This release significantly alters the previous layout of the library, making it more stable, more reliable, faster and solving a fundamental bug in the connection to DSGRN. Compatibility issues with DSGRN are also fixed.
With this version you can use NDMA to:
- reliably find "all" equilibria in a EMT Hill model with the boxy box algorithm
- find "all" equilibria in any Hill model, without the boxy box algorithm
- find saddle nodes w.r.t. vertical or horizontal paths
- crawl the DSGRN Morse graph looking for parameter regions with specific number of equilibria
- create parameter data points in a given DSGRN region (this feature is still under development and will se future expansions)
This code is companion to the paper "Global analysis of regulatory network dynamics: equilibria and saddle-node bifurcations" by Shane Kepley, Konstantin Mischaikow, and Elena Queirolo. All the results in the paper can be recreated by running this version, namely the codes:
TS_coherency.py (Figure 4)
nullclines_and_isolas.py (Figures 5 and 6)
main_heat_map.py (Figure 7)
EMT_DSGRNcoherency.py (Figure 8)
EMT_DSGRN_nonlocal_coherency.py (Figure 9 and 10)
EMT_pairwise_comparison.py (no figure)