This is the supplementary code and data for the paper Large-scale analysis of optimisation methods for parameter estimation problems in the life sciences by Stephan Grein, David R. Penas, Daniel Weindl, Polina Lakrisenko, Julio R. Banga, and Jan Hasenauer.
Information about the optimization runs is provided in the
optimizations/ directory.
Due to the large size of the raw data, we only provide summarized data that is
sufficient to reproduce the figures in the paper. These data are available in
the data/ directory.
Scripts for generating the figures in the paper are available in the
data_analysis/ directory.
The analysis environment is managed with uv. To reproduce all figures and tables, run:
cd data_analysis
./run_all.shThis installs the pinned Python environment (uv sync --frozen) and then
runs every notebook and script in the directory, in dependency order,
writing the generated figures and tables to data_analysis/out/.
Code is licensed under the BSD 3-Clause License (see LICENSE), and data is licensed under CC-BY-4.0 (see LICENSE-DATA).