Comparing automated recommendation methods across scenarios on simulated DBTL cycles.

Project structure

1. data/config_files_yml: contains all configurations of DBTL cycle processes for the simulation study.
2. results: all the results of the simulation study
3. models: consists of the bioprocess models
4. 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

Running your own simulated DBTL scenarios (TODO)

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