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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Datanator Resource Report Resource Website 1+ mentions |
Datanator (RRID:SCR_018651) | application programming interface, data access protocol, data or information resource, database, software resource, web application | Software toolkit for discovering data needed to build, calibrate, and validate mechanistic models of cells. Integrated database of molecular data for quantitatively modeling cellular behavior. Web application for identifying relevant data for modeling specific organism in specific environmental condition. | Data discovering, cell model, model cellular biochemistry, modeling specific organism, specific environmental condition, genomics, proteomics, epigenomics, metabolomics, system biology, bio.tools |
uses: BpForms is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NIBIB P41 EB023912; NIGMS R35 GM119771 |
DOI:10.1101/2020.08.06.240051 | Free, Freely available | biotools:datanator, r3d100013339 | https://github.com/karrlab/datanator, https://bio.tools/datanator, https://doi.org/10.17616/R31NJMSB | SCR_018651 | SciCrunch Registry | 2026-09-26 02:16:10 | 2 | ||||||
|
Protein Interactions Calculator Resource Report Resource Website 10+ mentions |
Protein Interactions Calculator (RRID:SCR_018574) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web server for inter residue interaction calculations in single site. Determines accessible surface area and residue depth, which is distance of residue from surface of protein. Recognizes specific kind of interactions, such as apolar–apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near surface or deep inside. Recognizes interactions including disulphide bonds, hydrophobic interactions, ionic interactions, hydrogen bonds, aromatic- aromatic interactions, aromatic-sulphur interactions and cation interactions within protein or between proteins in complex. | Protein interaction, interaction calculation, single site, accessible surface are, residue depth, protein surface, residue distance, residue interaction, protein complex, bio.tools |
is listed by: Debian is listed by: bio.tools |
Department of Biotechnology Government of India | PMID:17584791 | Free, Freely available | biotools:pic | https://bio.tools/pic | http://crick.mbu.iisc.ernet.in/~PIC | SCR_018574 | SciCrunch Registry | 2026-09-26 02:16:09 | 34 | |||||
|
LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG003749; NIDA U54 DA021519; NIEHS P30 ES06096; NIEHS U01 ES015675; NLM R01 LM008106 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | SciCrunch Registry | 2026-09-26 02:16:09 | 4 | ||||||
|
Plant Co-expression Annotation Resource Resource Report Resource Website 1+ mentions |
Plant Co-expression Annotation Resource (RRID:SCR_018429) | Plantannot | data access protocol, data or information resource, service resource, software resource, web service | Webserver for identifying targets for genetically modified crop breeding pipelines. Used to find proteins that have no annotation or function assigned and could be related to molecular mechanisms regarding abiotic stresses in plants. System aggregates orthology, coexpression networks and genomic data to filter genomes of plants downloaded from Phytozome and NCBI and select candidate proteins in that regard. | Omics, plant, annotation, function, breeding, genetically modified crops, abiotic stress in plant, plant genome, plant genomic data, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Phytozome is related to: NCBI is related to: Machado |
Embrapa | DOI:10.1101/2020.05.22.110510 | Free, Freely available | biotools:plantannot | https://www.machado.cnptia.embrapa.br/plantannot2, https://bio.tools/plantannot | SCR_018429 | SciCrunch Registry | Plantannot v2 | 2026-09-26 02:16:07 | 1 | ||||
|
GalaxyWEB Resource Report Resource Website 100+ mentions |
GalaxyWEB (RRID:SCR_018558) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for protein structure prediction and refinement. Used to predict protein structure from sequence by template based modeling. Used for refinement after providing starting model structure and locations of loops or termini to be refined. | Protein structure prediction, protein structure refinement, protein sequence, template based modeling, model structure, loop location, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
Ministry of Land ; Transport and Maritime Affairs of Korea ; National Research Foundation of Korea ; Seoul National University |
