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OpenScience / open science
10 years of CDK
Today marks (roughly) the tenth birthday of a fantastically successful open science project called the Chemical Development Kit (CDK). At the time the skeleton of the project was set down on my office whiteboard, I was still the lead developer … Continue reading
Posted in open science, Science, Software
3 Comments
Packmol
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 open science, Science, Software
13 Comments
Gwyddion – Open Source SPM analysis
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
Posted in open science, Science, Software
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If you’re going to do good science, release the computer code too
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
Posted in open science, Science, Software
1 Comment
Kitware has a blog!
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
Posted in open science, Software
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Being Scientific: Falsifiability, Verifiability, Empirical Tests, and Reproducibility
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, open science, Science
5 Comments
On Reproducibility
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, open science, Policy, Science
3 Comments
Sad news about Warren DeLano
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
Posted in open science, Science, Software
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What, exactly, is Open Science?
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, open science, Policy, Science
56 Comments
Machine learning open source software
Cheng Soon Ong just emailed me about mloss.org, a community creating a comprehensive open source machine learning environment. Mloss.org is essentially a community portal with lots of detailed information about each of the listed projects. One of the more interesting … Continue reading
Posted in open science, Software
3 Comments