Dynamic community metabolic modelling of a co-culture of Thermoanaerobacterium thermosaccharolyticum M5 and Clostridium acetobutylicum NJ4 from the publication Consolidated bioprocessing performance of a two-species microbial consortium for butanol production from lignocellulosic biomass .
The main steps in this project were:
- Automatic reconstruction of GEMs (CareveMe)
- Model validation and curation (COBRApy)
- Static modelling of individual strains (COBRApy)
- Dynamic modelling of individual strains (COMETS)
- Dynamic modelling of community (COMETS)
The GEM for the BiGG universal model, is located in the ../GEMs/ folder. The medium used for model reconstruction and simulation is in the medium.tsv file. The main results are presented in the notebooks m5_sim.ipynb, nj4_sim.ipynb, and community_sim.ipynb.
| Folder | Description |
|---|---|
| GEMs | Genome-scale metabolic models constructed for the case study strains, and GEMs from closely related strains |
| escher_maps/ | .json files to make escher map visualisations |
| exp_data/ | Experimental data retrieved from the case study |
| figures/ | All figures generated for the thesis |
| grid_search_results/ | Raw results from grid search over fermentation conditions |
| utils/ | Functions and scripts for simulations and analysis |
The utils/ folder contains functions and scripts to run simulation and analysis, here follows a overview of the content:
| File | Description |
|---|---|
| comets_functions.py | Functions to run single and sequential dFBA simulations |
| data_processing.py | Functions to clean the experimental data retrieved from case study publication |
| fermentation_optimisation.py | Script to run grid search over inoculation time, inoculation ratio, and xylan concentration |
| flux_coupling.py | Function to add flux coupling constraints |
| kinetic_params.py | Dictionary of kinetic parameter values |
| m5_modifications.py | Modifications for curation of M5 model |
| model_validation.py | Helper functions for model validation |
| nj4_modifications.py | Modifications for curation of NJ4 model |
| read_excel.py | Functions to read GEMs from Excel files |
| static_sim.py | Helper functions to run and plot FBA and FVA simulations |
| unit_conversion.py | Functions to perform unit conversions |
| Notebook | Description |
|---|---|
| community_sim.ipynb | Results for M5 and NJ4 community simulation |
| data.ipynb | Inspection and calculations on experimental data from publication |
| m5_sim.ipynb | Results from the M5 monoculture simulation |
| m5_validation.ipynb | Used to validate and curate the M5 GEM |
| nj4_sim.ipynb | Results from the NJ4 monoculture simulation |
| nj4_validation.ipynb | Used to validate and curate the NJ4 GEM |