PMID:22649060 | Free, Freely available | biotools:galaxyweb | https://bio.tools/galaxyweb | SCR_018558 | SciCrunch Registry | 2026-09-26 02:16:09 | 231 | ||||||
|
MaxAlign Resource Report Resource Website 10+ mentions |
MaxAlign (RRID:SCR_018552) | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, web service | Web tool for maximizing usable data in alignment. Maximizes number of characters that are present in gap free columns alignment area by selecting optimal subset of sequences. Removes sequences with many gaps in post process of alignments in order to improve alignment area. | Maximizing data, post process alignment, gap free column alignment area, sequence subset selection, improve alignment area, bio.tools |
is listed by: Debian is listed by: bio.tools |
Foundation for Science and Technology Portuguese Ministry of Science. | PMID:17725821 | Free, Available for download, Freely available | biotools:maxalign | https://bio.tools/maxalign | SCR_018552 | SciCrunch Registry | MaxAlign 1.1, MaxAlign 1.1 Server | 2026-09-26 02:16:09 | 11 | |||||
|
HPEPDOCK Server Resource Report Resource Website 50+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for blind peptide protein docking based on hierarchical algorithm. Blind peptide-protein docking by fast modeling of peptide conformations and global sampling of binding orientations. | Blind peptide protein docking, peptide conformation modeling, global sampling, blind orientation, protein, modeling, docking, bio.tools |
is listed by: bio.tools is listed by: Debian |
Huazhong University of Science and Technology ; National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | SciCrunch Registry | 2026-09-26 02:16:09 | 73 | ||||||
|
Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | SciCrunch Registry | 2026-09-26 02:16:14 | 56 | ||||||||
|
LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data analysis software, data processing software, software application, software resource | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agriculture and AgBioResearch at Michigan State University ; NSF IOS 1740874; United States Department of Agriculture National Institute of Food |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | SciCrunch Registry | 2026-09-26 02:16:14 | 15 | ||||||
|
metaXplor Resource Report Resource Website 1+ mentions |
metaXplor (RRID:SCR_019025) | data or information resource, software resource, web application | Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures. | Data storage, metagenomics, data filtering, data sharing, data exploration, metagenomic data, viral data, microbial data, data manager, datasets sharing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Restricted | biotools:metaxplor | https://metaxplor.cirad.fr/metaXplor/, https://bio.tools/metaxplor | SCR_019025 | SciCrunch Registry | 2026-09-26 02:16:14 | 1 | ||||||||
|
GigaSOM.jl Resource Report Resource Website 1+ mentions |
GigaSOM.jl (RRID:SCR_019020) | data processing software, data visualization software, software application, software resource | Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets. | Flow cytometry data, flow cytometry data clustering, data clustering, data visualization, Julia, datasets, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/2020.08.03.234187 | Free, Available for download, Freely available | biotools:GigaSOM.jl | https://bio.tools/GigaSOM.jl | SCR_019020 | SciCrunch Registry | 2026-09-26 02:16:14 | 2 | |||||||
|
TRAL Resource Report Resource Website 1+ mentions |
TRAL (RRID:SCR_018979) | TRAL | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions. | Annotation, tandem repeats annotation, amino acid repeats, nucleic data, statistical analysis, redundant predictions filtering, redundant annotation clustering, overlapping annotations clustering, false positive annotation filtering, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research ; and Innovation |
DOI:10.1093/bioinformatics/btv306 | Free, Freely available | biotools:tral | https://bio.tools/tral | SCR_018979 | SciCrunch Registry | Tandem Repeat Annotation Library | 2026-09-26 02:16:14 | 1 | ||||
|
PrognoScan Resource Report Resource Website 100+ mentions |
