GSOC bid draft

From Madagascar
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1. Describe your organization

Madagascar is a package for scientific data analysis. The existing user base focuses on the field of exploration geophysics (i.e., inverting acoustic data to obtain the deep structure of the earth). Madagascar, however, is designed as a general framework. It's key innovation is in integrating scientific publication with software, in a revolutionary approach known as "reproducible research".

It consists of many loosely coupled components, making it easy to extend. Madagascar has always been a pure open source effort, licensed under GPL and hosted at SOurceForge.

Organizationally, Madagascar is produced by an informal alliance of researchers at various companies and universities. More than 30 people have contributed to development so far.

However, more focused effort is needed to transform the package from its current beta version to a fully functional product. The Google Summer of Code may provide the necessary boost.

Please contact us directly through Dr. Michael Tobis at the Bureau of Economic Geology, at

2. Why is your organization applying to participate in GSoC 2008? What do you hope to gain by participating?

As an academic group, we thrive on the participation of students. As scientists, learning is key to our mission, so we always welcome fellow participants. In particular, we could direct;y benefit from the presence of ambitious students who are adept with modern software methodologies. We expect the learning to be bidirectional.

This said, we also have very high ambitions for our project. We believe that the idea of scientific reproducibility is greatly facilitated by our architecture. Our implementation can be used directly by any data-intensive discipline. More importantly, it can be used as a prototype for other sciences that seek to have computational assistance in the pursuit of reproducibility. We have found that reproducibility as implemented by our group facilitates the intellectual growth of the work group and the advancement of the field as a whole.

The lead author of Madagascar was a co-editor of a recent edition of IEEE COmputing in Science and Engineering, in which these concepts were described at length. Our hope is to expose this approach to a wider community.

3. Did your organization participate in past GSoCs? If so, please summarize your involvement and the successes and challenges of your participation.

Not yet.

4. If your organization has not previously participated in GSoC, have you applied in the past? If so, for what year(s)?

Not yet.

5. Who will your organization administrator be? Please include Google Account information.

Michael Tobis:

6. What license(s) does your project use?

GPL exclusively

7. What is the URL for your ideas page?

8. What is the main development mailing list or forum for your organization?

9. What is the main IRC channel for your organization?

None at present.

10. Does your organization have an application template you would like to see students use? If so, please provide it now.


11. Who will be your backup organization administrator? Please include Google Account information.

Sergey Fomel

12. Who will your mentors be? Please include Google Account information.

  1. Vladimir Bashkardin vbashkardin
  2. Sergey Fomel sergey.fomel
  3. Paul Sava paul.sava
  4. Michael Tobis mtobis

13. What criteria did you use to select these individuals as mentors? Please be as specific as possible.

All are active participants in the development of Madagascar, and have teaching and/or supervisory experience. Mr. Bashkardin is a graduate student with teaching experience and Mr. Bril an independent entrepreneur. The others hold PhD degrees in earth sciences.

14. What is your plan for dealing with disappearing students?

Other than a good faith effort to contact them, none. We would not seek to replace them until the summer of Code ends.

15. What is your plan for dealing with disappearing mentors?

We don't expect this, of course, but we will have a backup mentor ready for each project.

16. What steps will you take to encourage students to interact with your project's community before, during and after the program?

Before the project begins, we will encourage them to look at our online documentation and maximize contact with their mentor. During, we will encourage daily contact, weekly reports and code reviews, and participation in the mailing list. After the completion of the project, we will keep participants informed through our mailing list and invite them to our traditional annual meetings

Participating students with an interest in exploration geophysics will certainly improve their odds of being accepted for graduate work at one of the leading institutions where Madagascar is supported.

17. What will you do to ensure that your accepted students stick with the project after GSoC concludes?

We hope that some of the participants will come to uncerstand our approach to reproducibility in scientific software, and perhaps gain an interest in exploration geophysics,