Table of Contents: PLOS Computational Biology: Software


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The PLOS Computational Biology Software Section was launched in 2011 and has been steadily gathering momentum since its beginnings. Handled by our Software Editors, Software articles highlight and describe outstanding open source software of exceptional importance that has been shown to provide new biological insights, either as a part of the Software article, or published elsewhere. New articles will be added to the Software collection as they are published.


Research Articles

A RESTful API for Accessing Microbial Community Data for MG-RAST

Andreas Wilke, Jared Bischof, Travis Harrison, Tom Brettin, Mark D'Souza, Wolfgang Gerlach, Hunter Matthews, Tobias Paczian, Jared Wilkening, Elizabeth M. Glass, Narayan Desai, Folker Meyer

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

Markus Niklasson, Alexandra Ahlner, Cecilia Andresen, Joseph A. Marsh, Patrik Lundström

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond

NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles

Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi, Satoshi Tabata

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products

Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling

OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

Greg Finak, Jacob Frelinger, Wenxin Jiang, Evan W. Newell, John Ramey, Mark M. Davis, Spyros A. Kalams, Stephen C. De Rosa, Raphael Gottardo

CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion

Christophe Restif, Carolina Ibáñez-Ventoso, Mehul M. Vora, Suzhen Guo, Dimitris Metaxas, Monica Driscoll

A Toolbox for Representational Similarity Analysis

Hamed Nili, Cai Wingfield, Alexander Walther, Li Su, William Marslen-Wilson, Nikolaus Kriegeskorte

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond

rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Sergio Ruiz-Carmona, Daniel Alvarez-Garcia, Nicolas Foloppe, A. Beatriz Garmendia-Doval, Szilveszter Juhos, Peter Schmidtke, Xavier Barril, Roderick E. Hubbard, S. David Morley

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky

CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis

Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, Gregory W. Carter

ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data

André Yoshiaki Kashiwabara, Ígor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham

Using Biological Pathway Data with Paxtools

Emek Demir, Özgün Babur, Igor Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin Gross, Onur Selçuk Sümer, Gary D. Bader, Chris Sander

Software for Computing and Annotating Genomic Ranges

Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin T. Morgan, Vincent J. Carey

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

Umadevi Paila, Brad A. Chapman, Rory Kirchner, Aaron R. Quinlan

Chaste: An Open Source C++ Library for Computational Physiology and Biology

Gary R. Mirams, Christopher J. Arthurs, Miguel O. Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G. Fletcher, Daniel G. Harvey, Megan E. Marsh, James M. Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, David J. Gavaghan

Spartan: A Comprehensive Tool for Understanding Uncertainty in Simulations of Biological Systems

Kieran Alden, Mark Read, Jon Timmis, Paul S. Andrews, Henrique Veiga-Fernandes, Mark Coles

Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics

Hamish Cunningham, Valentin Tablan, Angus Roberts, Kalina Bontcheva

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes

Kishore R. Mosaliganti, Ramil R. Noche, Fengzhu Xiong, Ian A. Swinburne, Sean G. Megason

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

Eva Chovancova, Antonin Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlikova, Artur Gora, Vilem Sustr, Martin Klvana, Petr Medek, Lada Biedermannova, Jiri Sochor, Jiri Damborsky

Automated Tracking of Whiskers in Videos of Head Fixed Rodents

Nathan G. Clack, Daniel H. O'Connor, Daniel Huber, Leopoldo Petreanu, Andrew Hires, Simon Peron, Karel Svoboda, Eugene W. Myers

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

John A. Capra, Alexander G. Williams, Katherine S. Pollard

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

Alexander Favorov, Loris Mularoni, Leslie M. Cope, Yulia Medvedeva, Andrey A. Mironov, Vsevolod J. Makeev, Sarah J. Wheelan

AutoClickChem: Click Chemistry in Silico

Jacob D. Durrant, J. Andrew McCammon