This repository complements the manuscript "Computational modelling reveals and predicts flux differences in nucleotide metabolism in IL-4-treated Cyp27a1-KO bone marrow-derived macrophages". It contains metabolic models, scripts, spreadsheets and a tutorial on how to perform a gene knockout of interest, as well as performing downstream processing and vizualization schemes. The work has been performed on Macintosh M1 Pro 2021 machine running OSX Sonoma 14.5. Expected run time for the demo tutorial: less than 1 hr. Expected run time for the entire analysis: 1-2 days, where the bulk of the resources are used up by the sampling algorithm so it is recommended to use compute cluster to run this part of the analysis. No non-standard hardware is required.
- Sequence-level analysis:
STAR v2.7.11a (source: https://github.com/alexdobin/STAR)
Salmon v1.10.1 (source: https://combine-lab.github.io/salmon/getting_started/)
FastQC v0.12.1 (source: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Multiqc v1.16 (source: https://github.com/MultiQC/MultiQC)
- In MATLAB environment:
MATLAB v2023a
MATLAB v2019b (for running fastFVA algorithm)
RAVEN toolbox v2.8.4 (installation source: https://github.com/SysBioChalmers/RAVEN; includes core software resource: Task-driven Integrative Network Inference for Tissues, tINIT)
COBRA toolbox v3.4 (installation guide: https://opencobra.github.io/cobratoolbox/stable/installation.html)
Mouse1 Metabolic Model v1.7.0 (accessible from https://github.com/SysBioChalmers/Mouse-GEM)
Gurobi - optimization suite v9.5.2 (installation guide with free academic version: https://www.gurobi.com/academia/academic-program-and-licenses/)
IBM CPLEX v12.10 Optimization Studio (free academic version: https://www.ibm.com/support/pages/ibm-ilog-optimization-academic-initiative)
- In R environment (installation either with
install.packages()orBiocManagerpackage):
R v4.3.1
DESeq2 v1.40.2
tximeta v1.18.1
clusterProfiler v4.8.2
Typical install time for the following dependencies: less than 1 hour