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OpenFLUX2: (13)C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel
Mikhail S Shupletsov1,2, Lyubov I Golubeva3, Svetlana S Rubina4
1Ajinomoto-Genetika Research Institute, 117545, Moscow, Russian Federation. mikle.shupletsov@gmail.com.
This study introduces OpenFLUX2, an open-source software enhancing parallel labeling experiments (PLEs) for metabolic flux analysis (MFA). OpenFLUX2 improves intracellular flux precision by integrating complementary data from multiple labeling experiments.
Area of Science:
- Metabolic Engineering
- Systems Biology
- Computational Biology
Background:
- Steady-state (13)C-based metabolic flux analysis ((13)C-MFA) quantifies intracellular fluxes using experimental and computational methods.
- Traditional (13)C-MFA often relies on single labeling experiments (SLEs).
- Parallel labeling experiments (PLEs) offer improved flux precision by integrating complementary data from multiple labeling experiments.
Purpose of the Study:
- To extend the open-source software OpenFLUX for the analysis of PLE data.
- To improve the precision and resolution of intracellular flux quantification in metabolic flux analysis.
- To provide a user-friendly software environment for implementing PLE-based (13)C-MFA.
Main Methods:
- Extension of the OpenFLUX software to accommodate PLE data analysis.
- In silico simulations to validate improved flux precision with PLE data compared to SLE data.
- Optimization of experimental design for tracer selection to minimize flux variances.
- Computation of flux parameters, goodness-of-fit testing, flux identifiability analysis, and Monte Carlo-based determination of flux confidence intervals.
Main Results:
- OpenFLUX2 enables the computation of PLE data, demonstrating improved flux precision compared to SLE-based analysis.
- Efficient flux resolution is achieved through optimized experimental design in PLE-mediated analysis.
- The software provides comprehensive analysis including experimental design optimization, flux parameter computation, model adequacy testing, and precise flux confidence interval determination.
Conclusions:
- The open-source OpenFLUX2 software facilitates the implementation of PLEs for steady-state (13)C-MFA.
- It offers a user-friendly environment for both beginners and experienced users.
- OpenFLUX2 supports experimental design, quantitative flux evaluation, and statistical analysis for improved metabolic flux quantification.
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