Supercoiling-mediated feedback simulation dataset

Supercoiling-mediated feedback simulation dataset

Background
These files represent simulation datasets generated for the publication
"Supercoiling-mediated feedback rapidly couples and tunes transcription"
by Christopher Johnstone and Kate E. Galloway.

All figures in the paper can be replicated by using the code available at https://github.com/GallowayLabMIT/tangles_model (permalink) and these datasets.

File summary

• `unprocessed_datasets.zip` contains the merged Julia simulation files.
• `preprocessed_datasets.zip` contains the smaller, preprocessed datasets used for actuall plotting of data figures.

File format

• The preprocessed datasets are serialized Pandas dataframes (gzipped Parquet files).
• The unprocessed datasets are self-describing HDF/H5 files.

Usage
The main figure-plotting notebook, `notebooks/modeling_paper_figures.ipynb`, contained in the code repository mentioned above can use either the unprocessed or preprocessed datasets. If the preprocessed datasets are present, it will load them directly.  If the preprocessed datasets are not present, that Python notebook will preprocess the data.

License
This data is available under a CC-BY 4.0 International License.
Please attribute:

• Christopher Johnstone (cjohnsto@mit.edu)
• Kate E. Galloway (katiegal@mit.edu)