NDMA v1

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)

NDMA version 0

This is the initial release of NDMA: Network Dynamics Modeling and Analysis.

With this release, you can look at the Toggle Switch and the EMT models, search for saddle nodes, as well as track equilibria with continuation.

This library accompany the paper "Global analysis of regulatory network dynamics: equilibria and saddle-node bifurcations" by Shane Kepley, Konstantin Mischaikow, and Elena Queirolo, 2022

Developers: Shane Kepley, and Elena Queirolo