BioModels

In this tutorial, we will attempt to import models from BioModels into your account on Cell Collective.

Begin by importing the ccapi module into your workspace.

import ccapi

Now, let’s try creating a client object in order to interact with services provided by Cell Collective.

client = ccapi.Client()

Authenticate your client using a *password flow type authentication* scheme.

NOTE: Before you can authenticate using ccapi, you must first register an application of the appropriate type on `Cell Collective <https://cellcollective.org>`__. If you do not require a user context, it is read only.

client.auth(email = "test@cellcollective.org", password = "test")

Let’s import the `Hamey2017 - Blood stem cell regulatory network <https://www.ebi.ac.uk/biomodels/MODEL1610060000>`__ from BioModels into Cell Collective.

You can use the read_id routine from ccapi.services.biomodels to import a model into Cell Collective using a BioModels identifier.

from ccapi.services.biomodels import read_id

Pass a valid client object and a valid BioModels ID.

model = read_id(client, "e_coli_core", save = True)
model

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
<ipython-input-1-a3f54c5170fc> in <module>
----> 1 model = read_id(client, "e_coli_core", save = True)
      2 model

NameError: name 'read_id' is not defined

You can view details about this model by accessing the default version.

This can also be viewed on the UI.

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