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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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Rating: 5.0. From 5 votes.
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Posted in open science, Science, Software | 1 Comment

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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Rating: 5.0. From 3 votes.
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Posted in open science, Science, Software | 3 Comments

Relax – Molecular dynamics by NMR data analysis

Edward d’Auvergne pointed out the relax program, which looks like a useful way to connect experimental NMR spectra with molecular dynamics simulations. relax is designed for the study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other … Continue reading

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Rating: 5.0. From 1 vote.
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Posted in open science, Science, Software | Tagged , | Leave a comment

Quantum Espresso!

I just got email from Brandon Wood about an open source project called Quantum Espresso (formerly known as PWSCF), which is a rather extensive open-source project for DFT-based electronic structure calculations. It appears to be a refactoring of some established … Continue reading

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Rating: 5.0. From 1 vote.
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Posted in open science, Science, Software | 5 Comments

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

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Rating: 4.9. From 16 votes.
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Posted in Open Data, open science, Policy, Science | 53 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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Rating: 4.8. From 5 votes.
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Posted in open science, Science, Software | Leave a comment

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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Rating: 4.7. From 14 votes.
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Posted in open science, Science, Software | 13 Comments

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

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Rating: 4.5. From 2 votes.
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Posted in open science, Software | Leave a comment

Jmol goes JavaScript

About 10 years ago, I turned the Jmol project over to a series of fantastic lead developers (Jmol programmers regenerate in different bodies just like Doctor Who does).  Since then, the aspect of the new work on Jmol that has … Continue reading

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Rating: 4.4. From 8 votes.
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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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Rating: 4.3. From 6 votes.
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Posted in Open Data, open science, Science | 1 Comment