Biological Boolean Networks¶
A series of biological Boolean networks that can be directly loaded for experimentation.
-
cana.datasets.bio.
BREAST_CANCER
()[source]¶ Boolean network model of signal transduction in ER+ breast cancer
The network is defined in [ZSA17].
- Returns
(BooleanNetwork)
-
cana.datasets.bio.
BUDDING_YEAST
()[source]¶ The network is defined in [LLL+04].
- Returns
(BooleanNetwork)
-
cana.datasets.bio.
DROSOPHILA
(cells=1)[source]¶ Drosophila Melanogaster boolean model. This is a simplification of the original network defined in [AO03]. In the original model, some nodes receive inputs from neighboring cells. In this single cell network, they are condensed (nhhnHH) and treated as constants.
There is currently only one model available, where the original neighboring cell signals are treated as constants.
- Parameters
cells (int) – Which model to return.
- Returns
(BooleanNetwork)
-
cana.datasets.bio.
LEUKEMIA
()[source]¶ Boolean network model of survival signaling in T-LGL leukemia
The network is defined in [ZSY+08].
- Returns
(BooleanNetwork)
-
cana.datasets.bio.
MARQUESPITA
()[source]¶ Boolean network used for the Two-Symbol schemata example.
The network is defined in [MPR13].
- Returns
(BooleanNetwork)
-
cana.datasets.bio.
THALIANA
()[source]¶ 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
()[source]¶ 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)[source]¶ 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)[source]¶ 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)