Instructions:

1. Clone or Download the Repository

git clone https://github.com/EdwardCatoiu/StressME-DynamicME

2. From the root of the StressME-DynamicME folder (where the Dockerfile and new scripts are), build the docker image by running:

docker build -t stressme_with_dynamicme .

3. Still in the same folder/terminal, start the container with:

docker run -it -p 8888:8888 -v "$PWD":/app stressme_with_dynamicme

4. Open a browser and go to http://localhost:8888

To Run dynamicME

5. Modify config_dynamicME.yamlas needed
   • Important: Change project_name
   • Optional: Time, timestep, volume, mass, media concentration, uptake rates

project_name: 'demo' # change to avoid overwriting the demo results

6. Open terminal in Jupyter
   

7. Run from command line (/app #)

   • Results and config file saved to run_dynamicme_results/{project_name}/

python3 run_dynamicme.py config_dynamicME.yaml

8. Visualize the results using figures_dynamicme.ipynb
   • Plot growth rate and yield
   • Plot biomass composition
   • Plot tracked metabolite concentrations (demo --> media composition)
   • Plot protein translation rates
   • Plot complex formation rates
   • Plot proteome distribution (ProteoMap/Voronoi)

To Run stressME

9. Modify config_stressME.yaml as needed
   • Important: Change project_name
   • Optional: Modify stresses & substrates

project_name: 'demo' # change to avoid overwriting the demo results

10. Run from command line (/app #)
    • Results and config file saved to run_stressme_results/{project_name}/

python3 run_stressme.py config_stressME.yaml

11. Visualize the results using figures_stressme.ipynb
    • Plot proteome distribution (ProteoMap/Voronoi)