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Category Archives: Software
Playing with MultiGraph
I’ve been playing around with a cool JavaScript library called MultiGraph which lets you interact with graphical data embedded in a blog post. The data format is a simple little xml file called a “MUGL“. Here’s a sample … Continue reading
Posted in Open Data, open science, Science, Software, Uncategorized
Tagged javascript library, multigraph
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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
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
Posted in Science, Software
Tagged langevin equation, pseudo random number, random number generator, time reversibility
1 Comment
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
Posted in NMR spectroscopy, open science, Science, Software
Tagged molecular dynamics simulations, nmr data analysis
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Overture – A C++ toolkit for Solving PDEs in Complex Geometries
This looks useful! The partial differential equations (PDEs) we solve in my lab are the equations of motion for atoms in molecular dynamics. These are relatively easy to integrate numerically. Lots of labs work with harder PDE problems (like … Continue reading
SASSIE – Create atomistic models from Small Angle scattering data
Here’s a neat bit of “bridge” or “glue” software for today – SASSIE is a python-based suite for creating atomistic models of molecular systems in order to compare those models directly to data from small-angle X-ray scattering (SAXS) and small-angle … Continue reading
Posted in Science, Small-angle Scattering, Software
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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
Posted in open science, Science, Software
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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
Posted in open science, Science, Software
1 Comment
Why aren’t voting machines required to be Open Source?
If ever there was a need for the transparency that open source software brings it is in the realm of voting machine technology. This story makes that point crystal clear. There may or may not be shenanigans going on in … Continue reading
Posted in Policy, Software
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Open source fonts
Adobe released an open source font today called Source Sans Pro. It looks super clean and nearly perfect for user interfaces. Right now it comes in six weights, but a monowidth version is coming soon. (I’m most excited about … Continue reading