Automated Particle Tracking & Analysis Software

A LabView module to allow particle tracking in time-stack images.
Developed in the laboratory of Dr. Steve Gross, UCI.
For more information on this program and how well it does compared to other tracking programs, see our article on the Physical Biology website.


GPU Codes for 3D Modeling

We provide CUDA code for Nvidia GPUs of a 3D model of epidermal development. The model includes GPU implementation of the subcellular element method for 3D spatial cells, an intracellular gene network for each cell represented by a set of ODEs, cell-cell neighbor communication through Notch signaling as part of each cell's internal gene network, and cell behaviors of growth and division.

Download: GPU Codes for 3D Model of Epidermal Development

Gene Network Inference Tool

We provide our Objective-C (Cocoa for Mac, GNUstep for Linux/Windows) optimization framework to learn linear gene regulatory networks from various types of gene expression data. The optimization incorporates network sparsity constraint through L1 regularization as well as incorporation of existing network information. The framework can handle wild type, perturbation, gene knockout and heterozygous knockdown gene expression data.

Download: Gene Network Inference Tool

Stiff Reaction Diffusion Solvers

We provide Matlab and C codes based on a novel and efficient algorithm for Reaction-Diffusion equations that model spatial dynamics of complex biological systems. The numerical method used in the code is designed for effective treatment of stiff reactions in spatial systems.

Download: Software for Stiff Reaction Diffussion Solvers

Accelerated Stochastic Simulation Algorithm for Reaction Networks

This is an exact method for stochastic simulation of chemical reaction networks (Exact R-Leap) to accelerate the Stochastic Simulation Algorithm (SSA).

Download: Accelerated Stochastic Simulation Algorithm Software

Dynamical Grammar Simulator

Plenum is a simulation software written in Mathematica for dynamical grammar models. Dynamical grammars are an elegant language for representing complex processes that include stochastic events and continuous dynamics.

Download: Dynamical Grammar Simulator

BMC Systems Biology

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Molecular Systems Biology

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PLOS Computational Biology

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