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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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BioMoby Resource Report Resource Website 1+ mentions |
BioMoby (RRID:SCR_013386) | controlled vocabulary, data or information resource, ontology | The MOBY-S system defines an ontology-based messaging standard through which a client will be able to automatically discover and interact with task-appropriate biological data and analytical service providers, without requiring manual manipulation of data formats as data flows from one provider to the next. The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. Sponsors: Funding was provided by Genome Prairie and Genome Alberta A Bioinformatics Platform for Genome Canada''; Canadian Institutes for Health Research; The Natural Sciences and Engineering Research Council of Canada; The Heart and Stroke Foundation for BC and Yukon; The EPSRC through the myGrid (GR/R67743/01, EP/C536444/1, EP/D044324/1, GR/T17457/01) e-Science projects; The Spanish National Institute for Bioinformatics (INB) through Fundacin Genoma Espaa; The Generation Challenge Programme (GCP; http://www.generationcp.org) of the Consultative Group for International Agricultural Research. :Keywords: Ontology, Messaging, Standard, Client, Automatically, Discovery, Biological, Data, ANalytical, Service, Model, Organism, Database, Java, Platform, Semantic, Bioinformatics, |
is listed by: SoftCite is related to: BioExtract has parent organization: Pompeu Fabra University; Barcelona; Spain |
nif-0000-30186 | SCR_013386 | BioMoby | 2026-09-12 12:58:02 | 8 | ||||||||||
|
Glimmer Resource Report Resource Website 500+ mentions |
Glimmer (RRID:SCR_011931) | Glimmer | analysis service resource, data analysis service, production service resource, service resource, software resource | A software system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. | microbial, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Glimmer-MG is related to: GlimmerHMM has parent organization: Johns Hopkins University; Maryland; USA |
DOI:10.1093/nar/26.2.544 | Open unspecified license, OSI certified | OMICS_01486, biotools:glimmer | https://bio.tools/glimmer, https://sources.debian.org/src/tigr-glimmer/ | SCR_011931 | Glimmer - Microbial Gene-Finding System | 2026-09-12 12:57:42 | 687 | |||||
|
AutoDock Vina Resource Report Resource Website 1000+ mentions |
AutoDock Vina (RRID:SCR_011958) | AutoDock Vina | software resource | An open-source program for doing molecular docking. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Scripps Research Institute |
PMID:34278794 PMID:19499576 DOI:10.1002/jcc.21334 |
Open unspecified license | biotools:autodock_vina, OMICS_01595, OMICS_03790 | https://bio.tools/autodock_vina, https://sources.debian.org/src/avogadro/ | SCR_011958 | 2026-09-12 12:57:43 | 2447 | ||||||
|
MrBayes Resource Report Resource Website 10000+ mentions |
MrBayes (RRID:SCR_012067) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 28,2023. Software program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. | applet, mac os x, unix/linux, windows |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:22357727 DOI:10.1093/sysbio/sys029 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_04237 | https://sources.debian.org/src/mrbayes/ | SCR_012067 | 2026-09-12 12:57:44 | 10714 | |||||||
|
Mimics Resource Report Resource Website 1000+ mentions |
Mimics (RRID:SCR_012153) | Mimics | commercial organization, data processing software, image analysis software, image processing software, segmentation software, software application, software resource | Software for medical image processing. Use Mimics for the segmentation of 3D medical images (coming from CT, MRI, microCT, CBCT, Ultrasound, Confocal Microscopy) and the result will be highly accurate 3D models of your patient''s anatomy. You can then use these patient-specific models for a variety of engineering applications directly in Mimics or 3-matic, or export the 3D models and anatomical landmark points to 3rd party software, like statistical, CAD, or FEA packages. | segmentation, 3d-rendering, micro-ct, ct, mri, cbct, ultrasound, confocal microscopy, anatomy | is listed by: SoftCite | rid_000086 | SCR_012153 | Materialise MIMICS, Mimics - Medical Image Segmentation for Engineering on Anatomy | 2026-09-12 12:57:46 | 1029 | ||||||||
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SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, source code, web service | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-09-12 12:57:53 | 10996 | |||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-09-12 12:57:52 | 319 | ||||||||
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LaCyTools Resource Report Resource Website 10+ mentions |
LaCyTools (RRID:SCR_024525) | software resource, software toolkit | Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides. | Targeted Liquid Chromatography, Mass Spectrometry Data Processing, relative quantitation of glycopeptides, | is listed by: SoftCite | PMID:27267458 | Free, Available for download, Freely available | SCR_024525 | 2026-09-12 01:01:18 | 26 | |||||||||
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GOplot Resource Report Resource Website 100+ mentions |
