Implementing Reproducible Research

Tools knitr: A Comprehensive Tool for Reproducible Research in R Yihui Xie Reproducibility Using VisTrails Juliana Freire, David Koop, Fernando Chirigati, and Claudio T. Silva Sumatra: A Toolkit for Reproducible Research Andrew P. Davison, Michele Mattioni, Dmitry Samarkanov, and Bartosz Telenczuk CDE: Automatically Package and Reproduce Computational Experiments Philip J. Guo Reproducible Physical Science and the Declaratron Peter Murray-Rust and Dave Murray-Rust Practices and Guidelines Developing Open-Source Scientific Practice K. Jarrod Millman and Fernando Perez Reproducible Bioinformatics Research for Biologists Likit Preeyanon, Alexis Black Pyrkosz, and C. Titus Brown Reproducible Research for Large-Scale Data Analysis Holger Hoefling and Anthony Rossini Practicing Open Science Luis Ibanez, William J. Schroeder, and Marcus D. Hanwell Reproducibility, Virtual Appliances, and Cloud Computing Bill Howe The Reproducibility Project: A Model of Large-Scale Collaboration for Empirical Research on Reproducibility Open Science Collaboration What Computational Scientists Need to Know about Intellectual Property Law: A Primer Victoria Stodden Platforms Open Science in Machine Learning Mikio L. Braun and Cheng Soon Ong RunMyCode.org: A Research-Reproducibility Tool for Computational Sciences Christophe Hurlin, Christophe Perignon, and Victoria Stodden Open Science and the Role of Publishers in Reproducible Research Iain Hrynaszkiewicz, Peter Li, and Scott Edmunds Index