Master's thesis: A modelling framework for Synthetic Biology

The folder /framework contains the modeling framework for Synthethic Biolog: DTU-SB.

The folder /logic-synthesis contains the extension using the DTU-SB Framework.

The folder /GUI contains a GUI for the framework based on Java Swing.

All folders are Eclipse projects, the Logic Synthesis and GUI projects reference the DTU-SB Framework, thus to get this up and running locally the following steps should be followed:

1. Clone the entire repository: git clone git@bitbucket.org:jboysen/dtu-sb.git (or use the url https://bitbucket.org/jboysen/dtu-sb.git)

2. Navigate into the DTU-SB folder.

3. Import the project from /framework into Eclipse.

4. Import the project from /logic-synthesis and /GUI into Eclipse.

5. Done!

Alternatively the respective Ant targets of the folders can be used.

Usage

Further information for usage of the framework can be found on the framework main page.

For usage of the Logic Synthesis: Go to the Downloads tab and download the file DTU-SB-GUI.zip, which contains a pre-compiled JAR-file and required library files. The JAR-file can be executed out-of-the-box, and synthesising new genetic devices can be done by choosing "Truth Table" on the left. Though to ensure that enough memory is available to the simulator, the following execution will raise the memory limit to 2GB:

$ java -Xmx2g -jar DTU-SB-GUI.jar

Note that the library-files located in the library-folder must be on the same path-level as the JAR-file itself.

Under all circumstances we strongly recommend to download the JAR-file mentioned above (also for pure simulation purposes), as it is a lot easier to work with than the CLI.