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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | analysis service resource, service resource, data analysis service, production service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-07-27 09:33:49 | 4180 | ||||||
|
GenoREAD Resource Report Resource Website |
GenoREAD (RRID:SCR_012007) | GenoREAD | analysis service resource, service resource, data analysis service, production service resource | A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence. | clone, verification, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Virginia Bioinformatics Institute |
PMID:23042248 | Acknowledgement requested | OMICS_01823, biotools:genoread | https://bio.tools/genoread | SCR_012007 | GenoREAD - Sequencing Verification Pipeline | 2026-07-27 09:34:00 | 0 | |||||
|
DSAP Resource Report Resource Website 1+ mentions |
DSAP (RRID:SCR_013352) | DSAP | analysis service resource, service resource, data analysis service, production service resource | A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20478825 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dsap, OMICS_00357 | https://bio.tools/dsap | SCR_013352 | 2026-07-27 09:34:23 | 8 | ||||||
|
PubCrawler Resource Report Resource Website 1+ mentions |
PubCrawler (RRID:SCR_008235) | service resource, software resource | PubCrawler is a free alerting service that scans daily updates to the NCBI Medline (PubMed) and GenBank databases. PubCrawler helps keeping scientists informed of the current contents of Medline and GenBank, by listing new database entries that match their research interests. The free PubCrawler web service has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on a personalized web page whenever new articles appear in PubMed or when new sequences are found in GenBank that are specific to customized queries. The server also acts as an automatic alerting system by sending out short notifications or emails with the latest updates as soon as they become available. PubCrawler searches the NCBI PubMed (Medline) and Entrez (GenBank) databases daily using search parameters (keywords, author names, etc.) specified by the user. There is no limit on the number of searches that can be carried out. Previous search hits are stored and only the newest PubMed or GenBank records are shown each day. The results are presented as an HTML Web page, similar to the results of an NCBI PubMed or Entrez query. This Web page can be located on our computer (the PubCrawler WWW-Service), on your computer (the stand-alone program), or you can receive it via e-mail (set this up using the PubCrawler WWW-Service). The Web page sorts the results into groups of PubMed/GenBank entries that are zero-days-old, 1-day-old, 2-days-old, etc., up to a user-specified age limit. Sponsors: Development of PubCrawler was supported by EMBnet | training tools, bio.tools |
is listed by: 3DVC is listed by: bio.tools is listed by: Debian |
biotools:pubcrawler, nif-0000-21345 | https://bio.tools/pubcrawler | SCR_008235 | PubCrawler | 2026-07-27 09:33:01 | 9 | ||||||||
|
Yabi Resource Report Resource Website |
Yabi (RRID:SCR_005359) | Yabi | service resource, software resource | A web-based analytical environment framework for bioinformatics applications that can be customized for a diverse range of -omics applications. The software system is adaptable to a range of both pluggable execution and data backends in an open source implementation. Enabling seamless and transparent access to heterogenous HPC environments at its core, it then provides an analysis workflow environment that can create and reuse workflows as well as manage large amounts of both raw and processed data in a secure and flexible way across geographically distributed compute resources. Yabi can be used via a web-based environment to drag-and-drop tools to create sophisticated workflows. It can also be accessed through the Yabi command line which is designed for users that are more comfortable with writing scripts or for enabling external workflow environments to leverage the features in Yabi. Configuring tools can be a significant overhead in workflow environments. Yabi greatly simplifies this task by enabling system administrators to configure as well as manage running tools via a web-based environment and without the need to write or edit software programs or scripts. | grid computing, high performance computing, cloud computing, bioinformatics, pipeline, workflow, command line, python, linux, storage, compute, genomics, transcriptomics, proteomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Murdoch University; Perth; Australia |
PMID:22333270 | GNU General Public License, v3 | OMICS_01148, biotools:yabi | https://bio.tools/yabi | SCR_005359 | 2026-07-27 09:32:15 | 0 | ||||||
|
imDEV Resource Report Resource Website 1+ mentions |
imDEV (RRID:SCR_014674) | software application, systems interoperability software, software resource | A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data. | statistical analysis, statistical analysis package, r, r package, excel, data visualization, feature selection, omics, systems interoperability, software, metabolomics, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/bts439 | Supports Microsoft Excel versions 2003-2010 | biotools:imdev | https://sourceforge.net/projects/imdev/, https://bio.tools/imdev | SCR_014674 | Interactive modules for Data Exploration and Visualization, Interactive modules for Data Exploration and Visualization (imDEV) | 2026-07-27 09:34:42 | 8 | ||||||
|
Chromas Resource Report Resource Website 10+ mentions |
Chromas (RRID:SCR_000598) | Chromas | commercial organization, software resource | Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01016, biotools:chromas | https://bio.tools/chromas | SCR_000598 | 2026-07-27 09:31:00 | 16 | |||||||
|
epitopepredict Resource Report Resource Website 1+ mentions |
epitopepredict (RRID:SCR_019221) | software application, simulation software, software resource | Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. | Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:epitopepredict | https://epitopepredict.readthedocs.io/en/latest/, https://bio.tools/epitopepredict | SCR_019221 | 2026-07-27 09:35:54 | 2 | ||||||||