PrognoScan (RRID:SCR_018740) | analysis service resource, data or information resource, database, production service resource, service resource | Database for meta analysis of prognostic value of genes from server at Kyushu Institute of Technology. Collection of publicly available cancer microarray datasets with clinical annotation, as well as tool for assessing biological relationship between gene expression and prognosis. Provides platform for evaluating potential tumor markers and therapeutic targets. | Kyushu Institute of Technology, meta analysis, prognostic gene value, cancer microarray dataset, clinical annotation, gene expression, tumor marker, therapeutic target, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:19393097 | Free, Freely available | SCR_018741, biotools:prognoscan | http://dna00.bio.kyutech.ac.jp/PrognoScan/index.html, https://bio.tools/prognoscan | SCR_018740 | SciCrunch Registry | 2026-09-26 02:16:11 | 461 | |||||||
|
Evolutionary Couplings Server Resource Report Resource Website 10+ mentions |
Evolutionary Couplings Server (RRID:SCR_018745) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server provides functional and structural information about proteins from their evolutionary record using methods from statistical physics. Computes evolutionary couplings from sequence alignments and predicts 3D structure for your protein of interest. Allows to run former EVcouplings, EVmutation, EVfold and EVcomplex jobs. | Coevolutionary sequence analysis, evolutionary coupling, protein sequence, RNA sequence alignment, predict protein structure, evolutionary sequence covariantion, 3D protein structure prediction, , bio.tools |
is listed by: bio.tools is listed by: Debian |
DOE CSGF fellowship ; NIGMS R01 GM106303; NSF GRFP DGE1144152 |
PMID:30304492 | Free, Freely available | biotools:EVcouplings | https://github.com/debbiemarkslab/evcouplings, https://bio.tools/EVcouplings | SCR_018745 | SciCrunch Registry | EVcouplings | 2026-09-26 02:16:11 | 26 | |||||
|
VICMpred Resource Report Resource Website 1+ mentions |
VICMpred (RRID:SCR_019039) | data access protocol, software resource, web service | Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule. | Bacterial protein, protein functional classification, virulence factor, metabolism molecule, information molecule, cellular process, gram negative bacteria, functional proteins prediction, amino acid patterns, aminoacid composition, dipeptide composition, bacterial protein sequences., bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research and Department of Biotechnology ; Government of India |
PMID:16689701 | Free, Freely available | biotools:vicmpred | https://bio.tools/vicmpred | SCR_019039 | SciCrunch Registry | Cellular process and Metabolism molecule in the bacterial proteins., Information molecule, Prediction of Virulence factors | 2026-09-26 02:16:14 | 3 | |||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | data access protocol, data or information resource, software resource, web service | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Australian Research Council Laureate Fellowship ; Natural Sciences and Engineering Research Council of Canada ; NSERC Discovery Grant ; Ontario Early Researcher award ; Tier II Canada Research Chair |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | SciCrunch Registry | AnnoTree 1.2 | 2026-09-26 02:16:14 | 25 | |||||
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Pyntacle Resource Report Resource Website 1+ mentions |
Pyntacle (RRID:SCR_019030) | data analysis software, data processing software, network analysis software, software application, software resource | Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools. | Graph analysis, topology, group centrality, systems biology, parallel computing, data conversion tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:pyntacle | https://bio.tools/pyntacle | SCR_019030 | SciCrunch Registry | 2026-09-26 02:16:14 | 1 | ||||||||
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IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | SciCrunch Registry | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-09-26 02:16:14 | 4 | ||||||
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ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | SciCrunch Registry | 2026-09-26 02:16:14 | 1 | ||||||||
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DicomTypeTranslator Resource Report Resource Website 1+ mentions |
DicomTypeTranslator (RRID:SCR_018878) | data management software, software application, software resource | Open source software tool to extract metadata from DICOM files for indexing and storage in SQL database. | DICOM SQL conversion, DICOM file, metadata extraction, SQL database, indexing and storage, file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:dicomtypetranslation | https://bio.tools/dicomtypetranslation | SCR_018878 | SciCrunch Registry | 2026-09-26 02:16:13 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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