Building a Boolean-Based Model¶

This simple example demonstrates how to create a boolean-based model, its components, regulators, conditions and sub-conditions into Cell Collective.

We’ll attempt to reconstruct the Cortical Area Development authored by CE Giacomantonio.

Begin by importing the ccapi module into your workspace.

[1]:

import ccapi

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

[2]:

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.

[3]:

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

Creating a Base Model¶

Create a Base Model using ccapi and instantize it with an authenticated client.

[4]:

model = ccapi.Model("Cortical Area Development", client = client)
model.save()

[4]:

ID	163454
Name	Cortical Area Development
Memory Address	0x010d4ee490
Number of Versions	1
Versions	[<BooleanModel 163454 version 1 at 0x010d4ee650>]

A ccapi.Model consists of various ccapi.ModelVersion objects that help you build various versions to a model. By default, a ccapi.Model provides you a default model version of a boolean type.

[5]:

# get the default model version
boolean      = model.versions[0]
boolean.name = "Version 1"
boolean

[5]:

ID	163454
Version	1
Name	Version 1
Memory Address	0x010d4ee650
Number of Components	0
Components

Adding Components to a Boolean-Based Model¶

First, we need to create a list of component objects for this model.

[6]:

# create components
COUP_TFI = ccapi.InternalComponent("COUP-TFI")
EMX2     = ccapi.InternalComponent("EMX2")
FGF8     = ccapi.InternalComponent("FGF8")
PAX6     = ccapi.InternalComponent("PAX6")
Sp8      = ccapi.InternalComponent("Sp8")

Now let us add a list of components to our Boolean Model.

[7]:

# add components to model
boolean.add_components(COUP_TFI, EMX2, FGF8, PAX6, Sp8)

Saving a Model¶

Ensure you save your model in order to commit your work.

[8]:

model.save()

[8]:

ID	163454
Name	Cortical Area Development
Memory Address	0x010d4ee490
Number of Versions	1
Versions	[<BooleanModel 163454 version 1 at 0x010d4ee650 name='Version 1'>]

Adding Regulators, Conditions and Sub-Conditions¶

Let’s add a list of regulators and conditions to our components. A list of regulators and conditions as well as sub-conditions can all be added at once to a component.

[9]:

# add regulators to components
COUP_TFI.add_regulators(
    ccapi.NegativeRegulator(Sp8),
    ccapi.NegativeRegulator(FGF8)
)
EMX2.add_regulators(
    ccapi.PositiveRegulator(COUP_TFI),
    ccapi.NegativeRegulator(FGF8),
    ccapi.NegativeRegulator(PAX6),
    ccapi.NegativeRegulator(Sp8)
)
Sp8.add_regulators(
    ccapi.PositiveRegulator(FGF8),
    ccapi.NegativeRegulator(EMX2)
)
FGF8.add_regulators(
    # add conditions to regulators
    ccapi.PositiveRegulator(FGF8, conditions = [
        ccapi.Condition(components = Sp8)
    ])
)
PAX6.add_regulators(
    ccapi.PositiveRegulator(Sp8),
    ccapi.NegativeRegulator(COUP_TFI)
)

[10]:

model.save()

[10]:

ID	163454
Name	Cortical Area Development
Memory Address	0x010d4ee490
Number of Versions	1
Versions	[<BooleanModel 163454 version 1 at 0x010d4ee650 name='Version 1'>]

We’ve now got things within our Boolean Model.

[11]:

boolean.components

[11]:

ID	Name	Number of Positive Regulators	Number of Negative Regulators
3202260	COUP-TFI	0	2
3202258	EMX2	1	3
3202261	FGF8	1	0
3202257	PAX6	1	1
3202259	Sp8	1	1

[12]:

FGF8.positive_regulators

[12]:

ID	Name	Number of Conditions
4136618		1

Model Summary¶

You can view detailed summary of your model using the summary function provided.

[13]:

boolean.summary()

Internal Components (+, -) External Components
-------------------------- -------------------
COUP-TFI (0,2)
EMX2 (1,3)
FGF8 (1,0)
PAX6 (1,1)
Sp8 (1,1)

…or view detailed information within your jupyter notebook.

[14]:

boolean

[14]:

ID	163454
Version	1
Name	Version 1
Memory Address	0x010d4ee650
Number of Components	5
Components	COUP-TFI, EMX2, FGF8, PAX6, Sp8

Model Rendering¶

You can also attempt to visualize a Boolean Model using the draw function provided.

[15]:

