Reframing the role of the objective function in its proper context for metabolic network modeling

Mohammad Mazharul Islam; William Shao; Mariska Batavia; Roseanne M Ford; Bernhard O Palsson; Jens Nielsen; Costas D Maranas; Sang Yup Lee; Jason A Papin

doi:10.1016/j.cels.2025.101298

Reframing the role of the objective function in its proper context for metabolic network modeling

Cell Syst. 2025 Jun 18;16(6):101298. doi: 10.1016/j.cels.2025.101298.

Authors

Mohammad Mazharul Islam¹, William Shao¹, Mariska Batavia¹, Roseanne M Ford², Bernhard O Palsson³, Jens Nielsen⁴, Costas D Maranas⁵, Sang Yup Lee⁶, Jason A Papin⁷

Affiliations

¹ Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA.
² Department of Chemical Engineering, University of Virginia, Charlottesville, VA, USA.
³ Department of Bioengineering and Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
⁴ Division of Systems and Synthetic Biology, Chalmers University of Technology, Gothenburg, Sweden.
⁵ Department of Chemical Engineering, Penn State University, University Park, PA, USA.
⁶ Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science & Technology (KAIST), Daejeon, Republic of Korea.
⁷ Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA. Electronic address: papin@virginia.edu.

PMID: 40541323
DOI: 10.1016/j.cels.2025.101298

Abstract

The "objective function" is a core concept in metabolic network modeling. Its use has enabled the analysis of large data to drive deeper understanding of cellular metabolism. This commentary reframes how the objective function is discussed to enhance its value and clarify misunderstandings in metabolic network modeling.

MeSH terms

Humans
Metabolic Networks and Pathways* / physiology
Models, Biological*