Testing Binomiality of Chemical Reaction Networks Using Comprehensive Gröbner Systems
We consider the problem of binomiality of the steady state ideals of biochemical reaction networks. We are interested in finding polynomial conditions on the parameters such that the steady state ideal of a chemical reaction network is binomial under every specialisation of the parameters if the conditions on the parameters hold. We approach the binomiality problem using Comprehensive Gr\"obner systems. Considering rate constants as parameters, we compute comprehensive Gr\"obner systems for various reactions. In particular, we make automatic computations on n-site phosphorylations and biomodels from the Biomodels repository using the grobcov library of the computer algebra system Singular.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
When algebra twinks system biology: a conjecture on the structure of Gröbner bases in complex chemical reaction networks
We address the challenge of identifying all real positive steady states in chemical reaction networks (CRNs) governed by mass-action kinetics. Traditional numerical methods often require specific initial guesses and may …
Analysis of the Conradi-Kahle Algorithm for Detecting Binomiality on Biological Models
We analyze the Conradi-Kahle Algorithm for detecting binomiality. We present experiments using two implementations of the algorithm in Macaulay2 and Maple on biological models and assess the performance of the algorithm …
Algebraic approaches for the decomposition of reaction networks and the determination of existence and number of steady states
Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analys…
An Efficient Algorithm for Determining the Equivalence of Zero-one Reaction Networks
Zero-one reaction networks play a crucial role in cell signaling. Determining the equivalence of reaction networks is a fundamental computational problem in the field of chemical reaction networks. In this work, we devel…
Stress Testing BERT Anaphora Resolution Models for Reaction Extraction in Chemical Patents
The high volume of published chemical patents and the importance of a timely acquisition of their information gives rise to automating information extraction from chemical patents. Anaphora resolution is an important com…