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Reproducible Research Tools

Monday, January 24th, 2011

Here is an updated list of existing tools, software and methods that can be used to create or enhance a Reproducible Research Compendium.

  • Sweave -Create dynamic reports (based on LaTeX and R)
  • Babel extension-Babel is Emacs Org-mode ability to execute source codes (R, Octave, Matlab, Python, etc.) within the same document
  • SCons- A part of the Madagascar software package, based on SCons, for managing data processing flows and reproducible computational experiments
  • AMRITA-A system for communicating software-based ideas and information (does not run under Windows)
  • CDEpack-A tool that automatically packages up everything required to execute a Linux command on another computer without any installation or configuration
  • StatDocs-Create interactive statistical documents
  • DynDoc-A set of functions to create and interact with dynamic documents and vignettes in R
  • Cacher and CacheSweave-R packages for caching statistical analyses and Sweave computations
  • Python Tools for RR-Python tools for reproducible research on hyperbolic problems
  • MATLAB Report Generator- Automatically generate reports from MATLAB in a wide variety of formats
  • Emacs Speaks Statistics-Supports editing of scripts and interaction with various statistical analysis programs such S-Plus, R, SAS and Stata

[updates]

  • Sumatra- A tool for managing and tracking projects based on numerical simulation or analysis
  • VisTrails- Create and modify executable workflows and papers

Are you aware of other RR tools? Contact us

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Enhance the Visibility of Your Reproducible Research Compendia

Thursday, June 4th, 2009

… Researchers provide their research compendia on their personal or institutional websites all around the world. This method of providing access to research follows a distributed scheme and brings up some issues about the worldwide visibility of the research compendia.

In such a distributed system, good visibility and retrieval of information are essential for the successful delivery of services. Fortunately, many different systems have been established to improve the information retrieval, notably search engines.

While search engines are vital for the retrieval of information on the Web, they do not index websites equally and may not index new pages for months. This usually leads to a delay in the information retrieval whereas delayed indexing of scientific research is not desirable …

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Reproducible Research Librumbeta is going live!

Wednesday, May 13th, 2009

Reproducible Research Librum is an open directory for reproducible research where you can find many reproducible research compendia and simply add yours.

Reproducible Research Librum is an in-depth approach to provide a comprehensive list of reproducible research websites and compendia.

In brief, Librum aims to increase the visibility of reproducible research compendia over Internet and to facilitate the search and find process for end-users.

|Go to Librum| |Learn more about Librum|

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How to Best Share Your Reproducible Research Compendium

Wednesday, May 6th, 2009

[…] Reproducibility means publication over the internet. Now that you have created your research compendium, you can share it with other researchers in many different ways. For example, you can simply put it on your personal or institutional website. However, if your institution supports an OAI-compliant repository, it is much more advantageous to put your compendium on such a repository.

How to Best Share?

  • Self-Archiving— Providing Open Access to the Research Paper
  • Open Licensing— Providing Open Access to the Code and Data

[…]

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How to Build and Enhance Your Reproducible Research Compendium

Sunday, May 3rd, 2009

To create a reproducible research compendium, you should provide all components of the research that are necessary for others to understand and reproduce the research.

The components of a Reproducible Research Compendium are listed below:

1. The Research Paper
2. The Data
3. The Computational Environment
4. Results
5. Complementary Material

[…] Many different methods are proposed by researchers to enhance a reproducible research compendium and to make it easier for others to adapt and extend the reported research. In this spirit, Literate Programming techniques can be greatly used in the enhancement of a reproducible research compendium […]

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Understand Reproducible Research

Sunday, May 3rd, 2009

What is Reproducible Research?
• Reproducible research refers to the idea that the ultimate product of research is the paper along with the full computational environment used to produce the results in the paper such as the code, data, etc. necessary for reproduction of the results and building upon the research.

• The term reproducible research was first proposed by Professor Jon Claerbout at Stanford University.

• Aside from being a good practice, recent studies show that reproducible research increases the impact of publications. These studies argue that reproducible research compendia are used and cited more often in other papers.

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