Supercoiling-mediated feedback simulation dataset

<p><strong>Supercoiling-mediated feedback simulation dataset</strong></p> <p><strong>Background</strong><br> These files represent simulation datasets generated for the publication<br> &quot;Supercoiling-mediated feedback rapidly couples and tunes transcription&quot;<br> by Christopher Johnstone and Kate E. Galloway.</p> <p>All figures in the paper can be replicated by using the code available at <a href="https://github.com/GallowayLabMIT/tangles_model">https://github.com/GallowayLabMIT/tangles_model</a> (<a href="https://doi.org/10.5281/zenodo.7054394">permalink</a>) and these datasets.</p> <p><strong>File summary</strong></p> <ul> <li>`unprocessed_datasets.zip` contains the merged Julia simulation files.</li> <li>`preprocessed_datasets.zip` contains the smaller, preprocessed datasets used for actuall plotting of data figures.</li> </ul> <p><strong>File format</strong></p> <ul> <li>The preprocessed datasets are serialized Pandas dataframes (gzipped Parquet files).</li> <li>The unprocessed datasets are self-describing HDF/H5 files.</li> </ul> <p><strong>Usage</strong><br> 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.&nbsp; If the preprocessed datasets are not present, that Python notebook will preprocess the data.</p> <p><br> <strong>License</strong><br> This data is available under a CC-BY 4.0 International License.<br> Please attribute:</p> <ul> <li>Christopher Johnstone (cjohnsto@mit.edu)</li> <li>Kate E. Galloway (katiegal@mit.edu)</li> </ul>