Documentation • Python/notebook interface

Model input

Pint relies on Automata networks framework which encompasses asynchronous Boolean and multi-valued networks.

The python module allows a seamless importation of models in different file formats. The conversion is made automatically and is ensured to be exact. The next sections show how to load a model, access and update its initial state, and saving and exporting to different formats. Finally, we show how to get basic informations on the automata network model.

Loading a model

Pint supports multiple formats for specifying Boolean and multi-valued networks, in particular SBML-qual and GINsim. Most of the conversions are performed using BioLQM. See load() for the full list of supported formats. If you are missing one, please open an issue.

The loading of a model is done with the function pypint.load which returns an abstract object representing the automata network. The format is guessed from the file extension.

The argument can either be a local path to a file, or a URL which will be downloaded prior to loading:

In [2]:
m = pypint.load("http://ginsim.org/sites/default/files/drosophilaCellCycleVariants.zginml")
Downloading ‘http://ginsim.org/sites/default/files/drosophilaCellCycleVariants.zginml’ to ‘gen/pintaa2rr28wdrosophilaCellCycleVariants.zginml’
Source file is in zginml format, importing with logicalmodel
Invoking GINsim…
Simplifying model…
6 state(s) have been registered: NoCycD_Endocycle, G0, Cycle_Init, Syncytial_Cycles, Ago_Endocycle, Endocycle_init

The load function also supports importing models from CellCollective simply by supplying the URL to the model repository:

In [3]:
m2 = pypint.load("https://cellcollective.org/#4705/septation-initiation-network")
Downloading ‘http://api.cellcollective.org/model/export/4705?type=SBML’ to ‘gen/pintcjqoq6wr4705.zip’
Source file is in sbml format, importing with logicalmodel
Simplifying model…

Finally, within the Jupyter notebook web interface, a model can be uploaded by calling load without any argument. Once the file selected, it will be uploaded in the notebook, and loaded as a local file.

In [4]:
m3 = pypint.load()

Initial state

An automata network comes with an initial state, associating to each automaton its starting local state. Some formats, such as GINsim, allow to define different states that are identified with a name. In such a case, the load function displays the registered states.

The initial state of a model m is accessed using m.initial_state. It is a dict-like object which supports updating.

In [5]:
m.initial_state
Out[5]:
{'Ago': 0,
 'CycA': 0,
 'CycB': 0,
 'CycD': 0,
 'CycE': 0,
 'Dap': 0,
 'E2F': 0,
 'Fzr': 0,
 'Fzy': 0,
 'Notch': 0,
 'Rb': 0,
 'Rux': 0,
 'Stg': 0,
 'Wee1': 0}
In [6]:
m.initial_state["CycE"] = 1  # modification of the initial state
m.initial_state.nonzeros()   # display only initial automata local states different from 0
Out[6]:
{'CycE': 1}

Registered states are stored in m.named_states and can be directly assigned as the initial state:

In [7]:
m.initial_state = m.named_states["NoCycD_Endocycle"]
m.initial_state.changes() # display changes since the default initial state of the model
Out[7]:
{'Dap': 1, 'Fzr': 1, 'Notch': 1, 'Rb': 1, 'Rux': 1}

Instead of modifying in-place the model, one can use the method Model.having() to create a new copy of the model with supplied initial state modifications:

In [8]:
m.initial_state.reset()    # restore to default initial state
m2 = m.having(CycE=1)      # having can take keyword arguments
m2 = m.having({"Notch": 1, "Stg": 1})   # .. or a dictionnary
m2 = m.having("NoCycD_Endocycle")       # .. or the name of a registered state

Saving and exporting

A model can be saved to a local file, in Pint native format:

In [9]:
m.save_as("models/demo_droso.an")

Pint can also export the model to different formats, such as Petri net (PEP format with .ll extension or ROMEO with .xml extension) and NuSMV (.smv). See EXPORT_SUPPORTED_EXTENSIONS for the full list of supported exportation format.

Model description

Basic statistics on the model can be obtained with the summary method:

In [10]:
m.summary()
Out[10]:
{'max_local_states': 2,
 'nb_automata': 14,
 'nb_local_states': 28,
 'nb_states': 16384,
 'nb_transitions': 61}
  • max_local_states gives the number of local states of the largest automaton;
  • nb_automata is self explanatory
  • nb_local_states is the sum of the number of local states in each automaton
  • nb_states is the total number of global states (in our example, it corresponds to 2^14)
  • nb_transitions is the number of defined local transitions

The list of automata and their local states and transitions can be accessed as follows:

In [11]:
m.automata
Out[11]:
['Ago',
 'CycA',
 'CycB',
 'CycD',
 'CycE',
 'Dap',
 'E2F',
 'Fzr',
 'Fzy',
 'Notch',
 'Rb',
 'Rux',
 'Stg',
 'Wee1']
In [12]:
m.local_states
Out[12]:
{'Ago': [0, 1],
 'CycA': [0, 1],
 'CycB': [0, 1],
 'CycD': [0, 1],
 'CycE': [0, 1],
 'Dap': [0, 1],
 'E2F': [0, 1],
 'Fzr': [0, 1],
 'Fzy': [0, 1],
 'Notch': [0, 1],
 'Rb': [0, 1],
 'Rux': [0, 1],
 'Stg': [0, 1],
 'Wee1': [0, 1]}
In [13]:
m.local_transitions[:5]
Out[13]:
["Ago" 1 -> 0,
 "Dap" 1 -> 0 when "CycE"=0 and "Notch"=1,
 "CycA" 1 -> 0 when "Rb"=0 and "E2F"=0,
 "CycA" 1 -> 0 when "Rb"=0 and "E2F"=1 and "Fzr"=1 and "Fzy"=0,
 "CycA" 1 -> 0 when "Rb"=0 and "E2F"=1 and "Fzy"=1]

This later list is actually composed of LocalTransition and SynchronizedLocalTransitions objects. It allows for further programmatic treatment.

Finally, the method dependency_graph() returns a directed graph among automata, where an edge from b to a means that at least one transition of a depends on the local state of b. The returned object is a NetworkX digraph which can be further manipulated, or directly displayed in the jupyter notebook:

In [14]:
m.dependency_graph()
Out[14]:
../_images/doc_model_29_0.svg