moyanwoxin/ibiosim

iBioSim is a computer-aided design (CAD) tool aimed for the modeling, analysis, and design of genetic circuits. It is capable of importing and exporting models specified using the Systems Biology Markup Language (SBML). iBioSim also supports the Synthetic Biology Open Language (SBOL), an emerging standard for information exchange in synthetic biology.

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, 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): Chris Myers, Tramy Nguyen, Leandro Watanabe, Michael Zhang.

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 libSBML for validation and flattening.
6. Clone the iBioSim, libSBOLj, and SBOLDesigner GitHub repositories to your machine

Installing iBioSim

1. Clone libSBOLj (https://github.com/SynBioDex/libSBOLj.git) project (e.g. git clone https://github.com/SynBioDex/libSBOLj.git) in a location of your preference. Go to the directory where the libSBOLj is checked out and make sure you are on the develop branch. Perform mvn clean and then mvn install. This will build libSBOLj and install it into your local repository, which is used as a dependency in iBioSim.
2. Clone SBOLDesigner (https://github.com/SynBioDex/SBOLDesigner) project (e.g. git clone https://github.com/SynBioDex/SBOLDesigner.git) in a location of your preference. Go to the directory where the SBOLDesigner is checked out and perform mvn clean and then mvn install. This will build SBOLDesigner and install it into your local repository, which is used as a dependency in iBioSim.
3. 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. Go to the directory where the iBioSim is checked out and perform mvn clean install. This will install the local non-Maven dependencies into your local repository and then build iBioSim. (NOTE: if you do not want to generate javadocs, use the flag -Dmaven.javadoc.skip=true).

Running iBioSim

1. Build an executable jar for iBioSim by running mvn clean and then mvn install on the project root.
2. Copy gui/target/iBioSim-gui-3.0.0-SNAPSHOT-jar-with-dependencies.jar to the bin directory of your iBioSim project and rename iBioSim-gui-3.0.0-SNAPSHOT-jar-with-dependencies.jar to iBioSim.jar.
3. In the bin directory, run:
   • Windows: iBioSim.bat
   • Mac OS X: iBioSim.mac64
   • Linux: iBioSim.linux64

[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.
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
4. After compiling or downloading reb2sac and GeneNet, copy the compiled binaries into the bin directory in the local copy of your iBioSim.

[Optional] Setting up iBioSim in Eclipse

Importing iBioSim to Eclipse

1. Follow the installation instructions for iBioSim above.
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. Perform Update Project under Maven by right clicking on the iBioSim project.
6. If you want to import SBOLDesigner into Eclipse, then repeat the previous steps for SBOLDesigner. Make sure you execute Maven generate-sources to resolve some dependencies in SBOLDesigner as well.
7. If you want to update SBOLDesigner in iBioSim, then under Package Explorer in Eclipse, right click on the SBOLDesigner pom.xml file and click select Run As and click Maven clean. Do the same for Maven install. Alternatively, you can do this from the command-line as instructed in Installing iBioSim.

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. $PATH:path/to/iBioSim/bin).
• Set Arguments tab to the following information:
  • Program arguments: -Xms2048 -Xms2048 -XX:+UseSerialGC -Djava.library.path=/path/to/lib/
  • Note: for the java library path, /path/to/lib/ is the location where libSBML is installed. The libSBML is installed by default in /usr/local/lib in Linux and Mac OS X machines and C:\Program Files\SBML\libSBML-5.16.0-libxml2-x64 in Windows 64-bit machines.
• If you are running on Mac OS X, also set the following:
  • VM arguments: -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/src/resources/icons/iBioSim.jpg
• All run configurations are complete. Make sure to apply all your changes.