|
runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | web application, software resource | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NSF ; NIH |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | 2026-07-27 09:35:55 | 3 | |||||||
|
BioSimulators Resource Report Resource Website 1+ mentions |
BioSimulators (RRID:SCR_019111) | software repository, web application, software resource | Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects. | Containerized biosimulation tools, consistent interfaces, choosing simulator guide, supported modeling frameworks, simulation algorithms, modeling formats, bio.tools |
is used by: runBioSimulations is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; National Institutes of Health ; National Science Foundation |
Free, Freely available | biotools:biosimulators | https://bio.tools/biosimulators | SCR_019111 | 2026-07-27 09:35:57 | 5 | |||||||
|
AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | software application, workflow software, software resource, data processing software | Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications. | High Performance Computing, HPC environment, rRNA gene amplicons, rRNA marker, gene amplicon pipeline, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:31816087 | Free, Freely available | SCR_019113, biotools:amplicontagger | https://bitbucket.org/jtremblay514/nrc_pipeline_public/src/master/, https://jtremblay.github.io/amplicontagger_guide.html, https://bio.tolols/amplicontagger | SCR_019112 | 2026-07-27 09:35:52 | 3 | |||||||
|
MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | software application, simulation software, software resource | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | MP3 | 2026-07-27 09:35:59 | 2 | |||||
|
NMRProcFlow Resource Report Resource Website 10+ mentions |
NMRProcFlow (RRID:SCR_016592) | software application, data visualization software, software resource, data processing software | Software as graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics. | NMR, metabolomics, data, viewer, spectra, processing, graphical, interface, bio.tools |
uses: R Project for Statistical Computing is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
French National Infrastructure in Metabolomics and Fluxomics | DOI:10.1007/s11306-017-1178-y | Free, Available for download, Freely available | biotools:nmrprocflow, SCR_022777 | https://github.com/INRA/NMRProcFlow, https://bio.tools/nmrprocflow, https://github.com/inra/nmrprocflow | SCR_016592 | Nuclear Magnetic Resonance PROcessing FLOW, Nuclear Magnetic Resonance Processing Flow | 2026-07-27 09:35:19 | 23 | |||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | software application, image processing software, software resource, data processing software | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-07-27 09:35:19 | 64 | ||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | software application, image processing software, software resource, data processing software | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-07-27 09:35:27 | 106 | |||
|
Experimental Design Assistant Resource Report Resource Website 100+ mentions |
Experimental Design Assistant (RRID:SCR_017019) | EDA | service resource, web application, software resource | Web based tool to help in vivo researchers improve design, conduct, analysis and reporting of animal experiments.Provides automated feedback on proposed design and generates graphical summary that aids communication with colleagues, founders and regulatory authorities. Addresses causes of irreproducibility. | in vivo, design, conduct, analysis, reporting, animal, experiment, irreproducibility, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: NC3Rs |
PMID:28957312 | Free, Freely available | biotools:eda | https://bio.tools/eda | SCR_017019 | EDA, Experimental Design Assistant (EDA), Experimental Design Assistant | 2026-07-27 09:35:24 | 187 | |||||
|
PBSIM Resource Report Resource Website 10+ mentions |
PBSIM (RRID:SCR_002512) | software application, simulation software, software resource | Software that simulates PacBio reads by using either a model-based or sampling-based simulation. | pacbio simulation, model-based simulation, sampling-based simulation |
is listed by: OMICtools is listed by: Debian |
PMID:23129296 DOI:10.1093/bioinformatics/bts649 |
Free, Available for download, Freely available | OMICS_00253 | https://sources.debian.org/src/pbsim/ | SCR_002512 | PacBio reads simulator | 2026-07-27 09:31:30 | 11 | ||||||
|
Molecular Dynamics Workflow (BioKepler) Resource Report Resource Website 1+ mentions |
Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) | software application, workflow software, software resource, data processing software | A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like. | workflow, MD, molecular dynamics, simulation, software, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: bioKepler has parent organization: University of California at San Diego; California; USA |
NIGMS P41GM103426 | Requires Linux | biotools:ambergpumdsimulation | http://nbcr.ucsd.edu/data/downloads/workflows/, https://bio.tools/ambergpumdsimulation | SCR_014389 | Molecular Dynamics Workflow, AmberGPUMDSimulation, Molecular Dynamics Workflow Software, Amber GPUMD Simulation | 2026-07-27 09:34:37 | 1 | ||||||
|
HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | software application, workflow software, software resource, data processing software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
France Genomique National infrastructure ; Labex Deep ; European Research Coucil ; ERC Advanced Investigator award ; European Commission ; ABS4NGS project ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes ; Howard Hughes Medical Institute |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | 2026-07-27 09:35:34 | 206 | ||||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | data or information resource, organization portal, consortium, portal | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | 2026-07-28 09:39:58 | 3 |
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