Reproducible Papers

This is will become a curated list of papers that are computationally reproducible by modern standard.

Please make a PR to add new papers to the list. Papers may be cathegorized for topic and technology. See here.

Motivation

Implementing a perfectly replicable and reproducible code for scientific computing is a challenging task, and perfection is nearly impossible. However imperfect reproducibility is better than no reproducibility.

Thanks to the efforts of a few authors and new emerging technologies, a growing number of papers are more reproducible than ever before.

This list serves to highlight exemplary works that apply best-efforts in reproducibility using current tools. They may be not perfect, but they represent practical examples that can be readily followed by a broder scientific community.

Criteria for inclusion

• the paper has been peer-reviewed
• depends on open source software (e.g. python, R, not MATLAB)
• paper's software available in a public repository (github, bitbucket, etc.)
• use open data, available for download
• allows replicating the figures and results
• use some method to replicate the "exact" software environment (e.g. conda environments, docker container, etc.)

Reproducible Papers List

• How much of the world is woody?
  Richard G. FitzJohn, Matthew W. Pennell, Amy E. Zanne, Peter F. Stevens, David C. Tank, William K. Cornwell 2014
  DOI: 10.1111/1365-2745.12260
  Repository: https://github.com/richfitz/wood

• Adaptive Engagement of Cognitive Control in Context-Dependent Decision Making
  Michael L. Waskom, Michael C. Frank and Anthony D. Wagner. 2016
  DOI: 10.1093/cercor/bhv333
  Repository: https://github.com/WagnerLabPapers/Waskom_CerebCortex_InPress

• A data repository and analysis framework for spontaneous neural activity recordings in developing retina
  Eglen SJ, Weeks M, Jessop M, Simonotto J, Jackson T, Sernagor E. 2014
  DOI: 10.1186/2047-217X-3-3)
  Repository: https://github.com/sje30/waverepo

• Bivariate spatial point patterns in the retina: a reproducible review
  Eglen SJ,. 2016
  DOI: None. Paper
  Repository: https://github.com/sje30/eglen2015

• Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant
  Andreas Bremges, Irena Maus, Peter Belmann, Felix Eikmeyer, Anika Winkler, Andreas Albersmeier, Alfred Pühler, Andreas Schlüter and Alexander Sczyrba
  DOI: 10.1186/s13742-015-0073-6
  Repository: https://github.com/metagenomics/2015-biogas-cebitec