Locat-paper

Included

• locat-0.1 should be available separately and can be pointed to with the LOCAT01_PATH environment variable
• Updated locat-0.1 reproducibility notebooks under notebooks/figures/
• Updated simulation/runtime scripts under notebooks/figures/Simulations/
• Small and medium support files, result summaries, and selected figure outputs
• Dependency audit in manifests/repro_bundle_manifest.csv

Not Included

Some required data/derived objects are too large for a normal GitHub repo (hundreds of MB to multiple GB). These are listed in manifests/repro_bundle_manifest.csv with status excluded_large.

Folder Layout

The bundle mirrors the working folder structure used in the main LOCAT repo:

• notebooks/figures/FigS1_3kPBMC
• notebooks/figures/Fig2_Dermal_Condensate
• notebooks/figures/Fig3_ESC_Timecourse
• notebooks/figures/Perturb_PBMC
• notebooks/figures/Simulations
• data/ for smaller input and summary files

Path Note

Copied notebooks/scripts now resolve locat-0.1 from LOCAT01_PATH when set, or from a sibling locat-0.1 checkout. Notebook-adjacent support files were moved into support_files/ subfolders to keep the analytical notebooks and scripts visually clean.