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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Polbase Resource Report Resource Website |
Polbase (RRID:SCR_006107) | data or information resource, data repository, database, storage service resource, service resource | Repository of biochemical, genetic, and structural information about DNA Polymerases. Polbase is designed to compile detailed results of polymerase experimentation, presenting them in a dynamic view to inform further research. After validation, results from references are displayed in context with relevant experimental details and are always traceable to their source publication. Polbase is connected to other resources, including PubMed, UniProt and the RCSB Protein Data Bank, to provide multi-faceted views of polymerase knowledge. In addition to a simple web interface, Polbase data is exposed for custom analysis by external software. | dna polymerase repository, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: PubMed is related to: UniProt has parent organization: New England Biolabs |
Small Business Innovation Research ; NIGMS 1R44GM087021 |
PMID:21993301 | Free, Open unspecified license, Acknowledgement required | biotools:polbase, nlx_151580 | https://bio.tools/polbase | SCR_006107 | DNA Polymerase Database | 2026-08-05 10:44:22 | 0 | |||||
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959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | data or information resource, wiki, narrative resource | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | NematodeGenomes | 2026-08-05 10:44:22 | 2 | |||||
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MMMDB - Mouse Multiple tissue Metabolome DataBase Resource Report Resource Website 1+ mentions |
MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) | MMMDB | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. | metabolite, metabolome, cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, plasma, metabolomic pathway, capillary electropherograms time-of-flight mass spectrometry, electropherogram, mass spectrometry, annotation, isotope, fragment, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:22139941 | Free | nlx_151467, biotools:mmmdb | https://bio.tools/mmmdb | SCR_006064 | Mouse Multiple tissue Metabolome DataBase | 2026-08-05 10:44:22 | 1 | |||||
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InterEvol database Resource Report Resource Website 10+ mentions |
InterEvol database (RRID:SCR_006054) | InterEvol | data or information resource, database, software resource, data analysis service, production service resource, service resource, analysis service resource | InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface | structure, evolution, protein complex, interface, protein complex, sequence alignment, plug in, protein structure, visualization, pymol plugin, structural homolog, structural interolog, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: CEA; Gif sur Yvette; France |
Commissariat a lEnergie Atomique ; ANR HPGenVar |
PMID:22053089 | Free and open to all users - no login requirement | nlx_151453, biotools:interevol | https://bio.tools/interevol | SCR_006054 | 2026-08-05 10:44:22 | 10 | |||||
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UMD-BRCA1/ BRCA2 databases Resource Report Resource Website 10+ mentions |
UMD-BRCA1/ BRCA2 databases (RRID:SCR_006128) | UMD-BRCA1/ BRCA2 databases | data or information resource, data repository, database, storage service resource, service resource | The UMD-BRCA1/BRCA2 databases have been set up in a joined national effort through the network of 16 diagnostic laboratories to provide up-to-date information about mutations of the BRCA1 and BRCA2 genes identified in patients with breast and/or ovarian cancer. These databases currently contain published and unpublished information about the BRCA1/BRCA2 mutations reported in French diagnostic laboratories. This database includes 28 references and 5530 mutations (1440 different mutations and 786 protein variants) The databases of BRCA1 and BRCA2 mutations were built using the Universal Mutation Database tool. For each mutation, information is provided at several levels: * at the gene level: exon and codon number, wild type and mutant codon, mutation event, mutation name and, * at the protein level: wild type and mutant amino acid, binding domain, affected domain. If you want to submit a mutation, please contact R. Lidereau., S. Caputo. or E. Rouleau. | cancer, gene, mutation, exon, codon, wild type, mutant, mutation, protein, amino acid, binding domain, affected domain, brca1, brca2, variant, polymorphism, unclassified variant, unknown variant, female, woman, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: National Institute of Health and Medical Research; Rennes; France |
Breast cancer, Ovarian cancer | French National Cancer Institute ; European Union FP7/2007-2013; Association dAide a la Recherche Cancerologique de Saint Cloud |
PMID:22144684 | The UMD- BRCA1 Locus Specific Databases constitute the intellectual property of the curators of the database. Any unauthorized copying, Storage or distribution of this material without written permission from the curators would lead to copyright infringement with possible ensuing litigation. | nlx_151608, biotools:brca_share | https://bio.tools/brca_share | SCR_006128 | UMD-BRCA1 mutations database, UMD-BRCA1 / BRCA2 databases, UMD-BRCA1/BRCA2 databases | 2026-08-05 10:44:23 | 26 | |||
