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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
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
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
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
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
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
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
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
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
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
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
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
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
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
https://www.mpbio.com/fastprep-24-5g-instrument
Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion.
Proper citation: MP Biochemicals: FastPrep24 Sample Preparation (RRID:SCR_018599) Copy
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
http://covidnlp.tavlab.iiitd.edu.in/
Web Application for distilling systemic implications of COVID-19 pandemic with Natural Language Processing.
Proper citation: CovidNLP (RRID:SCR_018513) Copy
https://www.thelabworldgroup.com/mettler-toledo-pb303-precision-balance
Miligram balance that is used for weighing, tarring, percent weighing, and dynamic weighing for unstable samples. Has maximum capacity of 310 grams. Lab balance utilizes mono block weighing technology with permanent shock protection and built in overload protection as well as automatic calibration.
Proper citation: Mettler: PB303-S Milligram Balance (RRID:SCR_018592) Copy
Invitrogen benchtop automated cell counter. Can perform cell counts, viability calculations, hemocytometry, fluorescent protein expression, and measure fluorescence capabilities. There are also reusable slides, fluorescence capabilities, and brightfield fluorescence channels.
Proper citation: Thermo Fisher: Life Technologies: Countess Automated Cell Counter (RRID:SCR_018591) Copy
http://shiny.ieis.tue.nl/sprite/
Web app to generate possible distributions of data matching given mean, SD, sample size, and range. Used for recovering data from summary statistics. Implementation of SPRITE in R programming environment.
Proper citation: rSPRITE (RRID:SCR_018524) Copy
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