https://www.reproducibility.org
Madagascar is an open-source software package for multidimensional data analysis and reproducible computational experiments. Its mission is to provide
- a convenient and powerful environment
- a convenient technology transfer tool
for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by the users.
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Madagascar is a modern package. It started in 2003 and was publicly released in 2006. It was developed almost entirely from scratch. It is a relatively new package that follows modern software engineering practices such as module encapsulation and test-driven development. The rapid growth of a project of this scope (more than 1,000 main programs and more than 5,000 tests) would not be possible without standing on the shoulders of giants and learning from the 30 years of previous experience in open packages such as SEPlib and Seismic Unix. We have borrowed and reimplemented functionality and ideas from these other packages.
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Madagascar is a test-driven package. Test-driven development is not only an agile software programming practice but also a way of bringing a scientific foundation to geophysical research that involves numerical experiments. Bringing reproducibility and peer review, the backbone of any real science, to computational geophysics is the primary motivation for Madagascar's development. The package consists of two levels: low-level main programs (typically developed in the C programming language and working as data filters) and high-level processing flows (described using the Python programming language) that combine main programs and unambiguously document data processing histories for testing and reproducibility. Experience shows that high-level programming is easily mastered even by beginning students without any previous programming experience.
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Madagascar is an open-source package. It is distributed under the standard GPL open-source license, which does not restrict the usage and modification of the code. Moreover, access to modifying the source repository is not controlled by one organization but shared equally among developers. Sharing the responsibility enables an open collaboration among different groups spread worldwide, in the true spirit of the open-source movement.
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Madagascar uses a simple, flexible, and universal data format that can handle very large datasets but is not tied specifically to seismic data or any other particular kind. This "regularly sampled" format is borrowed from the traditional SEPlib. A universal data format allows us to share general-purpose data processing tools with scientists and engineers from other disciplines.
The primary source of information is the website:
https://www.reproducibility.org/
Additional information:
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Users' mailing list ("RSF-user"): https://lists.sourceforge.net/lists/listinfo/rsf-user
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Developers' mailing list ("RSF-devel"): https://lists.sourceforge.net/lists/listinfo/rsf-devel
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Development blog: http://ahay.org/blog/
See the INSTALL.txt document for build instructions.
While written from scratch, Madagascar borrows ideas from the design of SEPlib, a publicly available software package maintained by Bob Clapp at the Stanford Exploration Project (SEP). Generations of SEP students and researchers contributed to SEPlib. The most significant contributions came from Rob Clayton, Jon Claerbout, Dave Hale, Stew Levin, Rick Ottolini, Joe Dellinger, Steve Cole, Dave Nichols, Martin Karrenbach, Biondo Biondi, and Bob Clapp.
Madagascar was started in 2003 under the name RSF (Regularly Sampled Format) by Sergey Fomel. Since then, many other people have contributed to it. See the AUTHORS.txt file for an incomplete list.
