A chemical reaction network model of PURE

Data and models repository for the paper "A chemical reaction network model of PURE," along with additional simulations and validation experiments. The folder contains all Python scripts used to simulate protein expression and plot figures seen in the paper "A chemical reaction network model of PURE" by Zoila Jurado, Ayush Pandey, and Richard M. Murray. Additionally, all simulation runs and experimental results are included.

Installation

1. Run pip install -r requirements.txt from your terminal.

Or, if you prefer to install everything manually, you can:

1. Install biocrnpyler: pip install biocrnpyler>=1.1.1
2. Install bioscrape: pip install bioscrape>=1.2.0
3. If Step 2 fails, you can clone the Bioscrape repository and manually install the package. Run python setup.py install to install bioscrape once you meet all the installation requirements.
4. Install seaborn, holoviz, corner, svglib, scikit-learn, bokeh-catplot, openpyxl, bokeh, jupyter_bokeh ==2.0.0, and panel==0.13.1

How to navigate this repository

PURE CRN models

We use BioCRNpyler to generate chemical reaction network models to building a transcription (TX) and translation (TL) model for cell-free protein synthesis using PURE. The generation of all models are in the modeling/ directory in this repository.

Inferencing on TX-only data

Scripts and results for the parameter inferencing for the TX-only model on MGapt expression is under the Inferencing_MGapt directory.

Experimental data

All calibration data used of this repository is available under the Data_files directory. Additional calibration data use can be found under the 'Calibration_MGapt','Calibration_MGapt' directory. The plasmids used in this paper are available from myTXTL T7 Expression Kit.

Simulation Experiments

All simulations from the model are available under the Simulation_results directory in folders corresponding with model run. Subfolder Nuclues_Simulations contains, specific simulations around the separation of transcription and translation under different nucleus conditions.

SBML models

All generated SBML models are available in the Models directory.

Scripts

All scripts used to build model and plotting are located in the main folder.

References

The PURE CRN model is based on Matsuura 2017. For more details, see PURE simulatator.

Contact

Contact Zoila Jurado if you have any questions.