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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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biospytial Resource Report Resource Website 1+ mentions |
biospytial (RRID:SCR_018226) | data visualization software, software toolkit, data analysis software, data management software, software application, data processing software, software resource | Software package as spatial graph based computing engine for ecological big data. Modular open source knowledge engine designed to import, organize, analyse and visualize big spatial ecological datasets using power of graph theory. Handles species occurrences and their taxonomic classification for performing ecological analysis on biodiversity and species distributions. Data are linked with relationships that are stored in graph database, while tabular and geospatial data are stored in relational database management system. | spatial data infrastructure, biodiversity informatics, ecological knowledge engine, ecological data analysis, biodiversity, taxonomic classification, bio.tools |
is listed by: Debian is listed by: bio.tools |
CONACyT ; GBIF ; Lancaster University |
DOI:10.5524/100723 | Free, Available for download, Freely available | biotools:biospytial | https://bio.tools/biospytial | SCR_018226 | 2026-07-31 09:28:14 | 2 | ||||||
|
NetMHCpan Server Resource Report Resource Website 100+ mentions |
NetMHCpan Server (RRID:SCR_018182) | software resource, data access protocol, web service | Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs). | Quantitative prediction, peptide binding, MHC molecule, artificial neural network, Major Histocompatibilty Complex, peptide length, peptide binding affinity, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agencia Nacional de Promoción Científica y Tecnológica ; Argentina ; NIAID |
PMID:19002680 PMID:28978689 |
Free, Available for download, Freely Available | biotools:netmhcpan | https://bio.tools/netmhcpan, https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/ | SCR_018182 | NetMHCpan 1.0, NetMHCpan 3.0, NetMHCpan 2.0, NetMHCpan 4.1, NetMHCpan 4.0, NetMHCpan | 2026-07-31 09:28:14 | 138 | |||||
|
4See Resource Report Resource Website 1+ mentions |
4See (RRID:SCR_018014) | data visualization software, software application, data processing software, software resource | Software tool to visualize 4C data. | Visualize, 4C data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.3389/fgene.2019.01372 | Free, Available for download, Freely available | biotools:4see | https://bio.tools/4see | SCR_018014 | 2026-07-31 09:28:24 | 1 | |||||||
|
TDimpute Resource Report Resource Website 1+ mentions |
TDimpute (RRID:SCR_018306) | data processing software, data analysis software, software application, software resource | Software tool to transfer learning based deep neural network to impute missing gene expression data from DNA methylation data. | Transfer learning; gene expression prediction; DNA methylation; TCGA, neural network, missing gene expression, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/803692 | Free, Available for download, Freely available | biotools:tDimpute, BioTools:TDimpute | https://bio.tools/TDimpute, https://bio.tools/TDimpute, https://bio.tools/TDimpute | SCR_018306 | 2026-07-31 09:28:29 | 1 | |||||||
|
NeuroChaT Resource Report Resource Website 1+ mentions |
NeuroChaT (RRID:SCR_018020) | software toolkit, data analysis software, software application, software resource, data processing software | Software open source python toolbox to analyse neuronal signals recorded in vivo in freely behaving animal, with particular emphasis on spatial coding. Can be used as application programming interface, or as general user interface, and is designed to help simplify adoption of standardised analyses for behavioural neurophysiology and facilitate open data sharing and collaboration between laboratories. | Neuronal signal, analysis, freely behaving animal, spatial coding, behavioural neurophysiology, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Wellcome Trust | DOI:12688/wellcomeopenres.15533.1 | Free, Available for download, Freely available | biotools:NeuroChat | https://bio.tools/NeuroChaT | SCR_018020 | Neuron Characterisation Toolbox | 2026-07-31 09:28:12 | 2 | |||||
|
Online Peri-Event Time Histogram for Open Ephys Resource Report Resource Website 1+ mentions |
Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) | OPETH | data visualization software, software application, data processing software, software resource | Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them. | Open source, open ephys, optogenetics, behavior, electrophysiology data, neuroscience experiment, spike detection, behavior tagging, neuron, histogram, bio.tools |
is listed by: Debian is listed by: bio.tools |
Hungarian Academy of Sciences Lendület Program LP2015-2/2015; European Research Council Starting Grant 715043; Generalitat Valenciana Postdoctoral Fellowship Program APOSTD/2019/003 |
DOI:10.1101/783688 | Free, Available for download, Freely available | biotools:OPEtH | https://bio.tools/OPETH | SCR_018022 | Online Peri-Event Time Histogram | 2026-07-31 09:28:12 | 4 | ||||
|
ΔG prediction server Resource Report Resource Website 10+ mentions |
ΔG prediction server (RRID:SCR_018191) | software resource, data access protocol, service resource, web service | Web server to predict ΔGapp for membrane insertion of potential TM helix. Given amino acid sequence of putative transmembrane helix, server gives prediction of corresponding apparent free energy difference for insertion of this sequence into Endoplasmic Reticulum membrane by means of Sec61 translocon. | Amino acid sequence, putative transmembrane helix, free energy difference, sequence insertion, endoplasmic reticulum membrane, potential TM helix, predict energy difference, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stockholm University; Stockholm; Sweden |
Free, Freely available | biotools:deltag_prediction | http://dgpred.cbr.su.se/index.php?p=TMpred, https://bio.tools/deltag_prediction | SCR_018191 | ΔG prediction server v1.0 | 2026-07-31 09:28:27 | 12 | |||||||
|
Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | data visualization software, data analysis software, software application, software resource, data processing software | Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org, https://bio.tools/mvp_a | SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2026-07-31 09:28:12 | 1 | |||||
|
DichroWeb Resource Report Resource Website 50+ mentions |
DichroWeb (RRID:SCR_018125) | data analysis service, data access protocol, service resource, production service resource, software resource, analysis service resource, web service | Web server for analysis of protein circular dichroism spectra. Provides access to circular dichroism secondary structure calculation algorithms and reference databases. Used in analysis of protein secondary structures. | Analysis, protein, circular dichroism spectra, secondary structure, reference database, algorithm, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of London; London; United Kingdom |
BBSRC | PMID:17896349 PMID:15215473 |
Restricted | biotools:dichroweb | https://bio.tools/dichroweb | SCR_018125 | 2026-07-31 09:28:13 | 62 | ||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | data analysis software, service resource, software application, production service resource, software resource, sequence analysis software, data processing software, analysis service resource | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-07-31 09:28:12 | 5406 | |||||
|
Plant Co-expression Annotation Resource Resource Report Resource Website 1+ mentions |
Plant Co-expression Annotation Resource (RRID:SCR_018429) | Plantannot | data or information resource, data access protocol, 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 | Plantannot v2 | 2026-07-31 09:28:17 | 1 | ||||
|
GalaxyWEB Resource Report Resource Website 100+ mentions |
GalaxyWEB (RRID:SCR_018558) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | 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 |
National Research Foundation of Korea ; Ministry of Land ; Transport and Maritime Affairs of Korea ; Seoul National University |
PMID:22649060 | Free, Freely available | biotools:galaxyweb | https://bio.tools/galaxyweb | SCR_018558 | 2026-07-31 09:28:18 | 157 | ||||||
|
pepwheel Resource Report Resource Website 1+ mentions |
pepwheel (RRID:SCR_018398) | software resource, data access protocol, service resource, web service | Web tool to visualise protein sequences as helices. Draws helical wheel diagram for protein sequence. EMBOSS pepwheel displays peptide sequences in helical representation. | Computational proteomics, data analysis pipeline, label free quantification, mass spectrometry, quantitative proteomics, visualise protein sequence, helical wheel diagram, peptice sequence display, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: EMBOSS works with: Proteome Discoverer |
Free, Freely available | biotools:pepwheel | https://bio.tools/pepwheel | SCR_018398 | 2026-07-31 09:28:16 | 1 | ||||||||
|
