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SimThyr – simulation software for pituitary thyroid feedback

This is a bit outside our normal area of expertise, but it looks interesting. Thyroid hormones play an important role in metabolism, growth and differentiation. Therefore, exact regulation of thyroid hormone levels is vital for most organisms. The mechanism for the feedback … Continue reading

Rating: 5.0. From 12 votes.
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Posted in Science, Software | Tagged , | Leave a comment

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

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

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

Itzï

Itzï is a hydrologic and hydraulic model that simulates 2D surface flows on a regular grid using simplified shallow water equations. It uses GRASS GIS as a back-end for reading entry data and writing results. It simulates surface flows from direct rainfall … Continue reading

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

Reversible Random Number Generators

This news comes by way of John Parkhill, my new colleague here at Notre Dame. William G. Hoover (of the Nosé-Hoover Thermostat) and Carol G. Hoover issued a $500 challenge on arXiv to generate a time-reversible random number generator.  The … Continue reading

Rating: 5.0. From 1 vote.
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Posted in Science, Software | Tagged , , , | 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

Rating: 5.0. From 1 vote.
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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

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

Rating: 4.9. From 16 votes.
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Posted in Open Data, open science, Policy, Science | 52 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

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

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