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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DiANNA Resource Report Resource Website 10+ mentions |
DiANNA (RRID:SCR_018529) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | 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, | NSF DBI 0543506; Boston College |
PMID:16844987 PMID:15980459 |
Free, Freely available | http://bioinformatics.bc.edu/clotelab/DiANNA/ | SCR_018529 | DiANNA 1.1 | 2026-08-01 12:06:21 | 47 | |||||||
|
DAMBE Resource Report Resource Website 1+ mentions |
DAMBE (RRID:SCR_018528) | data analysis software, software application, software resource, sequence analysis software, data processing software | 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 |
Natural Science and Engineering Research Council of Canada ; University of Hong Kong ; Hong Kong Research Grant Council |
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 | 2026-08-01 12:06:14 | 7 | |||||
|
BepiPred-2.0 Resource Report Resource Website 1+ mentions |
BepiPred-2.0 (RRID:SCR_018499) | data access protocol, service resource, software application, production service resource, software resource, standalone software, web service, analysis service resource | 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 | 2026-08-01 12:05:59 | 4 | ||||||
|
JetFighter Resource Report Resource Website 1+ mentions |
JetFighter (RRID:SCR_018498) | web application, service resource, production service resource, software resource, analysis service resource | 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 | 2026-08-01 12:06:21 | 1 | |||||||||
|
AmberTools Resource Report Resource Website 500+ mentions |
AmberTools (RRID:SCR_018497) | software resource, software application, software toolkit, simulation software | 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 | 2026-08-01 12:06:14 | 642 | ||||||||||
|
DiscoTope Resource Report Resource Website 50+ mentions |
DiscoTope (RRID:SCR_018530) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | 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 | 2026-08-01 12:05:59 | 99 | |||||||||
|
AllerTop Resource Report Resource Website 100+ mentions |
AllerTop (RRID:SCR_018496) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | 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 | 2026-08-01 12:06:21 | 225 | ||||||||||
|
EpiModel Resource Report Resource Website 1+ mentions |
EpiModel (RRID:SCR_018539) | software toolkit, data analysis software, software application, software resource, data processing software | 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 |
NICHD R01 HD068395; NIMH R21 MH112449; NICHD R21 HD075662; NIDA P30 DA027828; NIAID P30 AI050409; NIAID P30 AI027757; NICHD T32 HD007543 |
PMID:29731699 | Free, Available for download, Freely available | biotools:epimodel | https://bio.tools/epimodel | SCR_018539 | 2026-08-01 12:05:59 | 7 | ||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data processing software, data analysis 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 | 2026-08-01 12:06:21 | 42 | ||||||
|
PhyDyn Resource Report Resource Website 10+ mentions |
PhyDyn (RRID:SCR_018544) | software resource, software application, simulation software | 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 |
NIGMS U01 GM110749; MRC Centre for Global Infectious Disease Analysis |
PMID:30422979 | Free, Available for download, Freely available | SCR_018544 | 2026-08-01 12:06:00 | 10 | ||||||||
|
Pyflakes Resource Report Resource Website |
Pyflakes (RRID:SCR_018422) | data processing software, data analysis software, software application, software resource | Software tool to check Python source files for errors. Passive checker of Python programs Used to analyze programs and detect various errors. Works by parsing source file, not importing it, so it is safe to use on modules with side effects. | Python, check Python source file, check file error, analyze program, detect error | Free, Available for download, Freely available | https://github.com/PyCQA/pyflakes | SCR_018422 | pyflakes 2.2.0 | 2026-08-01 12:06:13 | 0 | |||||||||
|
missForest Resource Report Resource Website 100+ mentions |
missForest (RRID:SCR_018543) | software resource, software application, simulation software | 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 | 2026-08-01 12:06:15 | 156 | ||||||||
|
Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | data or information resource, web service, data access protocol, software resource, application programming interface | 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 | 2026-08-01 12:06:20 | 2 | |||||||
|
PyRx Resource Report Resource Website 500+ mentions |
PyRx (RRID:SCR_018548) | software resource, software application, data processing software, simulation software | 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 | 2026-08-01 12:06:15 | 518 | |||||||||||
|
FHC: Platinum/Iridium microelectrode Resource Report Resource Website 1+ mentions |
FHC: Platinum/Iridium microelectrode (RRID:SCR_018426) | instrument resource | A platinum/iridium electrode use for stimulating tissue samples. Manufactured by FHC Neural microTargeting Worldwide. | stimulating electrode, microelectrode, metal microelectrode, platinum, platinum and iridium, Pt/Ir, FHC, stimtrode, platinum/iridium electrode, Pt/Ir electrode, stimtrode, Pt/Ir stimtrode | Restricted | SCR_018426 | 2026-08-01 12:06:14 | 8 | |||||||||||
|
DIANA Tools Resource Report Resource Website 10+ mentions |
DIANA Tools (RRID:SCR_018425) | project portal, data or information resource, portal, database, service resource, software resource, algorithm resource | Collection of tools to provide algorithms, databases and software for interpreting and archiving data in systematic framework ranging from analysis of expression regulation from deep sequencing data, annotation of miRNA regulatory elements and targets to interpretation of role of ncRNAs in various diseases and pathways. Includes target prediction algorithms microT v4 and microT-CDS, databases of experimentally verified miRNA targets on coding and non-coding RNAs like TarBase v7.0 and LncBase, and software capable of identifying potentially altered molecular pathways by expression of single or multiple miRNAs , mirPath. Provides Web Server (v5.0) to support series of workflows enabling users to perform miRNA analyses. | miRNA data, miRNA regulatory element, miRNA target annotation, ncRNA, target prediction algorithm, miRNA target database, miRNA analysis |
has parent organization: University of Thessaly; Thessaly; Greece provides: DIANA microT-CDS provides: DIANA-mirExTra provides: DIANA-mirPath provides: TarBase provides: TarBase |
Free, Freely available | SCR_018425 | 2026-08-01 12:06:20 | 47 | ||||||||||
|
ProSA-web Resource Report Resource Website 100+ mentions |
ProSA-web (RRID:SCR_018540) | data access protocol, service resource, production service resource, software resource, web service, analysis service resource | 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 | 2026-08-01 12:06:15 | 104 | |||||
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Barzooka Resource Report Resource Website 1+ mentions |
Barzooka (RRID:SCR_018508) | service resource, production service resource, software resource, algorithm resource, analysis service 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 | 2026-08-01 12:06:14 | 3 | ||||||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data visualization software, data analysis software, software application, software resource, data processing software | 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 | 2026-08-01 12:06:14 | 10 | ||||||||||
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Waters: Xevo TQ-XS mass spectrometer Resource Report Resource Website 1+ mentions |
Waters: Xevo TQ-XS mass spectrometer (RRID:SCR_018510) | instrument resource | Advanced benchtop tandem quadrupole mass spectrometer which expands scope of ultimate sensitivity analysis. Fatures probe design which allows users much easier maintenance, optimization and improved reproducibility between operators. Method transfer onto Xevo TQ-XS is made simple by Xtended Dynamic Range detector which allows six orders of linear dynamic range. Wider compound coverage without changing ionization technique is delivered by the revolutionary UniSpray source option. | Benchtop mass spectrometer, instrument, equipment, USEDit | is used by: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility | NIH S10 OD026962 | https://www.waters.com/waters/library.htm?cid=134889751&lid=134891088&locale=en_US, https://www.waters.com/webassets/cms/support/docs/715004990ra.pdf | SCR_018510 | TQ-XS Triple Quad Mass Spectrometer, Xevo TQ-XS, SUMS Xevo | 2026-08-01 12:06:21 | 7 |
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