This project uses Bayesian Survival Analysis (PYMC3) to study the rate of membrane electroporation events. The first electroporation times are obtained from coarse-grained molecular dynamics simulations using realistic membrane compositions with a constant external electric field. The simulations were run by prof. Lea Rems and the bayesian inference by myself, Dr. Sergio Pérez-Conesa. We are both members of the Delemottelab led by prof. Lucie Delemotte. All the explanations can be found in the article and the rest of code and data here
If you want to cite this code, please use CITE.bib, thank you!
Running the code
The code is based on the jupyter notebooks.
is used to convert the raw data into. Notebooks “ do the actual calculations.
Try out my binder to run the notebooks live on the cloud! It’s free
Unfortunatelly, you can’t train the models (too few memory on binder), but you can load them from the OSF repostory and analyze them in my binder.
Recreate conda environment
To recreate the conda environment used:
conda env create -f environment.yml
environment_exact.yml for the exact environment.
Getting additional data files
All the data, including the inference models, simulations etc. can be found in Open Software Foundation.
├── LICENSE │ ├── Makefile <- Makefile with commands like `make update_data` or `make format` │ ├── README.md <- The top-level README for developers using this project. ├── data │ ├── external <- Data from third party sources. │ ├── interim <- Intermediate data that has been transformed. │ └── processed <- The final, canonical data sets for modeling. │ ├── models <- Learned models │ ├── notebooks <- Jupyter notebooks. │ ├── reports <- Generated analysis as HTML, PDF, LaTeX, etc. │ ├── final_figures <- Generated graphics and figures to be used in final report. │ └── docs <- Generated LaTeX, pdf, word, powerpoint etc. │ ├── environment.yml <- The necessary packages to install in conda environment. │ ├── environment_exact.yml <- The exact package versions used. │ ├── src <- Source code for use in this project. │ ├── __init__.py <- Makes src a Python module │ │ │ └── data <- Scripts to download or generate data │ └──
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