GOplot (RRID:SCR_024419) | software resource, software toolkit | Software R package for visually combining expression data with functional analysis. | visually combining expression data with functional analysis, | is listed by: SoftCite | PMID:25964631 | Free, Available for download, Freely available | https://github.com/wencke/wencke.github.io | SCR_024419 | R GOplot | 2026-09-12 01:01:17 | 415 | |||||||
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geepack Resource Report Resource Website 1+ mentions |
geepack (RRID:SCR_024510) | software resource, software toolkit | Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data. | generalized estimating equations, fitting marginal generalized linear models to clustered data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024510 | generalized estimating equations pack | 2026-09-12 01:01:18 | 3 | |||||||||
|
DAGitty Resource Report Resource Website 10+ mentions |
DAGitty (RRID:SCR_024509) | software resource, software toolkit | Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models. | graphical analysis of structural causal models, drawing and analysing Directed Acyclic Graphs, | is listed by: SoftCite | PMID:28089956 | Free, Available for download, Freely available | https://github.com/jtextor/dagitty | SCR_024509 | 2026-09-12 01:01:18 | 25 | ||||||||
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FastMulRFS Resource Report Resource Website 1+ mentions |
FastMulRFS (RRID:SCR_024505) | software resource, software toolkit | Software pipeline for estimating species trees from multi copy gene trees. | estimating species trees, multi copy gene trees, | is listed by: SoftCite | PMID:32657396 | Free, Available for download, Freely available | SCR_024505 | 2026-09-12 01:01:18 | 1 | |||||||||
|
NOTUNG Resource Report Resource Website 1+ mentions |
NOTUNG (RRID:SCR_024484) | software resource, software toolkit | Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses. | inferring duplication dates, large scale analysis, dating gene duplications, optimizing gene family trees, | is listed by: SoftCite | PMID:11108472 | Free, Available for download, Freely available | SCR_024484 | Notung 2.9 | 2026-09-12 01:01:18 | 9 | ||||||||
|
CMplot Resource Report Resource Website 50+ mentions |
CMplot (RRID:SCR_024514) | software resource, software toolkit | Software drawing R package designed for Manhattan plot of genomic analysis. | drawing tool, Manhattan plot of genomic analysis, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/YinLiLin/CMplot | SCR_024514 | Circle Manhattan Plot | 2026-09-12 01:01:18 | 96 | ||||||||
|
maftools Resource Report Resource Website 100+ mentions |
maftools (RRID:SCR_024519) | software resource, software toolkit | Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files. | MAF summarize, MAF analyze, MAF visualize, Mutation Annotation Format files, driver gene identification, pathway, signature, enrichment, association analyses, somatic variants in Mutation Annotation Format, MAF | is listed by: SoftCite | PMID:30341162 | Free, Available for download, Freely available | https://bioconductor.org/packages/maftools/ | SCR_024519 | 2026-09-12 01:01:18 | 233 | ||||||||
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ASPicDB Resource Report Resource Website 1+ mentions |
ASPicDB (RRID:SCR_002102) | ASPicDB | data or information resource, database | A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation. | annotation, splicing pattern, gene, transcript, intron, protein, variant, alternative splicing, splicing, blast, exon, u2, u12, isoform |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bari; Bari; Italy |
Normal, Cancer | PMID:21051348 PMID:18388144 |
Free, Freely available | OMICS_01882 | http://srv00.ibbe.cnr.it/ASPicDB/ | SCR_002102 | Alternative Splicing Prediction Data Base, ASPicDB - A Database tool for alternative splicing analysis | 2026-09-12 01:01:24 | 8 | ||||
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SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-09-12 01:01:36 | 740 | |||||
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RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/, http://www.rnalocate.org/ | SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-09-12 01:00:47 | 24 | ||||||
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SRAMP Resource Report Resource Website 100+ mentions |
SRAMP (RRID:SCR_024500) | simulation software, software application, software resource | Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. | mammalian m(6)A site predictor, sequence derived features based predictor, | is listed by: SoftCite | PMID:26896799 | Free, Available for download, Freely available | SCR_024500 | Sequence-based Rna Adenosine Methylation site Predictor | 2026-09-12 01:00:48 | 452 | ||||||||
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RNAfold Resource Report Resource Website 100+ mentions |
RNAfold (RRID:SCR_024427) | data access protocol, software resource, web service | Web server predict secondary structures of single stranded RNA or DNA sequences. | predict secondary structures, single stranded RNA, DNA sequences, | is listed by: SoftCite | Free, Freely available | SCR_024427 | 2026-09-12 01:00:47 | 100 |
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