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We are pleased to announce the release of iBioSim 1.0, our first
official release. iBioSim is a tool that supports learning of genetic
circuit models, efficient abstraction-based analysis of these models,
and the design of synthetic genetic circuits. iBioSim includes
project management features and a graphical user interface that
facilitates the development and maintenance of genetic circuit models
as well as both experimental and simulation data records.

Models in iBioSim can be created using either an SBML editor or a
Genetic Circuit Model (GCM) editor. The SBML editor and the iBioSim
simulation engine support virtually all of SBML Level 2 Version 3
including reactions, rules, events, constraints, etc. The GCM editor
improves the efficiency of model development by supporting modeling at
a higher level
of abstraction than the molecular level supported by SBML. Namely, a
GCM includes only important species and their influences upon each
other. iBioSim can automatically translate from GCM to SBML models for
analysis.
A GCM can be either manually created or automatically learned from
time-series data. iBioSim also includes an efficient simulation engine
that supports ODE, stochastic, and Markov chain analysis of these
models. This engine
utilizes automatic abstraction to improve analysis time, often by one
to two orders of magnitude. Finally, iBioSim has a graphical editor
for visualizing both time series and event probability analysis results.

iBioSim has been applied successfully to numerous projects including
an analysis of the phage lambda decision circuit and the E. coli Fim
switch. It has also been applied to the design of a synthetic genetic
Muller C-element, an asynchronous state-holding gate. In these and
other efforts, the iBioSim tool with its support for automatic
abstraction has been shown to greatly improve the productivity of
researchers who are analyzing and designing genetic circuits.

Windows, Linux, and MacOS X versions of iBioSim are available for
download from our website:

http://www.async.ece.utah.edu/iBioSim/

To learn more, please visit with us at our arena at ICSB.

Cheers,

Chris

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