iBioSim is a computer-aided design (CAD) tool aimed 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 has also been tested successfully on the stochastic benchmark suite and the curated models in the BioModels database. iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.

Website: iBioSim

Video Demo: Tools Workflow

Contact: Chris Myers (@cjmyers) myers@ece.utah.edu

Contributor(s): Nathan Barker, Scott Glass, Kevin Jones, Hiroyuki Kuwahara, Curtis Madsen, Nam Nguyen, Tramy Nguyen, Tyler Patterson, Nicholas Roehner, Jason Stevens, Leandro Watanabe, Zhen Zhang, and Zach Zundel.

Pre-installation Requirement(s)

1. Create a GitHub account.
2. Setup Git on your machine.
3. Install Maven plugin on your machine.
4. Install Eclipse IDE for Java.
5. Clone the iBioSim GitHub repository to your machine.

Installing iBioSim in Eclipse

1. Clone the iBioSim project from command-line or any other method of your choice as instructed in the provided link.
2. Open up your Eclipse workspace that you want to import your iBioSim project to.
3. Select Import from the File Menu.
4. When given the option to select which project import, select Existing Maven Projects under Maven
   • Set Maven Projects:
     • Root Directory: full path to your iBioSim project (i.e. path/to/iBioSim)
     • Once root directory is set, all the pom.xml should be displayed under Projects. Select all pom.xml files.
     • All installation should be complete so click Finish
5. Under Package Explorer in Eclipse, right click on the iBioSim pom.xml file and click select Run As and click Maven clean
6. Perform Update Project under Maven by right clicking on the iBioSim project.

Setting up iBioSim Configurations

1. Open up iBioSim Run Configurations window and create a new Java Application in your Eclipse workspace

• Give the java application a name (i.e. iBioSim_GUI)

• Set the Main tab to the following information:

  • Project: iBioSim-gui
  • Main class: edu.utah.ece.async.ibiosim.gui.Gui

• Set the Environment tab to the following information:

  • Create 2 variables with the corresponding value:
    • BIOSIM: full path to your iBioSim project (i.e. path/to/iBioSim)
    • PATH: append your copy of iBioSim bin directory to whatever existing PATH already supplied to the value of this variable (i.e. $PATH:$BIOSIM/bin).
    • DDLD_LIBRARY_PATH: full path to the lib directory in the iBioSim project (i.e. $BIOSIM/lib64)

• Set Arguments tab to the following information:

  • Program arguments: -Xms2048 -Xms2048 -XX:+UseSerialGC

  If you are running on a MAC, also set the following:

  • VM arguments: -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/src/resources/icons/iBioSim.jpg

• All run configurations are complete. Make sure to apply all your changes.

Running iBioSim

1. Run the java application that you have created from the previous step (i.e. iBioSim_GUI) in Eclipse.
2. Alternatively is to build an executable jar for iBioSim by running mvn clean install on the project root. Once this is completed, you can run java -jar gui/target/iBioSim-gui-0.0.1-SNAPSHOT-jar-with-dependencies.jar, which will fire up the user interface for iBioSim. If you run this way, make sure to define the BIOSIM and DDLD_LIBRARY_PATH variables and modify the PATH variable as shown above.

[Optional] Building reb2sac and GeneNet dependencies.

1. So far, instructions on how to build, install, and run iBioSim from source have been presented. However, these steps only included source code that are native Java. iBioSim incorporates tools that are not Java-based, and therefore, have to be installed separately. In order to do so, you have to following the instructions below:
   • reb2sac
   • GeneNet