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Author Archives: Dan Gezelter
SimThyr, a numerical simulator of thyrotropic feedback control for education and research
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
Posted in Medical Sciences, Physiology
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The Up-Goer Five Research Challenge
I thought this was silly at first, but after struggling to do it for my own research, I now think it can be a profound exercise that scientists should attempt before writing their NSF broader impact statements. Here’s the challenge: … Continue reading
Posted in education, Fun, Science
2 Comments
DuMuX
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
Posted in Engineering
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mMass – Open Source Mass Spectrometry Tool
mMass is designed to be feature rich, yet still easy to use. Stay focused on your data interpretation, not on the software. *Supports multiple formats (mZML, mzXML, mzData, MGF, ASCII and copy-Past from clipboard) *Various data processing tools avalaible (Proteomics, … Continue reading
Posted in Analytical
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OpenChrom
OpenChrom is an open source software for chromatography and mass spectrometry based on the Eclipse Rich Client Platform (RCP). Its focus is to handle mass spectrometry systems (e.g. GC/MS, LC/MS, Py-GC/MS, HPLC-MS) data files natively. OpenChrom is able to import … Continue reading
Posted in Analytical
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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
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
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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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