Protocol for Thermodynamically Optimal Construction and Analysis of Metabolic Networks using ThermOptCOBRA

This directory contains the implementations and tools supporting the protocol to construct and analyze thermodynamically optimal genome-scale metabolic networks.

Directory Structure and Descriptions

All software packages and algorithms are located inside the Protocol_ThermOptCOBRA directory:

• ThermOptCOBRA: The core suite of MATLAB-based functions for incorporating thermodynamic constraints into metabolic network analysis. It contains:

  • ThermOptEnumerator: For enumerating all thermodynamically infeasible cycles (TICs) in a model.
  • ThermOptCC: For consistency checking and identifying thermodynamically blocked reactions.
  • ThermOptiCS: For constructing context-specific models (CSMs) under thermodynamic constraints.
  • ThermOptFlux: For post-processing flux distributions to remove cycle-related fluxes.
  • Associated Paper: Kumar & Bhatt (2025), iScience.

• Localgini: Contains the GiniReactionImportance.m implementation. This tool quantifies gene expression variability across samples using Gini coefficients to establish thresholding and extract core reactions for context-specific model reconstruction.

  • Associated Paper: Kumar & Bhatt (2025), npj Systems Biology and Applications.

• spectraCC: Contains the flux consistency checking modules (spectraCC.m, forwardcc.m, reverse.m) belonging to the SPECTRA framework. SPECTRA is a generalist method to reconstruct metabolic networks from multi-omics data at a large scale.

  • Associated Paper: Kumar et al. (2026), bioRxiv.

• looplessFluxSampler: An efficient toolbox utilizing the Adaptive Direction Sampling on a Box (ADSB) algorithm to sample the non-convex loopless and mass-balanced flux solution space of metabolic models.

  • Associated Paper: Saa et al. (2024), BMC Bioinformatics.

---

Citations and References

If you use these algorithms or resources in your research, please cite the respective papers:

1. ThermOptCOBRA

   • Kumar, S. P., & Bhatt, N. P. (2025). ThermOptCobra: Thermodynamically optimal construction and analysis of metabolic networks for reliable phenotype predictions. iScience, 28(8), 113005.
   • Journal Link / DOI

2. Localgini

   • Kumar, S. P., & Bhatt, N. P. (2025). Modelling reliable metabolic phenotypes by analysing the context-specific transcriptomics data. npj Systems Biology and Applications, 11(1), 23.
   • Journal Link / DOI

3. SPECTRA (spectraCC)

   • Kumar, S. P., Sridhar, S., Alsmadi, N., Mahadevan, R., & Bhatt, N. P. (2026). Generalist method to reconstruct metabolic networks from multi-omics data at large-scale. bioRxiv preprint.
   • Preprint Link / DOI

4. LooplessFluxSampler

   • Saa, P. A., Zapararte, S., Drovandi, C. C., & Nielsen, L. K. (2024). LooplessFluxSampler: An efficient algorithm for sampling the loopless flux solution space of metabolic models. BMC Bioinformatics, 25, 12.
   • Journal Link / DOI