Tool of Scalable Counting of Minimal Trap Spaces and Fixed Points in Boolean Networks

The repository is the tool of our CP2025 paper.

The tool counts the number of minimal trap spaces and fixed points of a Boolean network. The detailed can be found here: CP2025.

Clone the repo

git clone --recurse-submodules https://github.com/meelgroup/bn-counting.git

Dependencies

You need to install cmake, g++, re2c, and bison.

sudo apt install build-essential bison re2c cmake gringo clasp python3-pip

Install python packages

pip install networkx
pip install clingo
pip install biodivine-aeon

Compilation and install

You need to compile approxasp and install python package fASP and tsconj. The following command to do that:

chmod +x build.sh
./build.sh

Running first task: C-MTS-1 and C-FIX-1

Input:

• Boolean Network: a Boolean network (.bnet file)

For counting minimal trap spaces:

python3 script/run_minimal_trap_space.py -t 1 -bn tests/t1_244.bnet

it should print the count in line: C-MTS-1:

For counting fixed points:

python3 script/run_fixed_point.py -t 1 -bn tests/t1_244.bnet

it should print the count in line: C-FIX-1:

Running second task: C-MTS-2 and C-FIX-2

Input:

• Boolean network: a Boolean network (.bnet file)
• phenotype: a phenotype, we specify it in a file. You can see example in file phen_244.txt

For counting minimal trap spaces:

python3 script/run_minimal_trap_space.py -t 2 -bn tests/t1_244.bnet -phen tests/phen_244.txt

it should print the count in line: C-MTS-2:

For counting fixed points:

python3 script/run_fixed_point.py -t 2 -bn tests/t1_244.bnet -phen tests/phen_244.txt

it should print the count in line: C-FIX-2:

Running third task: C-MTS-3 and C-FIX-3

Input:

• Boolean network: a Boolean network (.bnet file)
• phenotype: a phenotype, we specify it in a file. You can see example in file phen_244.txt
• perturbation: a perturbation, we specify it in a file. You can see example in file pert_244.txt

For counting minimal trap spaces:

python3 script/run_minimal_trap_space.py -t 3 -bn tests/t1_244.bnet -phen tests/phen_244.txt -pert tests/pert_244.txt

it should print the count in line: C-MTS-3:

For counting fixed points:

python3 script/run_fixed_point.py -t 3 -bn tests/t1_244.bnet -phen tests/phen_244.txt -pert tests/pert_244.txt

it should print the count in line: C-FIX-3:

Preprocessing BNs

We used tsconj and fASP to encode BNs to ASP program, for minimal trap space and fixed points, respectively. The original implementation is modified for our usage.

Benchmark:

The benchmark of our CP2025 experiments is available at https://zenodo.org/records/19665913.

How to cite

If you use it, please cite our work:

@article{KTPM2025,
  title={Scalable counting of minimal trap spaces and fixed points in boolean networks},
  author={Kabir, Mohimenul and Trinh, Van-Giang and Pastva, Samuel and Meel, Kuldeep S},
  booktitle={CP},
  year={2025}
}

Contributors

• Mohimenul Kabir
• Van-Giang Trinh
• Samuel Pastva
• Kuldeep S Meel