MaxAlign Resource Report Resource Website 10+ mentions |
MaxAlign (RRID:SCR_018552) | data analysis service, data access protocol, service resource, production service resource, software resource, analysis service 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 | MaxAlign 1.1, MaxAlign 1.1 Server | 2026-07-31 09:28:17 | 11 | |||||
|
HPEPDOCK Server Resource Report Resource Website 10+ mentions |
HPEPDOCK Server (RRID:SCR_018561) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | 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 |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; Huazhong University of Science and Technology |
PMID:29746661 | Free, Freely available | biotools:hpepdock | https://bio.tools/hpepdock | SCR_018561 | 2026-07-31 09:28:18 | 46 | ||||||
|
GalaxyRefine Resource Report Resource Website 100+ mentions |
GalaxyRefine (RRID:SCR_018531) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | Web server for protein structure prediction, refinement, and related methods. First rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. | Protein structure prediction, protein, structure prediction, protein structure, molecular dynamics simulation, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Seoul National University; Seoul; South Korea |
National Research Foundation of Korea ; Seoul National University. |
PMID:23737448 | biotools:galaxyrefine | https://bio.tools/galaxyrefine | SCR_018531 | 2026-07-31 09:28:17 | 248 | |||||||
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EpiEstim Resource Report Resource Website 10+ mentions |
EpiEstim (RRID:SCR_018538) | software toolkit, data analysis software, software application, software resource, data processing software | Framework and software to estimate time varying reproduction numbers during epidemics. Tools to quantify transmissibility throughout epidemic from analysis of time series of incidence. Used to estimate time varying instantaneous reproduction numbers from incidence time series. | Estimate time varying, reproduction number, epidemics, quantify transmissibility, time series analysis, reproductionc number analysis, incidence time series, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
United Kingdom Medical Research Council | PMID:24043437 | Free, Available for download, Freely available | biotools:EpiEstim | https://bio.tools/EpiEstim | SCR_018538 | Estimate Time Varying Reproduction Numbers from Epidemic Curves | 2026-07-31 09:28:34 | 32 | |||||
|
DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | data analysis software, software application, software resource, data processing software, software tool | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2, https://bio.tools/deseq2 | SCR_015687 | 2026-07-31 09:27:44 | 43994 | |||||||
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FragGeneScan Resource Report Resource Website 100+ mentions |
FragGeneScan (RRID:SCR_011929) | data analysis software, software application, software resource, sequence analysis software, data processing software | A software application for finding fragmented genes in short reads and may be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. | microbiome, sequence analysis, fragment, gene, short read, bio.tools |
is listed by: OMICtools is listed by: Human Microbiome Project is listed by: bio.tools is listed by: Debian has parent organization: Indiana University; Indiana; USA |
Acknowledgement requested, Available for download | OMICS_01484, biotools:fraggenescan | http://omics.informatics.indiana.edu/FragGeneScan/, https://bio.tools/fraggenescan | SCR_011929 | 2026-07-31 09:27:04 | 183 | ||||||||
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Pilon Resource Report Resource Website 1000+ mentions |
Pilon (RRID:SCR_014731) | data analysis software, software application, software resource, sequence analysis software, data processing software | Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome. | automatically, improve, draft, assembly, variation, strain, genome, read, alignment, analysis, inconsistency, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: shovill is hosted by: GitHub |
DOI:10.1371/journal.pone.0112963 DOI:10.1371/journal.pone.0112963 |
Available for download, Acknowledgement requested | OMICS_14553, biotools:pilon | https://github.com/broadinstitute/pilon/wiki, https://bio.tools/pilon, https://sources.debian.org/src/pilon/ | SCR_014731 | 2026-07-31 09:27:33 | 3102 |
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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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