- data/config_files_yml: contains all configurations of DBTL cycle processes for the simulation study.
- results: all the results of the simulation study
- models: consists of the bioprocess models
- scripts: consists of the building of bioprocess models (build_models dir), the analysis (two directoreis), and a setup_configs for the construction of the config files for simulation.
BenchmarkProjectDSMF
├── data
│ ├── config_files_yml
├── figures
│ ├── figure1
│ ├── figure2
│ ├── figure3
│ ├── figure4
│ ├── figures_paper_old
│ ├── individual_variables
│ ├── metabolic_engineering_conference
│ ├── statistics
│ └── SupportingInfo
├── literature
├── models
│ ├── bioprocess_models
│ └── test_mlmodel
├── results
│ ├── optimization_results
│ ├── pathway_validation
│ ├── results_for_plots_paper
│ ├── statistics_combinatorial_exp
│ └── statistics_compare_coefficients
├── scripts
│ ├── analysis
│ ├── analysis_figures
│ ├── build_models
│ ├── scripts_dev
│ └── setup_configs
├── source
└── tests
Simulation datasets generated using the different config files can be found on the 4tu repository.
We provide a workflow for running simulated DBTL scenarios Step 1: Construct a config file using a command line interface or make a manual config setup python scripts inspired by one of the scripts used in this work