depth and expert evaluation of selected therapeutic areas. At the same time it also provides a showcase for pharmaceutical, biotechnology and academic organizations wishing to increase the exposure of their research to the drug development community. LeadDiscovery sits at the center of this sector helping companies to identify commercially viable R&D options from within small biotechs and the public sector. Additionally, it supports the drug discovery and pharmaceutical development community through three key services: DailyUpdates, UpdatesPlus and PharmaReports - DailyUpdates: Launched in 2002 this popular e-mail alert service delivers information on breaking research, new clinical trials, drug development news and recently published market research and pipeline analysis reports. Registration to receive the service is available here - UpdatesPlus: Developed in 2007 as an extension of DailyUpdates, UpdatesPlus provides a monthly in depth analysis of breaking research and development activity in high profile therapeutic areas. - PharmaReports: LeadDiscovery offers a wide range of in depth pharmaceutical reports. It''s reports include market research reports and pipeline analyses. You can search our entire portfolio using LeadDiscovery''s search engine. Alternatively as it are one of the few information providers that has extensive research and development experience, LeadDiscovery occupys a unique position of being able to source reports that accurately meet your needs. If we don''t have a report that fits your requirements, it can produce one through its pharmaceutical consultancy services. LeadDiscovery offers full reports in selected areas of the pharmaceutical and biotech sector. Each of the reports below has been especially selected by LeadDiscovery and categorized into relevant areas: - Oncology - Cancer Immunotherapy - Immunology & Inflammatory Diseases - Infectious Diseases - Psychiatric, Addictive & Sleep Disorders - Pain - Neurodegenerative & Neuroelectrophysiological Disorders - Metabolic & Hormonal Disorders - Cardiovascular Disorders - GenitoUrinary Tract Disorders - Technology - Diagnostics & Devices - Other Theraputic Areas, Pharmaceutical Strategy and Development | drug, e-mail, genitourinary tract disorder, addictive, analysis, biotech, biotechnology, cancer, cardiovascular, clinical trail, development, device, diagnostic, disease, hormonal, immunology, immunotherapy, infectious, inflammatory, life scientist, metabolic, neurodegenerative, neuroelectrophysiological, oncology, pain, pharmaceutical, psychiatric, research, sleep, strategy, technology, therapeutic | nif-0000-10279 | SCR_006464 | LeadDiscovery | 2026-02-12 09:44:32 | 0 | ||||||||||
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GeneAnswers Resource Report Resource Website 10+ mentions |
GeneAnswers (RRID:SCR_006498) | software resource, software application, data analysis software, data processing software, data visualization software | GeneAnswers provide an integrated tool for given genes biological or medical interpretation. It includes statistical test of given genes and specified categories. Microarray techniques have been widely employed in genomic scale studies for more than one decade. The standard analysis of microarray data is to filter out a group of genes from thousands of probes by certain statistical criteria. These genes are usually called significantly differentially expressed genes. Recently, next generation sequencing (NGS) is gradually adopted to explore gene transcription, methylation, etc. Also a gene list can be obtained by NGS preliminary data analysis. However, this type of information is not enough to understand the potential linkage between identified genes and interested functions. The integrated functional and pathway analysis with gene expression data would be very helpful for researchers to interpret the relationship between the identified genes and proposed biological or medical functions and pathways. The GeneAnswers package provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential relationship between them by means of statistical methods, and make user-friendly network visualization to interpret the results. Besides the package has a function to combine gene expression profile and category analysis together by outputting concept-gene cross tables, keywords query on NCBI Entrez Gene and application of human based Disease ontology analysis of given genes from other species can help people to understand or discover potential connection between genes and functions. Sponsors: This project was supported in part by Award Number UL1RR025741 from the National Center for Research Resources. | expression, function, gene, analysis, biological, genomic, medical, microarray, network, pathway, technique, transcription, visualization | has parent organization: Northwestern University; Illinois; USA | nif-0000-25387 | SCR_006498 | GeneAnswers | 2026-02-12 09:44:21 | 46 | |||||||||
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GWAMA Resource Report Resource Website 100+ mentions |
GWAMA (RRID:SCR_006624) | GWAMA | software resource, software application, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data. | meta, analysis, genome, association, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:20509871 DOI:10.1186/1471-2105-11-288 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gwama, OMICS_00235 | https://bio.tools/gwama https://sources.debian.org/src/gwama/ |
http://www.well.ox.ac.uk/GWAMA/ | SCR_006624 | Genome-Wide Association Meta Analysis | 2026-02-12 09:44:33 | 175 | ||||
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HOMER Resource Report Resource Website 5000+ mentions |
HOMER (RRID:SCR_010881) | HOMER | sequence analysis software, software resource, software application, data analysis software, data processing software | Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++. | motif, discovery, next, generation, sequencing, analysis, genomic, data |
is listed by: OMICtools is related to: findMotif.pl has parent organization: University of California at San Diego; California; USA |
NURSA consortium grant ; NIH HC088093; NIDDK DK063491; NCI CA52599; NIGMS P50 GM081892; Foundation Leducq Transatlantic Network Grant |
PMID:20513432 | OMICS_00483 | http://biowhat.ucsd.edu/homer/index.html | SCR_010881 | HOMER, Hypergeometric Optimization of Motif EnRichment, Homer, Homer v4.5 | 2026-02-12 09:45:14 | 5370 |
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