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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TimeZone Resource Report Resource Website 1+ mentions |
TimeZone (RRID:SCR_018564) | data analysis software, data processing software, software application, software resource | Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes. | Detect footprint, positive selection, functionally adaptive, point mutation, microbial genome | NIAID RC4 AI092828; NIGMS R01 GM084318 |
PMID:23471110 | Free, Available for download, Freely available | SCR_018564 | 2026-09-05 06:28:38 | 1 | |||||||||
|
Doric Neuroscience Studio Resource Report Resource Website 10+ mentions |
Doric Neuroscience Studio (RRID:SCR_018569) | data acquisition software, data processing software, software application, software resource | Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected. | Doric, Doric hardware control, data acquire | Restricted | SCR_018569 | 2026-09-05 06:28:38 | 23 | |||||||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data processing software, data visualization software, software application, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-09-05 06:28:38 | 61 | ||||||
|
DiANNA Resource Report Resource Website 50+ mentions |
DiANNA (RRID:SCR_018529) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Neural network and web server, which determines cysteine oxidation state and disulfide connectivity of protein, given only its amino acid sequence. Used to predict disulfide connectivity topology. Predicts which half-cystines are covalently bound to which other half-cystines. DiANNA 1.1 is extension of DiANNA web server for ternary cysteine classification. | Ternary cysteine classification, cysteine oxidation, disulfide protein connectivity, amino acid sequence, predict disulfide connectivity, connectivity topology, cysteine covalent bound, | Boston College ; NSF DBI 0543506 |
PMID:16844987 PMID:15980459 |
Free, Freely available | http://bioinformatics.bc.edu/clotelab/DiANNA/ | SCR_018529 | DiANNA 1.1 | 2026-09-05 06:28:37 | 55 | |||||||
|
DAMBE Resource Report Resource Website 10+ mentions |
DAMBE (RRID:SCR_018528) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Hong Kong Research Grant Council ; Natural Science and Engineering Research Council of Canada ; University of Hong Kong |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2026-09-05 06:28:37 | 12 | |||||
|
BepiPred-2.0 Resource Report Resource Website 1+ mentions |
BepiPred-2.0 (RRID:SCR_018499) | analysis service resource, data access protocol, production service resource, service resource, software application, software resource, standalone software, web service | Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Sequential predictor, B cell epitope, B cell epitope predictor, B-cell epitope, protein sequence, protein, epitope, sequence | has parent organization: Technical University of Denmark; Lyngby; Denmark | NIH HHSN272201200010C | PMID:28472356 PMID:16635264 |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.cbs.dtu.dk/services/BepiPred-1.0/ | SCR_018499 | BepiPred-1.0, BepiPred | 2026-09-05 06:28:37 | 7 | ||||||
|
JetFighter Resource Report Resource Website 1+ mentions |
JetFighter (RRID:SCR_018498) | analysis service resource, production service resource, service resource, software resource, web application | Web tool that automatically screens bioRxiv preprints for rainbow colormaps, which are not colorblind safe. Emails authors information on replacing these colormaps with colorblind safe alternatives. Screens preprints to improve data representation and colour-blind accessibility. | bioRxiv preprint screening, ranbow colormap, colorblind safe, replacing colormap, improve data, improve picture, ASWG | has parent organization: California Institute of Technology; Pasadena; USA | Free, Freely available | https://github.com/smsaladi/jetfighter | SCR_018498 | 2026-09-05 06:28:37 | 1 | |||||||||
|
AmberTools Resource Report Resource Website 500+ mentions |
AmberTools (RRID:SCR_018497) | simulation software, software application, software resource, software toolkit | Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. | Molecular dynamics simulation, water, Born solvent model, molecular dynamics, molecular modeling | DOI:10.1002/wcms.1121 | SCR_018497 | Amber, AmberTools20, AmberTools MD software packages | 2026-09-05 06:28:37 | 728 | ||||||||||
|
DiscoTope Resource Report Resource Website 100+ mentions |
DiscoTope (RRID:SCR_018530) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server to predict discontinuous B cell epitopes from protein three dimensional structures. | B cell epitope, B cell epitope prediction, discontinous B cell epitope prediction, protein, protein three dimentional structure, protein structure, 3D | European Union Seventh Framework Programme | PMID:23300419 | Free, Freely available | SCR_018530 | 2026-09-05 06:28:37 | 109 | |||||||||
|
AllerTop Resource Report Resource Website 100+ mentions |
