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.

Spring SaLaD

SpringSaLaD is a particle-based, stochastic, biochemical simulation platform most suitable for modeling mesoscopic systems, which are far too large to be modeled with molecular dynamics but which require more detail than obtainable with macroscopic continuum models.  In SpringSaLaD, molecules are modeled as a collection of impenetrable spheres (called “sites”) linked by stiff springs.  The sites are intended to represent mesoscopic protein domains, such as an SH2 domain or a catalytic domain, and each site can be associated with a number of biochemical states, such as “active” or “inactive” for a catalytic domain.  SpringSaLaD supports the full array of typical biochemical reactions:  zeroeth-order reactions which model particle creation, a variety of first-order reactions such as particle decay, dissociation, and state transitions, and second-order reactions between sites for bonding reactions.

A good example a system which is best modeled with SpringSaLaD is ligand-mediated receptor clustering, where coarse-grained particle-level interactions are required but atom-level information is not of interest.  In general, SpringSaLaD is best used to model mesoscopic particles (diameters of 1 – 10 nm, which could represent a functional protein domain), moderately sized systems (10 – 10,000 particles), and times scales on the order of 1 second, but no actual restriction is set on size or scale of the simulated system.

SpringSaLaD is available as JAR files for PC, Mac, and Linux.  It includes a user-friendly GUI which supports all aspects of model creation, running simulations, and data analysis. The downloadable zip file also include a user’s guide and tutorial which walks the reader through a full example from model creation to data analysis.

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.

Microfilament Detector

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.

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.

More information on available softwares can be found here.