Usage

Tutorial examples

There are two main examples which demonstrate the usage -

Multiple Biomolecular Subsystems Interactions -

In this example, we consider three models written in SBML (these models may be generated using the methods described in the previous example). There are two double phosphorylation subsystems and an incoherent feedforward loop subsystem model. We intend to have all of the three subsystems inside a synthetic cell. There are different kinds of interactions that occur which can be modeled using this toolbox. The methods in the Subsystem and System class have been used in this example.

• Shared cellular resources: A list of molecules present inside a cell which all subsystems share as common resources.
• Combine subsystems: If desired, all species with the same name that occur across different subsystems may be allowed to be shared among subsystems.
• Interactions between subsystem and systems: Membrane transport modeling, combining multiple subsystems with input and output species, and so on.

The tutorial_interconnection.ipynb uses SBML models of double phosphorylation and an incoherent feedforward loop to demonstrate the three interactions described above.

Run the following command from a terminal in the Sub-SBML directory to open a browser tab with the list of files inside the directory.

jupyter notebook

Click on the tutorial_interconnection.ipynb file to open the jupyter notebook and press Shift + Enter to run the cells.

Interaction Modeling

Tutorial coming soon....until then working code is available on the repository.

Creating new SBML models using simple commands

See the Enzymatic_Reaction_Tutorial.ipynb for a quick tutorial on how to create models easily using Sub-SBML.

For a detailed tutorial, Using simple commands available as the member functions of the SimpleModel and SimpleReaction classes, we can create models getting rid of the long and tedious approach when using libsbml directly. The tutorial_modeling.ipynb creates a Double Phosphorylration (DP) SBML model from scratch. Run the following command from a terminal in the Sub-SBML directory to open a browser tab with the list of files inside the tutorial folder in the directory.

jupyter notebook

Click on the tutorial_modeling.ipynb file to open the jupyter notebook and press Shift + Enter to run the cells.