Minimal Cut Sets (MCSs) analysis of a consortium of P. aeruginosa and S. aureus.
This repository uses aspefm to compute Minimal Cut Sets using Answer Set Programming (ASP).
The module mparser should be used for converting metabolic networks into ASP rules.
The repository contains our context-specific models used for the construction of the consortium.
The models in models and their compressed counterparts are adapted from the iPae1146 and iYS854 genome-scale models.
The repository also contains code for benchmarking our aspefm tool against CNApy and CoBAMP.
Example executions of the tools are found in the scripts folder.
Conversion of MCSs into enzyme targets using GPRs and ASP is described in the models/gpr folder.
And outputs used in our analysis of the consortium of P. aeruginosa and S. aureus are provided in outputs.
The latter include the protein structures and alignments of our retrieved consortium-level targets.
Further code for computing our study's figures and in particular for the analysis concerning the enzyme targets' protein structures is not provided here but is available on request.
The code requires Python version 3.
Requirements are detailed in requirements.txt.
clingo version 5.4.0, compilation of clingo with Python is mandatory
conda install -c potassco clingo
IBM cplex version 12.1.0 or above.
aspefm and mparser are submodules of this repository.
Please refer to their respective documentation.
The full repository and its submodules can be downloaded/cloned using:
git clone --recurse-submodules https://github.com/maxm4/paSAmcs
See more information: https://git-scm.com/book/en/v2/Git-Tools-Submodules
zip -F aspefm_consortium_size_16_1.5_days.zip --out aspefm_output.zip
unzip aspefm_output.zip
The zip and unzip utilies are pre-installed in any Linux distribution.
iPae1146 was published in the following paper: Bartell, J. A. et al. Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis. Nature Communications 8, 14631 (2017).
iYS854 was published in the following paper: Seif, Y. et al. Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits. Nat Commun 9, 3771 (2018).
CNApy was published in the following paper: Thiele, S., von Kamp, A., Bekiaris, P. S., Schneider, P. & Klamt, S. CNApy: a CellNetAnalyzer GUI in Python for Analyzing and Designing Metabolic Networks. Bioinformatics (2021)
CoBAMP was published in the following paper: Vieira, V. & Rocha, M. CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models. Bioinformatics 35, 5361–5362 (2019).
aspefm was published in the following paper: Mahout, M., Carlson, R. P. and Peres, S. Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism. Processes 8, 1649 (2020).
Please contact Maxime Mahout if you have any questions about the repository's content.