Peer-reviewedCC BY-NC-NDSTAR protocols8 Oct 2026

Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.

Pavan Kumar¹
Nirav Pravinbhai Bhatt

¹BioSystems Engineering and Control (BiSECt) Lab, Institute of Technology Madras, Chennai, Tamil Nadu, India; The Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras, Chennai, Tamil Nadu, India; Department of Data Science and AI, Wadhwani School of Data Science and AI, IIT Madras, Chennai, Tamil Nadu, India. Electronic address: [email protected].

Abstract

Thermodynamically infeasible cycles violate the second law of thermodynamics but are permitted by stoichiometric flux analysis. Here, we present a protocol for the construction and analysis of metabolic networks using ThermOptCOBRA, a MATLAB extension of the COBRA Toolbox. We describe steps for enumerating cycles (ThermOptEnumerator), determining feasible directions and blocked reactions (ThermOptCC), and building thermodynamically consistent context-specific models using omics data (ThermOptiCS). We then detail procedures for removing loops or sample loopless flux distributions (ThermOptFlux/ADSB-ThermOptFlux). For complete details on the use and execution of this protocol, please refer to Kumar and Bhatt.¹.

Tree-to-cycle transition scale characterizes trade-off between dissipation and construction cost in adaptive transport networks
J. Stark, C. Godin
bioRxiv2 Sep 2026PreprintCC BYFull textBiophysicsbioRxiv
Fecal Metabolic and Microbial Responses to Five Acute Fueling Strategies During a 60-Minute Rowing Protocol: A Randomized Crossover Multi-Omics Pilot Study.
Xiangyu Wang, Jian Huang
Metabolites28 Sep 2026Peer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMC
Single-cell sequencing reveals immune networks and metabolic reprogramming in gynecological malignancies
Li Ren, Xuemei Li
Frontiers in Immunology19 Oct 2026Peer-reviewedCC BY 4.0Full textMolecular biology & gene regulationCrossrefPMC
Modeling microbiome modulation of tumor metabolic networks to predict synergistic therapies
Annie J. Badenoch, Zeyang Pang, Carolina H. Chung +6
Cell Reports Methods13 Aug 2026Peer-reviewedCC BY-NC-ND 4.0Full text1 citedMolecular biology & gene regulationPMC
Gut-liver axis in liver pre-metastatic niche formation: immune networks, microbial, and metabolic and emerging therapeutic opportunities
Leyi Zhao, Qiutong Lin, Danyuan Zhang +8
Frontiers in Microbiology15 Oct 2026Peer-reviewedCC BY 4.0Full textMolecular biology & gene regulationCrossrefEurope PMCEurope PMCPMC

Cite

BibTeX RIS

BibTeX

@article{kumar2026protocol,
  title = {{Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.}},
  author = {Pavan Kumar and Nirav Pravinbhai Bhatt},
  journal = {STAR protocols},
  year = {2026},
  month = oct,
  doi = {10.1016/j.xpro.2026.104890},
  url = {https://europepmc.org/article/MED/42848515},
  note = {CC BY-NC-ND},
}

RIS

TY  - JOUR
TI  - Protocol for thermodynamically optimal construction and analysis of metabolic networks using ThermOptCOBRA.
AU  - Pavan Kumar
AU  - Nirav Pravinbhai Bhatt
PY  - 2026
DA  - 2026/10/08
JO  - STAR protocols
DO  - 10.1016/j.xpro.2026.104890
UR  - https://europepmc.org/article/MED/42848515
AB  - Thermodynamically infeasible cycles violate the second law of thermodynamics but are permitted by stoichiometric flux analysis. Here, we present a protocol for the construction and analysis of metabolic networks using ThermOptCOBRA, a MATLAB extension of the COBRA Toolbox. We describe steps for enumerating cycles (ThermOptEnumerator), determining feasible directions and blocked reactions (ThermOptCC), and building thermodynamically consistent context-specific models using omics data (ThermOptiCS). We then detail procedures for removing loops or sample loopless flux distributions (ThermOptFlux/ADSB-ThermOptFlux). For complete details on the use and execution of this protocol, please refer to Kumar and Bhatt.¹.
SN  - 2666-1667
ER  -

Abstract

Related

Cite