cthermgem-dev

This repository contains all code and data used to develop and analyze the iCBI655 genome scale model of C. thermocellum DSM1313.

If you use any part of this software please cite:

 Development of a genome-scale metabolic model of Clostridium thermocellum and its applications for integration of multi-omics datasets and strain design.
 Garcia, S.,Thompson, R.A., Giannone, R., Dash, S., Maranas, C., and Trinh, C. T. 
 In preparation.

Directory description

Models:

• iAT601: Published data for the starting model iAT601.
• Steps: Captures the initial development from iAT601 to the intermediate model iSG676.
• iSG: Files associated with the development of iSG676
• iSG676: Final state of the iSG676 model.
• iCBI: Contains the development of iCBI655 starting from iSG676.

Data:

• genome: Files related to the most update genome annotation of C. therm. DSM1313.
• datasets: Curated datasets from published literature.
• media: Different medium compositions to adjust simulation conditions.

Other:

• maps: Escher metabolic maps.
• analysis: Analyses done to the final iCBI655 model.
• test: Tests to ensure software and model work as intended.
• tools: General functions to analyze and configure the model.

Executing the code

The recomended approach is to use a python virtual environment:

# Install virtualenv in your system
virtualenv  ~/myenvs/cthermgem
source ~/myenvs/cthermgem/bin/activate
pip install -r requirements.txt

To run the environment in jupyter notebooks you must install the kernel. From within the cthermgem environment run:

pip install ipykernel # Already included in the requirements.txt
ipython kernel install --user --name=cthermgem

If you still experience issues with the Jupter kernel run:

python -m ipykernel install --user --name=cthermgem

To ensure that scripts can import modules from this project it needs to be added to the PYTHONPATH environment variable, e.g. in unix-derived OSs; export PYTHONPATH=$(pwd) from the project root directory. Alternatively, within python you can do import sys then sys.path.insert(0,'/path/to/project/root'), relative paths can also be used in that case , e.g. '../..' if the files is two directories below the root directory.

Notes/troubleshooting

• Earlier versions of cobrapy allowed to obtain the objective value from model.optimize().f in the most recent version (see requirements.txt) this is no longer valid, and instead model.optimize().objective_value needs to be used. Some files may still contain the outdated call, leading to unexpected behavior or errors. Run grep -R 'optimize().f' ./ to find affected instances.