APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://www.poissonboltzmann.org/>. Please register at http://goo.gl/LGVU5j before downloading!
Notice: RMG-Java is no longer in active development. Please find the latest version written in Python at http://reactionmechanismgenerator.github.io To see the website o the old Java version of RMG, visit http://rmg.sourceforge.net RMG (Java version) is an automatic chemical reaction mechanism generator that constructs kinetic models composed of elementary chemical reaction steps using a general understanding of how molecules react (currently limited to C, H, O, and S atoms).
Open Source home for the Virtual Cell platform (VCell). See http://vcell.org/ for details.
PCP (Pattern Classification Program) is an open-source machine learning program for supervised classification of patterns. PCP is a binary executable running on Linux and Windows (under Cygwin environment).
Implementation of HYCOM physical ocean model with coupled biogeochemical component to study nitrogen fixation in the Amazon plume. This project is still in development, the code may not be functional at this time.
BMDExpress is a bioinformatics tool used to analyze microarray dose-response data. The analysis provides benchmark dose estimates at which different cellular processes are altered in toxicogenomic experiments.
Old project for GS2. Now moved to the gyrokinetics project.
This is the old project for GS2: Gyrokinetic Turbulence Simulator. Low frequency, electromagnetic turbulence occurs in magnetic fusion experiments, astrophysical plasmas, and basic physics experiments. GS2 is a full-featured, portable, parallel code for gyrokinetic simulation.
This tools produces Gnu Make dependencies for Fortran Source files. The Fortran source files can be in fixed (f77) or free (f90) format. It generates dependencies for include file, #include files and modules.
A 2D Eulerian hydro code using Godunov method. Author Ed Dendy.
Simple console program intended for factor or principal components analysis. It calculates the optimal number of factors using the Horn's parallel analysis, computes the Kaiser-Meyer-Olkin and a few other measures of sampling adequacy.
RPowr is a simple calculator for planning correlational research. It computes the power of the Pearson correlation coefficient allowing adjustment for unreliability and range restriction of the variables (e.g. predictor and criterion measures).