PyParticles is a particle simulation toolbox entirely written in Python. It simulates a particle-by-particle model with the most popular integrations methods, including Euler, Runge Kutta, and Midpoint. It represents the results on an OpenGL or Matplotlib plot, and offers an easy-to-use API.
iNA is a computational tool for quantitative analysis of fluctuations in biochemical reaction networks. Such fluctuations, also known as intrinsic noise, arise due to the stochastic nature of chemical reactions and cannot be ignored for when some molecules are present only in very low copy numbers as is the case in living cells. The SBML-based software computes statistical measures such as means and standard deviations of concentrations within a given accuracy using the analytical system size expansion. The result of iNA’s analysis can be tested against the computationally much more expensive stochastic simulation algorithm.
h5tools provides third-party tools for working with data where the underlying storage object is HDF5. The toolkit currently has two utilities in it: The HDF5 NeXus writer API is a set of functions which allows writing data in the NeXus data format, using only HDF5 function calls. H5merge will merge any two HDF5 or NetCDF4 files.
F-Engrave generates g-code tool paths for CNC machines using CXF fonts, true type fonts (TTF), or a 2D DXF file. It can generate tool paths for engraving or v-carving text or a DXF design. The output of F-Engrave can be imported into EMC2, MACH3, or other machine controllers. F-Engrave output can be reopened by F-Engrave for later editing. F-Engrave designs can also be exported as SVG files.
Open Grid Scheduler/Grid Engine is a batch-queuing system for distributed resource management. It is used by many high-performance clusters and computation farms. Together with basic batch job scheduling, it supports advance reservation, array jobs, parallel make, parallel job management, and GPU management.
MakeHuman is software for the modelling of three-dimensional humanoid characters. Features that make this software unique include a highly intuitive GUI and a high quality mesh, optimized to work in subdivision surface mode (for example, Zbrush). Using MakeHuman, a photo-realistic character can be modelled in less than 2 minutes.
Chebfun is a collection of algorithms and a software system in object-oriented MATLAB that extends familiar powerful methods of numerical computation involving numbers to continuous or piecewise-continuous functions. It also implements continuous analogues of linear algebra notions like the QR decomposition and the SVD, and solves ordinary differential equations. The mathematical basis of the system combines tools of Chebyshev expansions, fast Fourier transform, barycentric interpolation, recursive zerofinding, and automatic differentiation.