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RAxML Resource Report Resource Website 10000+ mentions |
RAxML (RRID:SCR_006086) | RAxML | software resource, data processing software, software application, data analysis software | Software program for phylogenetic analyses of large datasets under maximum likelihood. | phylogeny, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: RAxML Next Generation works with: PAML |
PMID:24451623 PMID:16928733 PMID:15608047 DOI:10.1093/bioinformatics/btu033 |
GNU General Public License | biotools:raxml, OMICS_02242 | https://bio.tools/raxml, https://sources.debian.org/src/raxml/ | SCR_006086 | Randomized Axelerated Maximum Likelihood | 2026-08-05 10:44:26 | 12473 | |||||
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OGEE - Online GEne Essentiality database Resource Report Resource Website 1+ mentions |
OGEE - Online GEne Essentiality database (RRID:SCR_006080) | OGEE, OGEEdb | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | Online GEne Essentiality database containing genes that were tested experimentally for essentiality and their features; it also provides a set of tools to systematically explore and analyze these data. The main purpose of this project is to better understand gene essentiality by facilitating the comparisons of the differences and similarities between essential and non-essential genes. This is achieved by collecting not only experimentally tested essential and non-essential genes, but also associated gene features such as expression profiles, duplication status, conservation across species, evolutionary origins and involvement in embryonic development. We focus on large-scale experiments and complement our data with text-mining results. Genes are organized into data sets according to their sources. Genes with variable essentiality status across data sets are tagged as conditionally essential, highlighting the complex interplay between gene functions and environments. Linked tools allow the user to compare gene essentiality among different gene groups, or compare features of essential genes to non-essential genes, and visualize the results. Why is it different from existing databases? * we included both essential and non-essential genes so that we could better understand the gene essentiality by comparing the similarities and differences between the two gene sets; * we compiled a list of features for each gene, including whether they are duplicates or involved in development, the number of other homologous genes in the same genome, as well as their earliest expression stages during development. These features are keys to understand the essentiality of genes; * we also provide a set of tools to explore our data and visualize the results. For example, users can simply divide genes into two groups according to whether they are duplicates, calculate the proportion of essential genes (PE%) in each group and then visualize the results in a bar plot; or they can classify genes into multiple groups according to their earliest expression stages during evolution, compare the essentiality of genes that were expressed earlier with those were latter, and plot the results in a line chart. | genome-wide association study, essentiality, gene, essential gene, non-essential gene, growth, expression profile, duplication status, conservation, evolutionary origin, embryonic development, text-mining, gene function, environment, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
BMBF 0315450C | PMID:22075992 | Free | nlx_151488, biotools:ogee | https://bio.tools/ogee | SCR_006080 | Online GEne Essentiality database | 2026-08-05 10:44:25 | 2 | ||||
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PRED-GPCR Resource Report Resource Website 1+ mentions |
PRED-GPCR (RRID:SCR_006196) | PRED-GPCR | data or information resource, data set, data analysis service, production service resource, service resource, analysis service resource | A prediction tool for GPCR Family Classification from sequence alone based on a probabilistic method that uses family-specific profile Hidden Markov Models. The PRED-GPCR system is based on a probabilistic method that uses family specific profile HMMs in order to determine to which GPCR family a query sequence belongs or resembles. The approach proposed in this method exploits the descriptive power of profile HMMs along with an exhaustive discrimination assessment method to select only highly selective and sensitive profiles, for each family. The collection of these profiles constitutes a signature library, which is scanned, for significant matches with a given query sequence. The output report for a query sequence consists of two sections: * A ranked list of the profile HMM matches, below the selected individual motif E-value cutoff, along with their corresponding family. * A ranked list of the Combined P-values, E-values as well as the number of profiles matched for each family. To cross-evaluate your results you can browse through Swiss-Prot, Trembl, Pfam and Prosite family related entries. | g-protein coupled receptor, classification, hidden markov model, sequence, fasta, family classification, motif, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Athens Biophysics and Bioinformatics Laboratory |
PMID:15215415 | nlx_151741, biotools:pred-gpcr | https://bio.tools/pred-gpcr | SCR_006196 | PRED-GPCR: GPCRs Family classification from sequence alone | 2026-08-05 10:44:26 | 2 | ||||||
