MyersResearchGroup / iBioSim

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) [email protected]

Contributor(s): Nathan Barker, Pedro Fontanarrosa, 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.

Active Developer(s): Pedro Fontanarrosa, Chris Myers, Tramy Nguyen, Leandro Watanabe.

Running iBioSim

1. Download the iBioSim tool from the release page here:
2. After downloading the tool, run the corresponding start-up script:
   • Windows: iBioSim.bat
   • Mac OS X: iBioSim.mac64
   • Linux: iBioSim.linux64

[Optional] Installing iBioSim for Development

Pre-installation Requirements

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. Install the experimental version of libSBML 5.18.0 for validation and flattening.
6. Clone the iBioSim GitHub repository to your machine

Importing iBioSim to Eclipse

1. Clone the iBioSim (https://github.com/MyersResearchGroup/iBioSim.git) project (e.g. git clone https://github.com/MyersResearchGroup/iBioSim.git) to a location of your preference.
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

Setting up iBioSim Configurations in Eclipse

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 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. $PATH:path/to/iBioSim/bin)
    • DDLD_LIBRARY_PATH: path to the libSBML (i.e. path/to/lib). The libSBML is installed by default in /usr/local/lib in Linux and Mac OS X machines and libSBML-5.18.0-win64 in Windows 64-bit machines.
    • DYLD_LIBRARY_PATH: same as DDLD_LIBRARY_PATH.
• Set Arguments tab to the following information:
  • VM arguments: -Xms2048M -Xms2048M -XX:+UseSerialGC -Djava.library.path=/path/to/lib/
  • Note: for the java library path, /path/to/lib/ is the location where libSBML is installed.
  • VM arguments: -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/src/resources/icons/iBioSim.jpg
• All run configurations are complete. Make sure to apply all your changes.

Building iBioSim

1. Go to the directory where the iBioSim is checked out and perform mvn clean install (NOTE: if you do not want to generate javadocs, use the flag -Dmaven.javadoc.skip=true).

[Optional] Building reb2sac and GeneNet dependencies

1. iBioSim incorporates tools that are not Java-based, and therefore, have to be installed separately.
2. The easiest way to install reb2sac and GeneNet is to simply download the pre-compiled binaries for your operating system below:
   • reb2sac
   • GeneNet
3. Another way to install them is to compile these tools on your machine following the instructions below:
   • reb2sac
   • GeneNet
   • Yosys
4. After compiling or downloading reb2sac, GeneNet, and Yosys copy the compiled binaries into the bin directory in the local copy of your iBioSim.