«Reproducibility is the hallmark of good science.» http://www.scfbm.org/content/8/1/7/
Git (Version Control System)
Git is a decentralized and distributed version control system (VCS). It's
widely used in the software industry to maintain code repositories.
http://git-scm.com
LaTeX (Typesetting)
LaTeX is a high-quality typesetting system. LaTeX is the de facto standard for
the publication of scientific documents.
http://www.latex-project.org
latex-git-log can be used to typeset the complete Git version history as table written in LaTeX. The typeset output (PDF document) includes the Git revisions (short SHA-1 hash). http://www.ctan.org/tex-archive/support/latex-git-log
SQL Research Database (Snapshots)
All data of the registry is mirrored to a separate SQL database (research database). During the transfer process data transformations take place to bring the data into a tabular structure and to anonymize personal subject data. To ensure full reproducibility of SQL queries we create periodic snapshots of the research database. A snapshot is a complete immutable SQL database with a consistent naming convention (YYYY-MM-DD: e.g. 2013-12-29)
Sweave (R in LaTeX)
Sweave combines R codes and LaTeX documents for reproducing results. It makes it easy to embed R code into LaTeX.
Project Templates
For each new research project a template based Git repository is created. The
template contains a common folder layout, scripts and LaTeX templates. The
deployment of new repositories is managed with Puppet.
https://puppetlabs.com
Secure Shell Access (SSH)
Access control to the Git research repositories and to the SQL server with the research snapshot database is managed with SSH public/private keys.
GitWeb (Git Server)
Git repositories on a Git server have a URL and could be opened to the public by submitting links to the Git repository alongside manuscripts sharing them with reviewers. To lower technical barrier (installing and maintaining a Git server) web-based hosting service for Git repositories such as GitHub or Bitbucket could be used for the collaboration as well.
http://git-scm.com/book/ch4-6.html
About SCQM
The SCQM Foundation runs a scientific platform for prospective long-term studies on inflammatory rheumatic diseases
http://www.scqm.ch
