Biological Boolean Networks

A series of biological Boolean networks that can be directly loaded for experimentation.

cana.datasets.bio.BREAST_CANCER()

Boolean network model of signal transduction in ER+ breast cancer

The network is defined in [ZSA17].

Returns:

(BooleanNetwork)

cana.datasets.bio.BT474_ErbB_S()

Boolean network model of the control of HCC1954 Breast Cell Line Short-term ErbB Network model

The network is defined in [dHBH+14].

Returns:

(BooleanNetwork)

cana.datasets.bio.BUDDING_YEAST()

The network is defined in [LLL+04].

Returns:

(BooleanNetwork)

cana.datasets.bio.DROSOPHILA(cells=1)

Drosophila melanogaster boolean model. This was firt defined in [AO03]. Two models are available in CANA, the original parasegment (4 cells) and a single cell simplification of the model. In the original parasegment model, some nodes receive inputs from neighboring cells. In the single cell model, they are condensed (nhhnHH) and treated as constants.

Parameters:

cells (int) – Which model to return. Accepts either 1 or 4. Default is 1.

Returns:

(BooleanNetwork)

cana.datasets.bio.LEUKEMIA()

Boolean network model of survival signaling in T-LGL leukemia

The network is defined in [ZSY+08].

Returns:

(BooleanNetwork)

cana.datasets.bio.MARQUESPITA()

Boolean network used for the Two-Symbol schemata example.

The network is defined in [MPR13].

Returns:

(BooleanNetwork)

cana.datasets.bio.THALIANA()

Boolean network model of the control of flower morphogenesis in Arabidopsis thaliana

The network is defined in [CAES+06].

Returns:

(BooleanNetwork)

cana.datasets.bio.load_all_cell_collective_models()

Load all the Cell Collective models, instanciating +70 models.

Returns:

(list)

Note

See source code for full list of models.

cana.datasets.bio.load_cell_collective_model(name=None)

Loads one of the Cell Collective [HKM+12] models. Models collected on Aug 2020.

Parameters:

name (str) – the name of the model to be loaded. Accepts: [“Apoptosis Network”, “Arabidopsis thaliana Cell Cycle”, “Aurora Kinase A in Neuroblastoma”, …, “Wg Pathway of Drosophila Signalling Pathways”, “Yeast Apoptosis”]

Returns:

(BooleanNetwork)

Note

See source code for full list of models. Credits to Xuan Wang for compiling these models. We are working on making a Cell Collective direct loader.

Network Motifs

Simple network motifs in Networkx.DiGraph format that can be directly loaded.

cana.datasets.motifs.network_motif(name=None)

Graph motifs from [MSOI+02].

Parameters:

name (string) – The name of the motif. Possible values are : FeedForward, Fan, FeedForwardSelf1, FeedForwardSelf2, FeedForwardSelf3, FeedForwardSelf123, BiFan, CoRegulated, CoRegulating, BiParallel, TriParallel, Dominating4, Dominating4Undir, 3Loop, 4Loop, 3LoopSelf123, FourLoop, FourCoLoop, DirectedTwoLoop, BiParallelLoop, 5Chain, 3Chain, KeffStudy3, KeffStudy4, CoRegulatedSelf, KeffLine4, KeffLineLoop4, 3Full, 6Pyramid, 4Split, 5BiParallel, 6BiParallelDilation, 6BiParallelDilationLoop, 5combine, 4tree.

Returns:

The directed graph motif.

Return type:

(networkx.DiGraph)