kchemorion/RNMUpdate: v2.2 - Corrected 82-Node Topology from Authoritative Source Files

What's Changed This release corrects the network topology data to use the authoritative adjacency-list source files (Enriched_SP.xlsx and Initial_SP.xlsx), replacing the previously used edge-list file. Key fixes Correct enriched topology: 82 nodes, 199 edges (147 activation + 52 inhibition) from Enriched_SP.xlsx Added initial topology: 66 nodes, 86 edges from Initial_SP.xlsx for basal-only simulations Updated network loader: load_adjacency_list() now handles "NOTHING" entries and applies name harmonization (e.g., TGFRI → TGFBRI) All scripts switched from load_edge_list() to load_adjacency_list() Regenerated outputs 200-run paired simulation (basal + IL-1β + TLR) All figures (bar charts, boxplots, histograms, KDE, cluster plots) paired_statistics.csv with full statistical analysis model.xml SBML Level 3 Version 2 model Results validated against manuscript Basal steady state: 81/82 nodes match expected anabolic-high / catabolic-low profile IL-1β stimulation: c-Jun ↑, p65 (NF-κB) ↑, IkBα ↓ — consistent with experimental data TLR stimulation: same qualitative shift at attenuated magnitudes Network summary | Property | Value | |----------|-------| | Proteins (nodes) | 82 | | Directed interactions | 199 | | Activation edges | 147 | | Inhibition edges | 52 | | NP-specific corpus | 41.4% |