OpenScience / Software



SciDAVis

Posted on August 17, 2010 by Dan Gezelter

SciDAVis is a free application for Scientific Data Analysis and Visualization. It combines a shallow learning curve and an intuitive, easy-to-use graphical user interface with powerful features such as scriptability and extensibility. SciDAVis runs on GNU/Linux, Windows and MacOS X; … Continue reading →

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Posted in Visualization | Leave a comment

Ascalaph

Posted on July 29, 2010 by Dan Gezelter

Package of molecular graphics and dynamics with an interface to quantum chemistry. GPL Find Ascalaph at: http://www.biomolecular-modeling.com/Ascalaph/index.html

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Posted in Molecular Dynamics, Theoretical and Computational | Leave a comment

LiveGraph: Real-Time Plotter and Exploratory Data Analysis Tool

Posted on March 4, 2010 by Dan Gezelter

Plots data live – while it’s being produced by any application. * Very simple point-and-click interface. * Fully automatic intelligent graph layout. * Single click graph transformations: Linear, Logarithm, Unit Interval, etc. * Time axes support. * APIs for integration … Continue reading →

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Posted in 2D Plotting | Leave a comment

PyBLAW

Posted on March 1, 2010 by Dan Gezelter

PyBLAW is a lightweight Python framework for solving one-dimensional systems of hyperbolic balance laws of the form q_t + f(q)_x = s(q). Find PyBLAW at: http://memmett.github.com/PyBLAW/

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Posted in Numerical Methods | Leave a comment

PyWENO (Python WENO)

Posted on March 1, 2010 by Dan Gezelter

PyWENO is a Python implementation of one-dimensional Weighted Essentially Non-oscillatory (WENO) approximations over unstructured (non-uniform) grids. Find PyWENO (Python WENO) at: http://memmett.github.com/PyWENO/

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Posted in Numerical Methods | Leave a comment

Packmol

Posted on February 19, 2010 by Dan Gezelter

One of the biggest issues you face when you first start doing molecular dynamics (MD) simulations is how to create an initial geometry that won’t blow up in the first few time steps. Repulsive forces are very steep if the … Continue reading →

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Posted in open science, Science, Software | 13 Comments

Gwyddion – Open Source SPM analysis

Posted on February 11, 2010 by Dan Gezelter

We just discovered a very cool open source program for analyzing scanning probe microscopy (SPM) data files. There a number of incompatible and proprietary file formats for surface microscopies (AFM, MFM, STM, SNOM/NSOM) and getting data out from a microscope … Continue reading →

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If you’re going to do good science, release the computer code too

Posted on February 5, 2010 by Dan Gezelter

A very nice aarticle by Darrel Ince has just been posted over at the Guardian. It deals with the climate-gate email theft and the quality of academic science code has just been . An excerpt: Computer code is also at … Continue reading →

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Posted in open science, Science, Software | 1 Comment

Kitware has a blog!

Posted on January 29, 2010 by Dan Gezelter

Geoff Hutchinson just pointed us to the new blog over at Kitware (the makers of VTK).  I’ve found VTK enormously helpful in the past (particularly the source to vtkMath.cxx) and I’m glad they’ve made the commitment to Open Source. My … Continue reading →

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jHepWork

Posted on November 29, 2009 by Dan Gezelter

Data analysis framework Find jHepWork at: http://jwork.org/jhepwork/

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Posted in Computational | Leave a comment