TY - GEN A1 - Liu, Fei A1 - Assaf, George A1 - Chen, Ming A1 - Heiner, Monika T1 - A Petri nets-based framework for whole-cell modeling T2 - Biosystems N2 - Whole-cell modeling aims to incorporate all main genes and processes, and their interactions of a cell in one model. Whole-cell modeling has been regarded as the central aim of systems biology but also as a grand challenge, which plays essential roles in current and future systems biology. In this paper, we analyze whole-cell modeling challenges and requirements and classify them into three aspects (or dimensions): heterogeneous biochemical networks, uncertainties in components, and representation of cell structure. We then explore how to use different Petri net classes to address different aspects of whole-cell modeling requirements. Based on these analyses, we present a Petri nets-based framework for whole-cell modeling, which not only addresses many whole-cell modeling requirements, but also offers a graphical, modular, and hierarchical modeling tool. We think this framework can offer a feasible modeling approach for whole-cell model construction. KW - Whole-cell modeling KW - Systems biology KW - Petri nets KW - Modeling framework Y1 - 2021 UR - https://www.sciencedirect.com/science/article/abs/pii/S0303264721001738?via%3Dihub U6 - https://doi.org/10.1016/j.biosystems.2021.104533 SN - 0303-2647 SN - 1872-8324 VL - 210 ER - TY - GEN A1 - Colombo, Riccardo A1 - Damiani, Chiara A1 - Gilbert, David A1 - Heiner, Monika A1 - Mauri, Giancarlo A1 - Pescini, Dario T1 - Emerging ensembles of kinetic parameters to identify experimentally observed phenotypes T2 - BMC bioinformatics KW - Ensembles KW - Fluxes KW - Kinetic parameters KW - Mechanistic simulations KW - Metabolism KW - ODEs KW - Steady state KW - Systems biology Y1 - 2018 UR - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2181-7 U6 - https://doi.org/10.1186/s12859-018-2181-7 SN - 1471-2105 VL - 19 IS - Suppl. 7 SP - 46 EP - 59 ER -