Code for: Monotone and non-monotone pace along trajectories of nonlinear differential equations, with an application to the tempo of cell differentiation
Year: 2026
Type: software
Abstract: Code accompanying the article "Monotone and non-monotone pace along trajectories of nonlinear differential equations, with an application to the tempo of cell differentiation" (N. Okui). The archive contains:- notebooks/pace_GSE279710_v3.ipynb: a Jupyter notebook (Google Colab) that downloads the public single-cell RNA-seq time course GEO GSE279710 (Shen et al., Sci Data 12:1238, 2025) and reproduces the analysis in Section 8 of the article: naive and split-half estimates of sampled pace between day means, bootstrap intervals, and principal-component read-outs.- figures/fig1_examples.py: Figure 1 (closed-form examples).- figures/fig2_data.py and figures/summary_v3.json: Figure 2 and the summary statistics it is drawn from. Requirements: Python 3 with NumPy, SciPy, pandas, scikit-learn and Matplotlib. Random seed 0. Released under the MIT licence.
Author: Okui, Nobuo
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225459042