ArticleMicrobial cell factories2009
OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis.
Article in Microbial cell factories, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Metabolic engineering of Corynebacterium glutamicum for high-yield de novo biosynthesis of 5-aminovaleramide, a promising bio-based monomer.Microbial cell factories · 2026Article
- GlobalNature metabolism · 2024Article
- INCAWrapper: a Python wrapper for INCA for seamless data import, -export, and -processing.Bioinformatics advances · 2024Article
- HMicroorganisms · 2023Article
- Quantitative insight into the metabolism of isoprene-producing Synechocystis sp. PCC 6803 using steady statePhotosynthesis research · 2022Article
- Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas.RSC advances · 2022Review
- Genotypic and phenotypic diversity among Komagataella species reveals a hidden pathway for xylose utilization.Microbial cell factories · 2022Review
- GC/MS-basedMicrobial cell factories · 2022Article
- The Metabolic Flux Probe (MFP)-Secreted Protein as a Non-Disruptive Information Carrier forInternational journal of molecular sciences · 2021Article
- Stable Isotopes for Tracing Cardiac Metabolism in Diseases.Frontiers in cardiovascular medicine · 2021Review
- Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes.Metabolites · 2020Review
- DynamiciScience · 2020Article
- Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale.Biotechnology for biofuels · 2020Article
- Metabolic Rearrangements Causing Elevated Proline and Polyhydroxybutyrate Accumulation During the Osmotic Adaptation Response ofFrontiers in bioengineering and biotechnology · 2020Article
- Impact framework: A python package for writing data analysis workflows to interpret microbial physiology.Metabolic engineering communications · 2019Article
- Snail-Overexpression Induces Epithelial-mesenchymal Transition and Metabolic Reprogramming in Human Pancreatic Ductal Adenocarcinoma and Non-tumorigenic Ductal Cells.Journal of clinical medicine · 2019Article
- Elevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts.BMC microbiology · 2019Article
- EMUlator: An Elementary Metabolite Unit (EMU) Based Isotope Simulator Enabled by Adjacency Matrix.Frontiers in microbiology · 2019Article
- The Design of FluxML: A Universal Modeling Language forFrontiers in microbiology · 2019Article
- High extracellular lactate causes reductive carboxylation in breast tissue cell lines grown under normoxic conditions.PloS one · 2019Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe quantitative analysis of metabolic fluxes, i.e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on 13C substrates, (ii) 13C labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis.
resultsWe have developed OpenFLUX as a user friendly, yet flexible software application for small and large scale 13C metabolic flux analysis. The application is based on the new Elementary Metabolite Unit (EMU) framework, significantly enhancing computation speed for flux calculation. From simple notation of metabolic reaction networks defined in a spreadsheet, the OpenFLUX parser automatically generates MATLAB-readable metabolite and isotopomer balances, thus strongly facilitating model creation. The model can be used to perform experimental design, parameter estimation and sensitivity analysis either using the built-in gradient-based search or Monte Carlo algorithms or in user-defined algorithms. Exemplified for a microbial flux study with 71 reactions, 8 free flux parameters and mass isotopomer distribution of 10 metabolites, OpenFLUX allowed to automatically compile the EMU-based model from an Excel file containing metabolic reactions and carbon transfer mechanisms, showing it's user-friendliness. It reliably reproduced the published data and optimum flux distributions for the network under study were found quickly (<20 sec).
conclusionWe have developed a fast, accurate application to perform steady-state 13C metabolic flux analysis. OpenFLUX will strongly facilitate and enhance the design, calculation and interpretation of metabolic flux studies. By providing the software open source, we hope it will evolve with the rapidly growing field of fluxomics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.