Supporting data for "Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision" by Chevalier et al., 2020

Code, data, and notebooks used for the synthesis and simulations of ensembles of Boolean networks for the tumor invasion model introduced in (Cohen et al, 2015)

Visualize online:

Simulations - Mutant analysis.ipynb

 Tumour - Synthesis with BoNesis.ipynb

The notebooks can be executed within the CoLoMoTo Docker image 2020-07-01:

pip install -U colomoto-docker
colomoto-docker -V 2020-07-01 --bind .

The synthesis additionally requires executing the following command (within the Docker image):

pip install --user bonesis-preview-20200514.zip

The ensembles have been generated with the following commands.

python synthesis.py synthesis --exact-pkn --globalfps
python synthesis.py synthesis --exact-pkn --globalfps --mutant p53 --mutant NICD

本数据集涵盖用于合成与模拟（Cohen等，2015）提出的肿瘤侵袭模型所对应的布尔网络（Boolean networks）集成体的代码、数据及Jupyter Notebook文件。

在线可视化文件如下：
- 「模拟-突变体分析.ipynb」
- 「肿瘤-BoNesis合成.ipynb」

上述Notebook可在CoLoMoTo Docker镜像2020-07-01环境中运行，前置部署命令如下：
bash
pip install -U colomoto-docker
colomoto-docker -V 2020-07-01 --bind .

若需执行布尔网络合成流程，还需在Docker镜像内运行以下额外依赖安装命令：
bash
pip install --user bonesis-preview-20200514.zip

该布尔网络集成体可通过以下命令生成：
bash
python synthesis.py synthesis --exact-pkn --globalfps
python synthesis.py synthesis --exact-pkn --globalfps --mutant p53 --mutant NICD