Dynamic modeling

Load a curated SBML model
Plot the model
Solve the model
Peak identification
Pathway studies

Obs.

This should be general enough to be performed on any similar models on the Biomodels database.



In [ ]:

    
## Here you should call the whole task, to be completed in one single call.
import DM
DM.run()

Load a dynamical model

Use the biomodels database to load a dynamical model. Here is one example:

http://www.ebi.ac.uk/biomodels-main/BIOMD0000000006

To parse the model either use BeautifulSoup, or the standard XML parser.



In [ ]:

    
import DM
model_link = ""
DM.load_model()

Plot the model

Parametrize the model and plot all species independently starting from a given concentration and parameters dictionary. Use for example odeint from scipy.

Save plots and actual values in files in the project's data folder.



In [ ]:

    
inidic = {} #dictionary of innitial concentrations and parameter values
DM.plot()

Solve the model

Solve the ODE system describing this model either using scipy or PyDST. Plot the results.

Optionally, you can further investigate the model with PySCeS. Save the results as you see fit.



In [ ]:

    
DM.solve()

Peak identification

Identify concentration peaks using scipy's pakages for optimization.



In [ ]:

    
DM.get_peaks()

Pathway studies

Try to annotate your model automatically using the Entrez database through BioPython. Plot the model plus annotations as a graph and save it in graphml.



In [ ]:

    
DM.annotations()