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ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-08-05 10:44:22 | 77 | |||||
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COLT-Cancer Resource Report Resource Website 10+ mentions |
COLT-Cancer (RRID:SCR_006485) | COLT-Cancer | data or information resource, database, data analysis service, production service resource, service resource, analysis service resource | The COLT-Cancer database is a collection of shRNA dropout signatures profiles, covering ~16000 human genes, and derived from more than 70 Pancreatic, Ovarian and Breast human cancer cell-lines using the microarray detection platform developed in the COLT (CCBR-OICR Lentiviral Technology) facility at the Moffat Lab. All shRNA dropout profiles are freely available through download or queries via this website. | gene, shrna profile, shrna, functional genetics, cancer, cell line, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Toronto; Ontario; Canada |
Pancreatic cancer, Ovarian cancer, Breast cancer | Ontario Institute for Cancer Research ; Terry Fox Research Institute ; Canadian Institutes of Health Research ; Canada Foundation for Innovation ; Ontario Research Fund |
PMID:22102578 | Free | biotools:colt-cancer, nlx_149426 | https://bio.tools/colt-cancer | SCR_006485 | CCBR-OICR Lentiviral Technology Cancer, COLT-Cancer database | 2026-08-05 10:44:29 | 11 | |||
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Phenotypes and eXposures Toolkit Resource Report Resource Website 50+ mentions |
Phenotypes and eXposures Toolkit (RRID:SCR_006532) | PhenX Toolkit | data or information resource, narrative resource, data set, catalog, database, standard specification, service resource | Set of measures intended for use in large-scale genomic studies. Facilitate replication and validation across studies. Includes links to standards and resources in effort to facilitate data harmonization to legacy data. Measurement protocols that address wide range of research domains. Information about each protocol to ensure consistent data collection.Collections of protocols that add depth to Toolkit in specific areas.Tools to help investigators implement measurement protocols. | PhenX project, genome, phenotype, genome-wide association study, genetic variation, genomic study, substance abuse, addiction, substance use, environmental exposure, disease susceptibility, outcome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: RTI International has parent organization: Consensus Measures for Phenotype and Exposure has parent organization: Trans-Omics for Precision Medicine (TOPMed) Program has organization facet: PhenX Phenotypic Terms is organization facet of: Consensus Measures for Phenotype and Exposure |
NHGRI U01 HG004597; NHGRI U41HG007050; NIDA ; OBSSR ; NIMH ; NHLBI ; NIMHD ; TRSP ; NHGRI U24 HG012556; ODP ; NINDS ; NCI |
PMID:21749974 | Restricted | SCR_017475, biotools:PhenX_toolkit, nlx_144102 | https://bio.tools/PhenX_Toolkit | SCR_006532 | Phenotypes and eXposures Toolkit | 2026-08-05 10:44:29 | 61 | ||||
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Flycircuit Resource Report Resource Website 50+ mentions |
Flycircuit (RRID:SCR_006375) | data or information resource, database, atlas, storage service resource, service resource | FlyCircuit is a public database for online archiving, cell type inventory, browsing, searching, analysis and 3D visualization of individual neurons in the Drosophila brain. | drosophila, fly brain, neuron reconstruction, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Virtual Fly Brain has parent organization: National Tsing Hua University; Hsinchu; Taiwan |
PMID:21129968 | r3d100012173, nif-0000-07738, biotools:FlyCircuit | https://bio.tools/FlyCircuit, https://doi.org/10.17616/R3293N | SCR_006375 | Fly Circuit - A Database of Drosophila Brain Neurons, Fly Circuit, Flycircuit database, Fly Circuit Database, FlyCircuit - A Database of Drosophila Brain Neurons | 2026-08-05 10:44:26 | 50 | |||||||
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HUDSEN Resource Report Resource Website 1+ mentions |
HUDSEN (RRID:SCR_006324) | HUDSEN | community building portal, data or information resource, portal | Forum for researchers in human developmental biology and related fields to meet and establish links. | development, genetics, embryology, embryonic, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: eMouseAtlas is related to: aGEM has parent organization: Newcastle University; Newcastle upon Tyne; United Kingdom is parent organization of: HUDSEN Electronic Atlas of the Developing Human Brain is parent organization of: HUDSEN Human Gene Expression Spatial Database |
nlx_152025, biotools:hudsen | https://bio.tools/hudsen | SCR_006324 | Human Developmental Studies Network | 2026-08-05 10:44:27 | 5 | |||||||
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bioRxiv Resource Report Resource Website 1000+ mentions |
bioRxiv (RRID:SCR_003933) | bioRxiv | community building portal, data or information resource, portal, database | A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version. | preprint, life science, bio.tools, FASEB list |
is used by: PrePubMed is listed by: LabWorm is listed by: bio.tools is listed by: Debian is related to: Overleaf has parent organization: Cold Spring Harbor Laboratory |
Free, Acknowledgement requested, The community can contribute to this resource | nlx_158302, biotools:bioRxiv | https://bio.tools/bioRxiv | SCR_003933 | bioRxiv - the preprint server for biology | 2026-08-05 10:43:57 | 1246 | ||||||
