OpenScience / Software



OpenAPIs for scientific instrumentation?

Posted on June 17, 2013 by Dan Gezelter

An interesting question from Dale Smith:  Are there OpenAPIs for remote sensing and monitoring of scientific instruments?  Dale pointed us at this very cool RSOE EDIS alert map as an example of what could be possible with distributed consumer-grade sensors … Continue reading →

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

Playing with MultiGraph

Posted on May 21, 2013 by Dan Gezelter

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 →

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SimThyr – simulation software for pituitary thyroid feedback

Posted on May 20, 2013 by Dan Gezelter

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 →

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Reversible Random Number Generators

Posted on May 14, 2013 by Dan Gezelter

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 →

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Posted in Science, Software | Tagged , , , | 3 Comments

Relax – Molecular dynamics by NMR data analysis

Posted on May 9, 2013 by Dan Gezelter

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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Multigraph

Posted on March 21, 2013 by Dan Gezelter

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 →

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Posted in Visualization | Leave a comment

emgr – Empirical Gramian Framework

Posted on February 28, 2013 by Dan Gezelter

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 →

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Posted in Numerical Methods | Leave a comment

relax

Posted on February 21, 2013 by Dan Gezelter

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 →

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Posted in NMR | Leave a comment

SimThyr, a numerical simulator of thyrotropic feedback control for education and research

Posted on February 11, 2013 by Dan Gezelter

SimThyr is a simulation program for the pituitary thyroid feedback control that is based on a parametrically isomorphic model of the overall system. Applications of this program cover research, including development of hypotheses, and education of students in biology and … Continue reading →

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Posted in Medical Sciences, Physiology | Leave a comment

DuMuX

Posted on January 10, 2013 by Dan Gezelter

DuMuX, DUNE for multi-{phase, component, scale, physics, …} flow and transport in porous media, is a free and open-source simulator for flow and transport processes in porous media. It is based on the Distributed and Unified Numerics Environment DUNE, dune-project.org. … Continue reading →

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Posted in Engineering | Leave a comment