CRN Steady-State Ideals (Gröbner Basis Computation)

A collection of Macaulay2 scripts that build steady-state ideals for biochemical reaction-network models and compute their reduced Gröbner bases. Each script follows the same structure:

1. declare a rational-function coefficient field in the rate constants and conserved totals,
2. create a polynomial ring ordered lexicographically,
3. define the mass-action steady-state equations,
4. add linear conservation laws,
5. generate the ideal and compute a reduced Gröbner basis.

In some examples, certain rate constants are assigned values a priori.

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Repository layout

file	model	key reference
ex_ERK.m2	ERK core	Loman et al. 2023
ex_TGFb.m2	TGF-β receptor network	Samal et al. 2016
ex_GRN.m2	Gene Regulatory Network	Conradi et al. 2017
ex_minimal_mapk.m2	Minimal MAPK Cascade	Hadač et al. 2017
ex_Wnt.m2	WNT signalling pathway	Gross et al. 2016
ex_toy.m2	Toy Network	Berra et al. 2024
ex_toy2.m2	Another Toy Network	Berra et al. 2024

Requirements

• Macaulay2 ≥ 1.21