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Git Resource Report Resource Website 50+ mentions |
Git (RRID:SCR_003932) | software development tool, version source control system, software application, software resource | A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows. | version control, distributed, bio.tools |
is used by: DataLad is used by: G-Node Data Infrastructure Services is listed by: bio.tools is listed by: Debian works with: git-annex |
GNU General Public License, v2 | nlx_158301, biotools:Git | https://bio.tools/Git | SCR_003932 | 2026-08-05 10:43:57 | 66 | ||||||||
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PubChem Resource Report Resource Website 10000+ mentions |
PubChem (RRID:SCR_004284) | data or information resource, data repository, database, storage service resource, service resource | Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI). | collection, information, data, chemical, structure, biological, property, small, molecule, siRNA reagent, bio.tools |
uses: ChEMBL is used by: NIF Data Federation is used by: Pathway Analysis Tool for Integration and Knowledge Acquisition is used by: GEROprotectors is listed by: OMICtools is listed by: re3data.org is listed by: NIH Data Sharing Repositories is listed by: bio.tools is listed by: Debian is related to: NCBI Structure is related to: Molecular Libraries Program is related to: NIH Data Sharing Repositories is related to: PubChem BioAssay has parent organization: NCBI is parent organization of: PubChem Substance works with: MiMeDB |
NLM | PMID:21418625 PMID:21272340 PMID:20970519 PMID:20298522 PMID:19825798 |
Free, Freely Available | biotools:pubchem, nlx_42691, nlx_29861, r3d100010538, OMICS_01587 | https://bio.tools/pubchem, https://doi.org/10.17616/R3GW37 | SCR_004284 | 2026-08-05 10:44:00 | 13540 | ||||||
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PDBe - Protein Data Bank in Europe Resource Report Resource Website 50+ mentions |
PDBe - Protein Data Bank in Europe (RRID:SCR_004312) | PDBe | data or information resource, data repository, database, storage service resource, service resource | The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules. | x-ray, nmr, cryo-em, hybrid method, dna, protein, rna, sugar, ligand, virus, compound, fold, enzyme, 3d spatial image, structure, macromolecule, protein-protein interaction, gold standard, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: DNA DataBank of Japan (DDBJ) is related to: EMDataResource.org is related to: Worldwide Protein Data Bank (wwPDB) is related to: Biological Magnetic Resonance Data Bank (BMRB) is related to: DNA DataBank of Japan (DDBJ) is related to: Worldwide Protein Data Bank (wwPDB) is related to: PDBj - Protein Data Bank Japan is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: European Bioinformatics Institute is parent organization of: Electron Microscopy Data Bank at PDBe (MSD-EBI) works with: MOLEonline |
European Molecular Biology Laboratory; Heidelberg; Germany ; Wellcome Trust ; BBSRC ; NIH ; European Union ; MRC ; CCP4 |
PMID:21045060 PMID:21460450 PMID:19858099 |
r3d100012791, biotools:pdbe, nlx_32372 | https://bio.tools/pdbe, https://doi.org/10.17616/R3J226 | SCR_004312 | Protein DataBank Europe, Protein DataBank in Europe, PDBe, Protein Data Bank in Europe, Protein Data Bank Europe, Macromolecular Structure Database | 2026-08-05 10:44:01 | 52 | |||||
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NeuroMatic Resource Report Resource Website 100+ mentions |
NeuroMatic (RRID:SCR_004186) | software resource, data processing software, software application, data analysis software | NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC | epsc, epsp, event, fit, acquisition, data management, ipsc, ipsp, nclamp, software, spike, spike train, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University College London; London; United Kingdom |
PMID:29670519 | nif-0000-00073, biotools:neuromatic | https://bio.tools/neuromatic | SCR_004186 | NeuroMatic | 2026-08-05 10:43:59 | 301 | |||||||
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RatMine Resource Report Resource Website 1+ mentions |
RatMine (RRID:SCR_004190) | data or information resource, web service, data access protocol, software resource, database, data analysis service, production service resource, service resource, analysis service resource | RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites. | disease, interaction, proteins, single nucleotide, gene ontology, mammalian phenotype, publication, genomics, pathway, quantitative trait loci, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Medical College of Wisconsin; Wisconsin; USA |
biotools:RatMine, nlx_21635 | https://bio.tools/RatMine | SCR_004190 | 2026-08-05 10:43:59 | 5 | |||||||||
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DER Finder Resource Report Resource Website 1+ mentions |
DER Finder (RRID:SCR_004250) | DER Finder | data processing software, software library, software application, software toolkit, software resource | R package for differential expression analysis of RNA-seq data. | differential expression, rna-seq, false discovery rate, genomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24398039 | Free, Public | biotools:derfinder, OMICS_02208 | https://bio.tools/derfinder | SCR_004250 | derfinder | 2026-08-05 10:44:00 | 5 |
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