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).


Center/Contributor: Center for Complex Biological Systems

Contact: Eric Mjolsness

Advanced Correlation Techniques Group

Working group to discuss research advances and applications related to correlation techniques in advanced microscopy imaging tools.

 

Center/Contributor: Center for Complex Biological Systems

Contact: Michelle Digman

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.


Center/Contributor: Center for Mathematical and Computational Biology

Contact: Qing Nie

Automated Particle Tracking and Analysis

A LabView module to allow particle tracking in time-stack images.

Center/Contributor: Center for Complex Biological Systems

Contact: Steven Gross

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.

Contributor/Center: Center for Mathematical and Computational Biology

Contact: Qing Nie

Gene Network Inference

Provides 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.


Center/Contributor: Center for Mathematical & Computational Biology

Contact: Qing Nie

Globals for Images

Software analysis tools for image files derived from multiple spectroscopic techniques.

Center/Contributor: Laboratory of Fluorescence Dynamics

Contact: wrightj@illinois.edu

GPU Codes for 3D Modeling

Provides 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.


Center/Contributor: Center for Complex Biological Systems

Contact: Qing Nie

Hybrid Continuos_Discrete Method for Stochastic Reaction-Diffusion Process

We provide a guide and source codes for the hybrid method along with its application to two morphogen systems.
 
Contributor/Center: Center for Mathematical and Computational Biology
 
Contact: Qing Nie

Laboratory for Fluorescence Dynamics

The Laboratory for Fluorescence Dynamics (LFD) is a national research resource center for biomedical fluorescence spectroscopy. The LFD's main activities are i) Services and Resources for state-of-the-art fluorescence measurements, microscopy and spectroscopy, ii) Research and Development to design, test, and implement advances in the technology of hardware, software, and biomedical application, and iii) Training and Dissemination of knowledge relevant to fluorescence spectroscopic principles, instrumentation, and applications.

Center/Contributor: Laboratory of Fluorescence Dynamics (LFD)

Contact: lfd@uci.edu

Metabolomics Interest Group

The Metabolomics Interest Group provides an informal venue for both current research groups, as well as new users, to i) more effectively utilize campus metabolomics resources, ii) obtain user support and provide community feedback, and iii) promote opportunities for collaborative interactions.

Center/Contributor: Center for Complex Biological Systems

Contact: Felix Grün

Mitochondrial Special Interest Group

The Mitochondrial Special Interest Group focuses on discussions of research related to mitochondrial functions in health and disease. The group meets monthly.

Center/Contributor: Center for Complex Biological Systems

Contact: Susan Rafelski

Modeling and Theoretical Biology Interest Group

The Modeling and Theoretical Biology Interest Group focuses on discussions of research in modeling approaches and advances in theoretical biology. The group meets monthly.


Center/Contributor: Center for Complex Biological Systems

Contact: Abed Alnaif

National Short Course in Systems Biology: Mmorphogenesis & Spatial Dynamics

This national short course in Systems Biology focuses on the Morphogenesis and Spatial Dynamics. The 3-week course is held annually in January at UCI.


Center/Contributor: Center for Complex Biological Systems

Contact: Felix Grün

Parismi Dataset

This dataset represents ~45,000 cells, imaged at high resolution in their native environment and segmented in three dimensions, for use in the "Parismi" pipeline. The dataset, which is unusual in its breadth and level of manual curation, will be valuable for researchers seeking to develop new machine learning and computer vision methods for automated biological image analysis.


Center/Contributor: Center for Complex Biological Systems

Contact: Olivier Cinquin

Pipeline for 3D Seqmentation and Analysis of Biological Sample Images

We are releasing the code for “Parismi” - our 3D image segmentation and cell cycle analysis pipeline so that the results reported in our publications can easily be reproduced, and to enable researchers to utilize and/or modify this tool for other applications.

A high-resolution annotated image dataset of 45,000 cells is also avaible.

 

Center/Contributor: Center for Complex Biological Systegs

Contact: Olivier Cinquin

Plenum 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.

Center/Contributor: Center for Complex Biological Sciences

Contact: Eric Mjolness

Scientific Inference Systems Tools

A collection of software and packages for modeling and image analysis on systems inferences.

Center/Contributor: Center for Complex Biological Systems

Contact: Eric Mjolsness

Sigmoid

The SIGMOID project is intended to produce a database of cellular signaling pathways and models thereof, to marshall the major forms of data and knowledge required as input to cellular modeling software and also to organize the outputs.


Center/Contributor: Institute for Bioinformatics and Genomics (UCI), Beckman Institute of the California Institute of Technology and Bioengineering Department at Johns Hopkins University

Contact: Eric Mjolsness

Stiff Reaction Diffusion Solvers

Fast Numerical Algorithms for Stiff Reaction-Diffusion Equations. Provides 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.

Center/Contributor:Center for Mathematical and Computational Biology

Contact: Qing Nie

2011 UCI Resources, Software & Databases. Copyright © 2013. The Center for Complex Biological Systems, UC Irvine
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