# boolean.draw()

Exception in thread Thread-4:
Traceback (most recent call last):
  File "/usr/local/opt/python/Frameworks/Python.framework/Versions/3.7/lib/python3.7/threading.py", line 926, in _bootstrap_inner
    self.run()
  File "/Users/achillesrasquinha/.venv/lib/python3.7/site-packages/pygraphviz/agraph.py", line 44, in run
    chunk = self.pipe.read()
  File "/Users/achillesrasquinha/.venv/lib/python3.7/site-packages/gevent/_fileobjectposix.py", line 164, in readall
    data = self.__read(DEFAULT_BUFFER_SIZE)
  File "/Users/achillesrasquinha/.venv/lib/python3.7/site-packages/gevent/_fileobjectposix.py", line 158, in __read
    wait_on_watcher(self._read_watcher, None, None, self.hub)
  File "src/gevent/_hub_primitives.py", line 326, in gevent._gevent_c_hub_primitives.wait_on_watcher
  File "src/gevent/_hub_primitives.py", line 350, in gevent._gevent_c_hub_primitives.wait_on_watcher
  File "src/gevent/_hub_primitives.py", line 304, in gevent._gevent_c_hub_primitives._primitive_wait
  File "src/gevent/_hub_primitives.py", line 46, in gevent._gevent_c_hub_primitives.WaitOperationsGreenlet.wait
  File "src/gevent/_hub_primitives.py", line 46, in gevent._gevent_c_hub_primitives.WaitOperationsGreenlet.wait
  File "src/gevent/_hub_primitives.py", line 55, in gevent._gevent_c_hub_primitives.WaitOperationsGreenlet.wait
  File "src/gevent/_waiter.py", line 151, in gevent._gevent_c_waiter.Waiter.get
  File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
  File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
  File "src/gevent/_greenlet_primitives.py", line 65, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
  File "src/gevent/_gevent_c_greenlet_primitives.pxd", line 35, in gevent._gevent_c_greenlet_primitives._greenlet_switch
greenlet.error: cannot switch to a different thread
Exception in thread Thread-5:
Traceback (most recent call last):
  File "/usr/local/opt/python/Frameworks/Python.framework/Versions/3.7/lib/python3.7/threading.py", line 926, in _bootstrap_inner
    self.run()
  File "/Users/achillesrasquinha/.venv/lib/python3.7/site-packages/pygraphviz/agraph.py", line 44, in run
    chunk = self.pipe.read()
  File "/Users/achillesrasquinha/.venv/lib/python3.7/site-packages/gevent/_fileobjectposix.py", line 164, in readall
    data = self.__read(DEFAULT_BUFFER_SIZE)
  File "/Users/achillesrasquinha/.venv/lib/python3.7/site-packages/gevent/_fileobjectposix.py", line 158, in __read
    wait_on_watcher(self._read_watcher, None, None, self.hub)
  File "src/gevent/_hub_primitives.py", line 326, in gevent._gevent_c_hub_primitives.wait_on_watcher
  File "src/gevent/_hub_primitives.py", line 350, in gevent._gevent_c_hub_primitives.wait_on_watcher
  File "src/gevent/_hub_primitives.py", line 304, in gevent._gevent_c_hub_primitives._primitive_wait
  File "src/gevent/_hub_primitives.py", line 46, in gevent._gevent_c_hub_primitives.WaitOperationsGreenlet.wait
  File "src/gevent/_hub_primitives.py", line 46, in gevent._gevent_c_hub_primitives.WaitOperationsGreenlet.wait
  File "src/gevent/_hub_primitives.py", line 55, in gevent._gevent_c_hub_primitives.WaitOperationsGreenlet.wait
  File "src/gevent/_waiter.py", line 151, in gevent._gevent_c_waiter.Waiter.get
  File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
  File "src/gevent/_greenlet_primitives.py", line 61, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
  File "src/gevent/_greenlet_primitives.py", line 65, in gevent._gevent_c_greenlet_primitives.SwitchOutGreenletWithLoop.switch
  File "src/gevent/_gevent_c_greenlet_primitives.pxd", line 35, in gevent._gevent_c_greenlet_primitives._greenlet_switch
greenlet.error: cannot switch to a different thread

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-15-61b8d2fd863a> in <module>
----> 1 boolean.draw()

~/dev/dev/hl/ccapi/src/ccapi/model/model/boolean/__init__.py in draw(self, type_, **kwargs)
    154             graph.add_nodes_from([c.name for c in self.components])
    155
--> 156             layout = graphviz_layout(graph)
    157
    158             nx.draw_networkx_nodes(graph, layout,

~/.venv/lib/python3.7/site-packages/networkx/drawing/nx_agraph.py in graphviz_layout(G, prog, root, args)
    235     This is a wrapper for pygraphviz_layout.
    236     """
--> 237     return pygraphviz_layout(G, prog=prog, root=root, args=args)
    238
    239

~/.venv/lib/python3.7/site-packages/networkx/drawing/nx_agraph.py in pygraphviz_layout(G, prog, root, args)
    283         args += f"-Groot={root}"
    284     A = to_agraph(G)
--> 285     A.layout(prog=prog, args=args)
    286     node_pos = {}
    287     for n in G:

~/.venv/lib/python3.7/site-packages/pygraphviz/agraph.py in layout(self, prog, args)
   1420         """
   1421         fmt = "dot"
-> 1422         data = self._run_prog(prog, " ".join([args, "-T", fmt]))
   1423         self.from_string(data)
   1424         self.has_layout = True

~/.venv/lib/python3.7/site-packages/pygraphviz/agraph.py in _run_prog(self, prog, args)
   1377             t.start()
   1378
-> 1379         self.write(child_stdin)
   1380         child_stdin.close()
   1381

~/.venv/lib/python3.7/site-packages/pygraphviz/agraph.py in write(self, path)
   1256         fh = self._get_fh(path, "w")
   1257         try:
-> 1258             gv.agwrite(self.handle, fh)
   1259         except OSError:
   1260             print("IO error writing file")

~/.venv/lib/python3.7/site-packages/pygraphviz/graphviz.py in agwrite(g, file)
     86
     87 def agwrite(g, file):
---> 88     return _graphviz.agwrite(g, file)
     89
     90 def agisundirected(g):

TypeError: not a file handle

[ ]: