OpenScience / Science



Octopus – A cool open source TDDFT code

I just found out about Octopus, a quantum mechanics package that does time-dependent density functional theory (TDDFT) calculations using pseudopotential approximations. It works in parallel using MPI and OpenMP and scales to tens of thousands of processors. It also has … Continue reading

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Posted in open science, Science, Software | 3 Comments

Computational Chemistry Highlights

Computational Chemistry Highlights (CCH) is an interesting new overlay journal that identifies important contributions to the field of computational and theoretical chemistry published within the last 1-2 years.  I’m involved in this particular overlay journal – I’ll be concentrating on recent developments … Continue reading

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

Advice to junior faculty who want to do get promoted doing Open Science

I recently sent some advice to a colleague who is coming up for tenure at another university.  He’s quite well known in the Open Science community and is trying to figure out how best to make the case to his … Continue reading

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An informal definition of OpenScience

Over at the open-science mailing list at okfn.org, Michael Nielsen just posted a great “informal” definition of open science:   Open science is the idea that scientific knowledge of all kinds should be openly shared as early as is practical … Continue reading

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Posted in open science, Science | Tagged , | 7 Comments

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

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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

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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

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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

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Posted in open science, Science, Software | 1 Comment

Being Scientific: Fasifiability, 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

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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

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