This repository contains the data and scripts (Python and R) that were used in generation of a pan-genome and 252 A. fumigatus strain genome-scale metabolic models (GEMs) and their interaction simulations with the lung microbiome described by Mirhakkak et al. (2023). Running the scripts in A_fumigatus_GEM/src/ will generate the results in A_fumigatus_GEM/res/.
For instance, one can use the following Terminal command to regenerate the strain GEMs.
$ python A_fumigatus_GEM/src/build_strain_gem.py
Or the following in interactive python (e.g. ipython3)
%run A_fumigatus_GEM/src/build_strain_gem.py
Python Dependencies
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COBRApy 0.17.1
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IBM CPLEX 12.8.0.0
Python Modules:
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glob
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pickle
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numpy
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copy
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pandas
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re
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timeit
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itertools
R packages
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ggplot2 3.3.6
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ggrepel 0.9.1
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ComplexHeatmap 2.10.0
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circlize 0.4.15
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RColorBrewer 1.1-3
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ggtree 3.2.1
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ape 5.6-2
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tidyverse 1.3.2
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ggstance 0.3.5
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viridis 0.6.2
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dplyr 1.0.9
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ggsignif 0.6.3
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vegan 2.6-2
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tibble 3.1.8
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stringr 1.4.0
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phyloseq 1.34.0
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ggpubr 0.4.0
Citation
Mirhakkak, M. H., Chen, X., Ni, Y., Heinekamp, T., Sae-Ong, T., Xu, L. L., ..., Schäuble, S. & Panagiotou, G. (2023). Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome. Nature Communications, 14(1), 4369.