Open Source Linux Mathematics Software

This is a Matlab software package for single molecule FRET data analysis.

MORphological PHenotype Extraction (MORPHE) is a suite of automated image processing, visualization, and classification algorithms to facilitate the analysis of heritable and clonal red-to-green transitions that occurred during the growth of a colony.

This software has moved to http://www.poissonboltzmann.org/.

Develop a basic understanding of the behavior of polar spherical coordinates through selected examples. Provide sample files for diverse mathematics engines

Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with nontrivial insights into the origins of stochasticity, in total however they constitute a patchwork of different theoretical analyses. Here we present a flexible and generally applicable noise decomposition tool, that allows us to calculate contributions of individual reactions to the total variability of a system’s output. With the package it is therefore possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that it is possible to infer noise contributions resulting from individual reactions directly from experimental data. This is the first computational tool that allows to decompose noise into contributions resulting from individual reactions.

Collection of utilities based on two basics classes: Matematica and VarData. Matematica) performs math operations on vectors and matrices for smoothing, interpolation, convolution, image processing... VarData) manipulate a structure of points connected by links. Addraw) openGL engine. ElPoly) analyze mechanical properties of polymer and membrane like structures. Addyn) perform molecular dynamics and Monte Carlo simulations and has a solver for 4th oder PDE. Avvis) perform all the operation of Matematica on different sets of data visualized on a Qt graphical interface. DrImage) image manipulation on the Matematica filters. The program is intended to use as less as possible external libs (optional: openGL, gsl, fftw, cgal, png, tiff, boost, MPI, Qt...).

This project provides visual interactive interfaces to custom algorithms used in genomes research.

gfit creates an interface between computational models and experimental data and provides tools for their analysis

GLARE is a library and a software for product based optimization of reagent lists in the context of a chemical combinatorial library design. Large virtual combinatorial libraries containing 10^12 products have been optimized within a second.

SpecMark (spectral Markov) is a method for calculating the joint probability distribution over species in a regulatory network.

Little b is a Lisp-based language which allows scientists to build shareable, reusable mathematical models of complex systems based on shared parts. The initial focus is molecular and multicellular networks. Project web page: http://www.littleb.org