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Author Archives: Dan Gezelter
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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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
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
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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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PhD Comics tackles Open Access
Fantastic comic / video by Jorge Cham on Open Access over at PhD Comics: www.phdcomics.com/comics.php?f=1533 The voices behind the video are Jonathan Eisen and Nick Shockey (director of the Right to Research Coalition), and the discussion covers the insanity of … Continue reading
Posted in Open Access, open science
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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
Data visualization and Digital Research tools
Two new collections of tools that may be of interest to the OpenScience community. Not everything on these lists is Open Source, but many of the visualization and research tools look to be very useful. Hat tip to Eric … Continue reading
Posted in Open Data, open science, Software
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