OpenScience / Software



mMass – Open Source Mass Spectrometry Tool

Posted on November 24, 2012 by Dan Gezelter

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 →

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Posted in Analytical | Leave a comment

OpenChrom

Posted on November 24, 2012 by Dan Gezelter

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 →

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Posted in Analytical | Leave a comment

Overture – A C++ toolkit for Solving PDEs in Complex Geometries

Posted on November 16, 2012 by Dan Gezelter

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 →

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SASSIE – Create atomistic models from Small Angle scattering data

Posted on November 8, 2012 by Dan Gezelter

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 →

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Posted in Science, Software | 1 Comment

Jmol goes JavaScript

Posted on November 7, 2012 by Dan Gezelter

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 →

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Octopus – A cool open source TDDFT code

Posted on November 6, 2012 by Dan Gezelter

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 →

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Posted in open science, Science, Software | 3 Comments

Why aren’t voting machines required to be Open Source?

Posted on November 5, 2012 by Dan Gezelter

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 →

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Posted in Policy, Software | Leave a comment

Open source fonts

Posted on September 6, 2012 by Dan Gezelter

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 →

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Posted in Fun, Software | 1 Comment

Data visualization and Digital Research tools

Posted on September 3, 2012 by Dan Gezelter

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 →

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

pyofss – Python-based optical fibre system simulator

Posted on July 9, 2012 by Dan Gezelter

Pyofss allows optical component modules to be grouped together into a system. An optical field is propagated through the system and the evolution of the field viewed at each module. Fibre effects include attenuation, dispersion, self-phase modulation, self-steepening, and Raman … Continue reading →

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Posted in Optics | Leave a comment