iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). It can import all levels and versions of SBML and is able to export Level 3 Version 1. It supports all core SBML modeling constructs except some types of fast reactions, and also has support for the hierarchical model composition, layout, flux balance constraints, and arrays packages. It was the first tool to produce correct results for all examples in the SBML benchmark suite. It has also been tested successfully on the stochastic benchmark suite and the curated models in the BioModels database. Finally, it is one of the first tools to also support the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.
- Before installing iBioSim, check that the following are installed on your system:
- Java Runtime Environment (Version 1.7 or higher)
- Graphviz (optional)
Other Useful Information
The iBioSim tool is being developed by Chris Myers research group at the University of Utah.
This project has involved many students including Nathan Barker, Scott Glass, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam Nguyen, Tramy Nguyen, Tyler Patterson, Nicholas Roehner, Jason Stevens, Leandro Watanabe, Michael Zhang, Zhen Zhang, and Zach Zundel.
The iBioSim tool makes use of several critical community developed libraries to enable it to better support standards such as SBML, SBOL, SED-ML, and the COMBINE Archive format. In particular, we would like to acknowledge the community of developers of libSBML, JSBML, jlibSEDML, and libSBOLj, the developers of the COMBINE Archive java library at the University of Rostock, and the developers of the Virtual Parts API at Newcastle University.