Author Archives: Dan Gezelter

Packmol

Posted on February 19, 2010 by Dan Gezelter

One of the biggest issues you face when you first start doing molecular dynamics (MD) simulations is how to create an initial geometry that won’t blow up in the first few time steps. Repulsive forces are very steep if the … Continue reading →

Posted in Science, Software, open science | 1 Comment

Gwyddion – Open Source SPM analysis

Posted on February 11, 2010 by Dan Gezelter

We just discovered a very cool open source program for analyzing scanning probe microscopy (SPM) data files. There a number of incompatible and proprietary file formats for surface microscopies (AFM, MFM, STM, SNOM/NSOM) and getting data out from a microscope … Continue reading →

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Open Science on “Future Tense”

Posted on February 5, 2010 by Dan Gezelter

Yesterday’s “Future Tense” radio program on Australian Broadcasting was just posted online. The topic was Open Science, and I managed to get interviewed for the show. The interview with Anthony Funnell was a great conversation, and he’s pulled out some … Continue reading →

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If you’re going to do good science, release the computer code too

Posted on February 5, 2010 by Dan Gezelter

A very nice aarticle by Darrel Ince has just been posted over at the Guardian. It deals with the climate-gate email theft and the quality of academic science code has just been . An excerpt: Computer code is also at … Continue reading →

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Kitware has a blog!

Posted on January 29, 2010 by Dan Gezelter

Geoff Hutchinson just pointed us to the new blog over at Kitware (the makers of VTK).  I’ve found VTK enormously helpful in the past (particularly the source to vtkMath.cxx) and I’m glad they’ve made the commitment to Open Source. My … Continue reading →

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Being Scientific: Fasifiability, Verifiability, Empirical Tests, and Reproducibility

Posted on December 1, 2009 by Dan Gezelter

If you ask a scientist what makes a good experiment, you’ll get very specific answers about reproducibility and controls and methods of teasing out causal relationships between variables and observables. If human observations are involved, you may get detailed descriptions … Continue reading →

Posted in Open Data, Science, open science | 1 Comment

On Reproducibility

Posted on November 23, 2009 by Dan Gezelter

I just got back from a fascinating one-day workshop on “Data and Code Sharing in Computational Sciences” that was organized by Victoria Stodden of the Yale Internet Society Project. The workshop had a wide-ranging collection of contributors including representatives of … Continue reading →

Posted in Conferences, Open Data, Policy, Science, open science | 3 Comments

Sad news about Warren DeLano

Posted on November 7, 2009 by Dan Gezelter

I just heard the sad news about Warren DeLano, one of the giants of open source scientific software (and the author of PyMOL). Warren passed away suddenly a few days ago. Like everyone else, I’m stunned and saddened by this … Continue reading →

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What, exactly, is Open Science?

Posted on July 28, 2009 by Dan Gezelter

I was recently asked to define what Open Science means. It would have been relatively easy to fall back on a litany of “Open Source, Open Data, Open Access, Open Notebook”, but these are just shorthand for four fundamental goals: … Continue reading →

Posted in Open Data, Policy, Science, open science | 26 Comments

Saros: Distributed Pair Programming

Posted on June 26, 2009 by Dan Gezelter

I’m a big fan of pair programming, which is one of the primary modes of software development in my research group. Usually, two people sitting together can spot errors that one alone can’t, and the pace of the coding and … Continue reading →

Posted in Science, Software | 1 Comment