Software
• 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.
• A 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.
• A GPU Code for 3D Model of Epidermal Development
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.
• Fast Methods for High-Spatial Dimensions
We provide Matlab codes based on an efficient algorithm for partial differential equations that contain cross derivative terms in reaction diffusions and Fokker-Planck equations. The numerical method used in the code is designed for effective treatment of diffusion operators in high spatial dimensions.
• Anisotropic Subcellular Methods for Cells in 3D
We provide OpenCL code for an efficient parallel implementation of the Anisotropic Subcellular Element Method in 3D. This implementation supports both symmetric and asymmetric cell division. Also included are examples demonstrating polar cell - cell adhesion and non-polar cell - cell adhesion.
• Discrete Cell Codes for Crypt (GPU)
We provide an OpenCL code of a 3D hybrid model for crypt homeostasis, consisting of GPU implementation of subcellular element model for cellular dynamics, cell-cell interaction, cell growth and division, as well as a chemical reaction-diffusion equation system for Wnt signaling.
• Sub Cellular Element Models for Early Embryo Development
We provide codes for subcellular element models in both 2D and 3D.