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University of Connecticut Health Center - Know Better Care Richard D. Berlin
Center for Cell Analysis & Modeling

CCAM Software

CCAM Software is produced by the faculty and staff of CCAM. Our flagship application, the Virtual Cell, serves as a National Resource for Cell Analysis and Modeling. The software below ranges from applications for analyzing FRAP and other image data, (Virtual FRAP Tool, Microfilament Detector, 5D Visualization MicroApp) to tools for generating models (BioNetGen, SyBiL) and model parameters (Gfit).

 

Virtual Cell

http://vcell.org/login/login.html
The Virtual Cell has been specifically designed to be a web-based research tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. Likewise the creation of models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Users can build complex models with a web-based Java interface to specify compartmental topology and geometry, molecular characteristics, and relevant interaction parameters. The Virtual Cell automatically converts the biological description into a corresponding mathematical system of ordinary and/or partial differential equations.
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CCAM Software

CCAM Events Calendar

Director

Dr. Leslie Loew
les@volt.uchc.edu
860-679-3568

Deputy-Director

Dr. Ann Cowan
acowan@nso2.uchc.edu
860-679-1449

Administrative Contact

Karen Zucker
zucker@nso2.uchc.edu
Center for Cell Analysis & Modeling
Phone: 860- 679-1452
Fax: 860-679-1039

Virtual FRAP Tool

"The Virtual FRAP tool  is  designed to analyze FRAP, Fluorescence Recovery after Photobleaching, experiments. It is available as a tool within the VCell software, and can be used to analyze experiments that collect all of the fluorescence associated with the cell, and where the bleach region does not vary through the Z dimension. Currently, Virtual FRAP can be used to fit D and %R for either one or two diffusing components of cytosolic (soluble) proteins, or to fit off rates for binding to immobile components. It does not analyze lateral diffusion within the plasma membrane.
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BioNetGen

http://vcell.org/bionetgen
Cellular signaling events are frequently mediated by protein-protein interactions via motifs, domains and subunits. Combined with the vast number of possible post translational modifications, the number of possible protein-protein configurations are sufficiently large to be considered combinatorically complex. Rule-based models of biochemical systems- including signal transduction, metabolic, and genetic regulatory networks- is the approach used by BioNetGen for the specification and simulation of such systems. Rule-based models allow the biologist and modeler to generate complex networks that emerge from the logical consequences of knowledge and assumptions about the mechanistic details.
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Microfilament Detector

http://wiki.vcell.uchc.edu/twiki5/bin/view/VCell/MicroFilaments%20
Gfit is an open-access software tool for performing global analysis of large, heterogenous data sets. Global analysis performs simultaneous regression analysis for mutliple parameters in the biological system. The tools allows for researchers to rapidly evaluate the system model in relation to experimental data where the numerous data sets act to constrain the possible values obtained through global fitting. This tool and approach has been used successfully with Fluorescence Correlation Spectroscopy data and Surface Plasmon Resonance to study nuclear transport, transciption and DNA-protein interactions.
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SyBil/SBPax


Sybil is short for Systems Biology Linker. It is a software currently able to load, analyze and display BioPAX data. Biological pathways, reaction and signaling networks are made publicly availabel in formats standardized to the Biological Pathway eXchange format (BioPAX). Simulation tools for biological pathways are standardized to other Markup languages such as Systems Biology Markup Language (SBML) and Virtual Cell Markup Language (VCML). To take full advantage of scientific advances requires the mapping and integration of simulation markup languages with BioPAX. Sybil is developed to convert models between BioPAX and SBML/VCML and builds an SBML-BioPAX joint repository using SBPAX.
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5D Visualization MicroApp

http://www.ccam.uchc.edu/research/apps/QuickTime_PluginsMultiMod.jar
This ImageJ plugin overlays separate grayscale 4D movies into a combined 5D display. This allows comparison of separate 4D microscopy recordings, combination of different microscopy channels, or overlay of microscopy and model data in 4 dimensions. Specifically, the 5D Visualization MicroApp overlays and navigates multiple QuickTime or QuickTimeVR Object movies in a single HyperStack window, with complete freedom to select and adjust lookup tables for display of each channel.
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