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Author Archives: Dan Gezelter
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
Not a kickstarter for science, a prize clearinghouse
Yesterday’s post on the reversible random number generators received some interesting reactions from my colleagues. They were uniformly impressed with the solution to what everyone thought was a hard problem, but surprisingly, most of the scientists I talked to were … 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
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
Posted in open science, Science, Software
Tagged molecular dynamics simulations, nmr data analysis
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Multigraph
Multigraph is a program for creating 2-dimensional scientific data graphs in web pages. It can read data in a variety of formats, and allows you to customize the appearance of the graph to your liking. Multigraph provides interactive pan and … Continue reading
Posted in Visualization
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The Tyranny of Pi day
March 14th is -day in the US (and perhaps day in Europe). The idea of a day devoted to celebrating an important irrational number is wonderful — I’d love to see schools celebrate e-day as well, but February 71st isn’t on … Continue reading
Posted in education, Science
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emgr – Empirical Gramian Framework
Empirical gramians can be computed for linear and nonlinear control systems for purposes of model order reduction or system identification. The emgr framework is a compact open source toolbox for gramian-based model reduction and compatible with OCTAVE and MATLAB. Find … Continue reading
Posted in Numerical Methods
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Fantastic news on the Open Access front
The White House just posted a new policy memorandum in response to the Open Access petition: Expanding Public Access to the Results of Federally Funded Research. This is great news for Open Science!
Posted in Open Access, open science, Policy, Science
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relax
relax is a program designed for the study study of molecular dynamics of organic molecules, proteins, RNA, DNA, sugars, and other biomolecules through the analysis of experimental NMR data. It supports exponential curve fitting for the calculation of the R1 … Continue reading
Posted in NMR
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Do.abl.es
Do you want to know how to measure DNA contour lengths using ImageJ? Perhaps you want to stain a C. Elegans embryo for imaging? Or possibly, you might want to test whether or not you have gotten an immune response using ELISA? Martin … Continue reading
Posted in Open Access, open science, Science
Tagged biology experiments, c elegans, open source, open source software, protocols, Science, Software
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