AllerTop (RRID:SCR_018496) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin. | Allergen, allergen prediction, physicochemical protein property, protein, protein property, allergen exposure | National Research Fund of the Ministry of Education and Science ; Bulgaria |
PMID:23735058 | SCR_018496 | 2026-09-05 06:28:37 | 352 | ||||||||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics. | Infectious disease, mathematical modeling, simulation, analysis, infectious disease dynamic, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIAID P30 AI027757; NIAID P30 AI050409; NICHD R01 HD068395; NICHD R21 HD075662; NICHD T32 HD007543; NIDA P30 DA027828; NIMH R21 MH112449 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-09-05 06:28:38 | 8 | ||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-09-05 06:28:38 | 46 | ||||||
|
PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | simulation software, software application, software resource | Sofware package for performing Bayesian phylogenetic inference under models that deal with structured populations with complex population dynamics. Enables simultaneous estimation of epidemiological parameters and pathogen phylogenies. Epidemiological modelling in BEAST. | Bayesian phylogenetic inference, epidemiological modelling, epidemiological parameter estimation, pathogen phylogeny estimation |
is related to: BEAST2 is related to: BEAST |
MRC Centre for Global Infectious Disease Analysis ; NIGMS U01 GM110749 |
PMID:30422979 | Free, Available for download, Freely available | SCR_018544 | 2026-09-05 06:28:38 | 10 | ||||||||
|
missForest Resource Report Resource Website 100+ mentions |
missForest (RRID:SCR_018543) | simulation software, software application, software resource | Software R package to impute missing values particularly in case of mixed type data. Non parametric, mixed type imputation method for any type of data for statistical software R. Predicts missing values. | Missing value prediction, mixed type data, non parametric, missing value, mixed data, predictor | is related to: CRAN | PMID:22039212 | Free, Available for download, Freely available | http://stat.ethz.ch/CRAN/ | SCR_018543 | 2026-09-05 06:28:38 | 173 | ||||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | application programming interface, data access protocol, data or information resource, software resource, web service | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-09-05 06:28:36 | 2 | |||||||
|
PyRx Resource Report Resource Website 500+ mentions |
PyRx (RRID:SCR_018548) | data processing software, simulation software, software application, software resource | Open source virtual screening software for computational drug discovery with intuitive user interface. Runs on operating systems Linux, Windows, and Mac OS. Used to screen libraries of compounds against potential drug targets. | Virtual screening, computational drug discovery, drug, medicinal chemistry, target compound, compound screening, compound library, library screening | Restricted | SCR_018548 | 2026-09-05 06:28:38 | 645 | |||||||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling. | Protein structure, protein, protein structure refinement, protein structure validation, protein structure prediction, protein structure modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
FWF Austria ; University of Salzburg ; Austria. |
PMID:17517781 | Free, Freely available | biotools:prosa-web | https://bio.tools/prosa-web | SCR_018540 | Protein Structure Analysis web | 2026-09-05 06:28:38 | 109 | |||||
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Barzooka Resource Report Resource Website 1+ mentions |
Barzooka (RRID:SCR_018508) | algorithm resource, analysis service resource, production service resource, service resource, software resource | Software automated screening tool that detects bar graphs of continuous data in preprints submitted to bioRxiv. Used for detection of bar graphs for continuous data in BioRxiv preprints. | Bar graph detection, continuous data, preprint, bioRxiv, bar graph, ASWG | PMID:35822444 | Free, Available for download, Freely available | SCR_018508 | 2026-09-05 06:28:37 | 5 | ||||||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. | Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization | NSF IIS 1251151 | Free, Available for download, Freely available | SCR_018511 | 2026-09-05 06:28:37 | 11 | ||||||||||
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MP Biochemicals: FastPrep24 Sample Preparation Resource Report Resource Website 10+ mentions |
MP Biochemicals: FastPrep24 Sample Preparation (RRID:SCR_018599) | instrument resource | Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion. | Sample Preparation, Instrument, Equipment, USEDit, ABRF, MP Biochemicals | is listed by: USEDit | SCR_020301, Model_Number_FastPrep24 | https://www.mpbio.com/media/productattachment/LS042019-EN-Sample-Preparation-Brochure.pdf | SCR_018599 | 2026-09-05 06:28:39 | 34 |
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