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http://clavius.bc.edu/~clotelab/DiANNA/

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.

Proper citation: DiANNA (RRID:SCR_018529) Copy   

•   Source: SciCrunch Registry

http://dambe.bio.uottawa.ca/DAMBE/dambe.aspx

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.

Proper citation: DAMBE (RRID:SCR_018528) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/BepiPred/index.php

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.

Proper citation: BepiPred-2.0 (RRID:SCR_018499) Copy   

•   Source: SciCrunch Registry

https://jetfighter.ecrlife.org

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.

Proper citation: JetFighter (RRID:SCR_018498) Copy   

•   Source: SciCrunch Registry

https://ambermd.org/AmberTools.php

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.

Proper citation: AmberTools (RRID:SCR_018497) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/DiscoTope/

Web server to predict discontinuous B cell epitopes from protein three dimensional structures.

Proper citation: DiscoTope (RRID:SCR_018530) Copy   

•   Source: SciCrunch Registry

https://www.ddg-pharmfac.net/AllerTOP/

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.

Proper citation: AllerTop (RRID:SCR_018496) Copy   

•   Source: SciCrunch Registry

https://www.epimodel.org/

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.

Proper citation: EpiModel (RRID:SCR_018539) Copy   

•   Source: SciCrunch Registry

https://github.com/blackrim/phyutility

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.

Proper citation: Phyutility (RRID:SCR_018545) Copy   

•   Source: SciCrunch Registry

https://github.com/mrc-ide/PhyDyn

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.

Proper citation: PhyDyn (RRID:SCR_018544) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pyflakes/

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.

Proper citation: Pyflakes (RRID:SCR_018422) Copy   

•   Source: SciCrunch Registry

https://github.com/stekhoven/missForest

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.

Proper citation: missForest (RRID:SCR_018543) Copy   

•   Source: SciCrunch Registry

https://github.com/lmb-embrapa/machado

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.

Proper citation: Machado (RRID:SCR_018428) Copy   

•   Source: SciCrunch Registry

https://pyrx.sourceforge.io/

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.

Proper citation: PyRx (RRID:SCR_018548) Copy   

•   Source: SciCrunch Registry

https://www.fh-co.com/product/metal-microelectrodes/

A platinum/iridium electrode use for stimulating tissue samples. Manufactured by FHC Neural microTargeting Worldwide.

Proper citation: FHC: Platinum/Iridium microelectrode (RRID:SCR_018426) Copy   

•   Source: SciCrunch Registry

http://diana.imis.athena-innovation.gr/DianaTools

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.

Proper citation: DIANA Tools (RRID:SCR_018425) Copy   

•   Source: SciCrunch Registry

https://prosa.services.came.sbg.ac.at/prosa.php

Web service is extension of classic ProSA program used for refinement and validation of experimental protein structures and in structure prediction and modeling.

Proper citation: ProSA-web (RRID:SCR_018540) Copy   

•   Source: SciCrunch Registry

https://github.com/quest-bih/barzooka

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.

Proper citation: Barzooka (RRID:SCR_018508) Copy   

•   Source: SciCrunch Registry

https://github.com/OHDSI/CohortMethod

Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.

Proper citation: CohortMethod (RRID:SCR_018511) Copy   

•   Source: SciCrunch Registry

https://mass-spec.stanford.edu/instruments

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.

Proper citation: Waters: Xevo TQ-XS mass spectrometer (RRID:SCR_018510) Copy   

•   Source: SciCrunch Registry