To run DFBA models in iBioSim tool, you need to:
- Download iBioSim 3.0
- Install from source
- Open up the tool as instructed here.
- Create a project by clicking on File->New->Project and specify the location and name of the project.
To create DFBA models, you need to follow these steps:
- Create a model by clicking on File->New->Model and the name of the model.
- Create a model for each required module as described in the guidelines
- Specify the SBO term of each module by clicking on the Model button in the toolbar.
- Once all the submodels have been created, you click on Tools->Analysis Tool and specify a name for the analysis. You can leave it empty for a default value.
- In the analysis view, select Monte Carlo as the Analysis Type and select Mixed-Hierarchical as the simulator.
- Click on the run button in the toolbar.
- Navigate to the TSD Graph to view the simulation results.
To run DFBA models from COMBINE Archives, you need to follow these steps:
- Once a project is created, you can import our examples.
- Click on File->Import->Archive and selecting the appropriate omex file.