Apoptosis is not the dominant axis: an evidence reappraisal of the Acorus tatarinowii–Polygala tenuifolia herb pair in vascular cognitive impairment
Year: 2026
Type: software
Abstract: 1. What this repository contains Directory Contents scripts/ Numbered analysis scripts (01–14). Each step reads from data/ or results/ and writes to results/ or figures/. manuscript/ manuscript.md — the full article text; dock_local.py / VCI_docking_colab.ipynb — molecular docking pipeline. results/ All intermediate and final result tables (CSV). Every figure and table in the paper can be regenerated from these files. figures/ Figures 1–8 and Supplementary Figure S1. Scripts and utilities related only to local machine troubleshooting or journal-specific formatting (wsl_setup.sh, fix_miniforge.sh, fix_python312.sh, render_poses.sh, cleanup_paths.py, check_docx.py, 13_md_to_docx.py, make_release_zip.py) were not included: they are not part of the analysis and are machine-specific. They remain available in the authors' working copy. 2. Requirements Python ≥ 3.10 with: numpy pandas scipy matplotlib requests For molecular docking only (optional step, dock_local.py): rdkit, vina, and either meeko or openbabel. These were run under Linux (WSL2/Ubuntu) because no precompiled Windows wheel was used; the Colab notebook provides a zero-install alternative. All scripts resolve paths relative to their own location, so the repository can be placed anywhere on the filesystem. 3. Reproduction pipeline Run from the repository root: python scripts/01_prepare_matrix.py # expression matrix, collapse technical replicatespython scripts/02_diff_expr.py # differential expression (limma-style linear model + BH)python scripts/03_enrichment.py # Enrichr multi-library enrichmentpython scripts/04_animal_cch.py # rodent chronic cerebral hypoperfusion datasetspython scripts/05_compound_targets.py # constituent structures (PubChem / ChEMBL)python scripts/06_celltype.py # brain cell-type signature scoringpython scripts/07_targets_network.py # disease / pathway / constituent target assemblypython scripts/08_integration_network.py # four-layer intersection, STRING PPI, ADMETpython scripts/09_cross_species.py # cross-species convergence testpython scripts/10_figures.py # Figures 1–6python scripts/11_docking_analysis.py # ligand efficiency, size-bias test, Figures 7–8python scripts/12_pose_prepare.py # binding-site residues and hydrogen bondspython scripts/14_render_poses_mpl.py # Supplementary Figure S1 (pure-CPU 3D rendering) Molecular docking (manuscript/dock_local.py, 6 targets × 9 constituents = 54 runs) requires the docking stack listed above and reads the receptor structures listed in the manuscript's Appendix. Step 11 onward depends on its output (results/docking_results.csv). 4. Data sources All primary data are public and were retrieved programmatically; none contain identifiable human information beyond the original studies' own releases. Dataset Source Role GSE122063 Gemma (UBC), https://gemma.msl.ubc.ca/rest/v2/datasets/GSE122063 Human cortical transcriptome (VaD / AD / control), primary analysis GSE199508.2 Gemma Rodent chronic hypoperfusion model A, cross-species validation GSE210666 / BCAS Gemma Rodent model B, cross-species validation Enrichr https://maayanlab.cloud/Enrichr/ Functional enrichment Open Targets Platform v4 GraphQL API https://api.platform.opentargets.org/api/v4/graphql Disease–target associations PubChem / ChEMBL REST APIs — Constituent structures, physicochemical descriptors, measured activities STRING API — Protein–protein interaction network RCSB PDB (1UKI, 4S0O, 5ELI, 2Z7X, 4LVT, 2J30) — Receptor structures for docking data/ holds the processed local copies consumed by scripts/01. It is not redistributed here due to size; re-download it from Gemma using the dataset IDs above, or request it from the corresponding author. 5. Ethics This study re-analysed previously published, publicly available datasets. No new human or animal experiments were performed; accordingly no additional ethical approval was required. Original dataset usage terms apply. 6. Licence Code: GPL-3.0. Result tables and figures derived from public data: CC BY 4.0. Please cite the associated article when reusing these materials.
Author: guo, chunyu
Language: English
Subfield: Complementary and alternative medicine
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W7214764880