Reproducible Research conferences in 2011

January 12, 2011 Links No comments

A sign of reproducible research becoming a mainstream idea is six different events happening this year:

  1. Minisymposium The Digitization of Science: Reproducibility and Interdisciplinary Knowledge Transfer at AAAS Annual Meeting in Washington (organized by Victoria Stodden from Columbia University) on February 19:
    http://aaas.confex.com/aaas/2011/webprogram/Session3166.html
  2. Minisymposium Verifiable, Reproducible Research and Computational Science at SIAM CSE conference in Reno (organized by Jarrod Millman from UC Berkeley) on March 4:
    http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11844
    http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11845
  3. Minisymposium Reproducible Science and Open-Source Software in the Geosciences at SIAM Geosciences conference in Long Beach (organized by Bernd Flemisch from University of Stuttgart, Kristin Flornes from IRIS, and Atgeirr Rasmussen from SINTEF) on March 22-23:
    http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11822
    http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11823
  4. Special session Reproducible Research at Interface 2011 (Statistical, Machine Learning, and Visualization Algorithms) in Cary (organized by Jürgen Symanzik from Utah State University) on June 1:
    http://www.interfacesymposia.org/Interface2011/
  5. Workshop Reproducible Research: Tools and Strategies for Scientific Computing at Applied Mathematics Perspectives conference in Vancouver (organized by Randall LeVeque from University of Washington, Ian Mitchell from UBC, Cleve Moler from Mathworks, and Victoria Stodden from Columbia University) on July 13-16:
    http://www.mitacs.ca/goto/amp_reproducible
  6. Minisymposium Reproducible Research in Computational Science: What, Why and How at ICIAM in Vancouver (organized by Randall LeVeque from University of Washington, Ian Mitchell from UBC, and Victoria Stodden from Columbia University) on July 18-22:
    http://meetings.siam.org/sess/dsp_programsess.cfm?SESSIONCODE=11435

Introducing tkMadagascar – Graphical frontend for Madagascar

January 7, 2011 Programs No comments

I’m pleased today to introduce tkMadagascar, a graphical front end for Madagascar.   tkMadagascar is a very poweful, but simple way for users to create processing flows for Madagascar without needing to use the command line or a text editor.  

Here are some images of tkMadagascar in action:

Creating and configuring Flows, Plots and Results:

Viewing Madagascar program self-documentation:

Most users (>75%) will probably find that they can use tkMadagascar solely in place of command line tools and/or text editors.  However, power users will likely find that it is somewhat limiting (e.g. no Python command support).  

You can dive into tkMadagascar if you are using the development version by updating, and reinstalling Madagascar.  

Additional documentation and tutorials can be found here.

OC-seislet

December 28, 2010 Documentation No comments

A new paper is added to the collection of reproducible documents:
OC-seislet: seislet transform construction with differential offset continuation

Random lines

December 14, 2010 Documentation No comments

Another old paper is added to the collection of reproducible documents:
Random lines in a plane

Modeling fractal media

November 19, 2010 Documentation No comments

Another old paper is added to the collection of reproducible documents:
Modeling 3-D anisotropic fractal media

Banana-doughnut traveltime sensitivity kernels

November 8, 2010 Documentation No comments

Another old paper is added to the collection of reproducible documents:
Traveltime sensitivity kernels: Banana-doughnuts or just plain bananas?

Eikonal perturbation with respect to the source location

October 27, 2010 Documentation No comments

A new paper is added to the collection of reproducible documents:
An eikonal based formulation for traveltime perturbation with respect to the source location

Elastic reverse-time migration

September 18, 2010 Documentation No comments

A new paper is added to the collection of reproducible documents:
Isotropic angle-domain elastic reverse-time migration

Normalization of illumination

September 12, 2010 Documentation No comments

A new paper is added to the collection of reproducible documents:
Stacking angle-domain common-image gathers for normalization of illumination

Addressing the credibility crisis

August 31, 2010 Links No comments

Reproducible Research, a manifest-like paper by a number of authors from different scientific disciplines, is published by Computing in Science and Engineering.

Progress in computational science is often hampered by researchers’ inability to independently reproduce or verify published results. Attendees at a roundtable at Yale Law School formulated a set of steps that scientists, funding agencies, and journals might take to improve the situation. We describe those steps here, along with a proposal for best practices using currently available options and some long-term goals for the development of new tools and standards.