Journal: BMC Bioinformatics

Article Title: iMS2Flux – a high–throughput processing tool for stable isotope labeled mass spectrometric data used for metabolic flux analysis

doi: 10.1186/1471-2105-13-295

Figure Lengend Snippet: Comparison of iMS2Flux and other available MS correction tools

Article Snippet: Similar to MSCorr , the OpenFLUX correction is provided as a function in MATLAB (corrMatGen) which requires the user to enter the chemical formula and other specifics about each compound individually.

Techniques: Labeling, Software

Journal: Frontiers in Cardiovascular Medicine

Article Title: Stable Isotopes for Tracing Cardiac Metabolism in Diseases

doi: 10.3389/fcvm.2021.734364

Figure Lengend Snippet: Resources for network reconstruction, simulation and visualization of metabolic flux analysis using stable-isotope tracers.

Article Snippet: OpenFLUX , MATLAB-base modeling software for 13 C-MFA; includes EMU simulation algorithm , https://github.com/lakeeeq/OpenFLUX , ( ) .

Techniques: Phospho-proteomics, Sequencing, Functional Assay, Concentration Assay, Software, Quantitative Proteomics, Labeling, In Situ, Microscopy, Mass Spectrometry, Combined Bisulfite Restriction Analysis Assay, Biomarker Discovery

Journal: Microbial Cell Factories

Article Title: OpenFLUX2: 13 C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments

doi: 10.1186/s12934-014-0152-x

Figure Lengend Snippet: Workflow of OpenFLUX2. Green boxes represent the two main components of OpenFLUX(2): PARSER for automatic stoichiometric and isotopomer model generation and the MATLAB-based box for the 13 C-MFA of the generated model. A gray background indicates options offered by OpenFLUX(2). A yellow background indicates options added during OpenFLUX2 development.

Article Snippet: OpenFLUX2 can be downloaded from SourceForge ( http://sourceforge.net/projects/openflux2 ).

Techniques: Generated

Journal: Microbial Cell Factories

Article Title: OpenFLUX2: 13 C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments

doi: 10.1186/s12934-014-0152-x

Figure Lengend Snippet: Experimental design studies for the identification of mixtures of [1- 13 C]/[U- 12 C]/[U- 13 C]-glucose isotopomers for “general” optimization or for the best resolution (“partial” optimization) of θ 31 , θ 14 , θ 22 fluxes (I) , results of these flux estimations (II) obtained through 13 C-MFA of the simulated SLEs ( A – F ) or PLEs ( G ) with the mentioned mixed tracers: A − SLE, 0/50/50, %% (partially optimized for θ 12 ); B − SLE, 10/44/46, %% (partially optimized for θ 22 ); C − SLE, 13/0/87, %% (partially optimized for θ 31 ); D − SLE, 66/0/34, %% (partially optimized for θ 14 ); E − SLE, 89/0/11, %% (partially optimized for θ 10 ); F −78/0/22, %% (generally optimized); G − PLE consisting of five LEs using the same tracers as in A – E for each experiment (red 68% CI boxes); (III) the normalized flux precision function values for the confidence level of γ = 0.95 computed for these (A – G) experiments. Green 68% CI boxes in (II) indicate flux estimation resulted from 13 C-MFA of SLE optimized for best resolution of this flux. The results of the experimental design studies computed by OpenFLUX2 were visualized in the form of a ternary plot generated by commercially available OriginPro 9.1 (Originlab Corp., Northampton, MA, USA) software.

Article Snippet: OpenFLUX2 can be downloaded from SourceForge ( http://sourceforge.net/projects/openflux2 ).

Techniques: Generated, Software

Journal: ACS Synthetic Biology

Article Title: FreeFlux: A Python Package for Time-Efficient Isotopically Nonstationary Metabolic Flux Analysis

doi: 10.1021/acssynbio.3c00265

Figure Lengend Snippet: Optimization-Based Computational Tools Available for 13 C MFA

Article Snippet: OpenFLUX2 , isotopic steady state , yes , MATLAB, Java , Windows , ∼20 min single run with a Corynebacterium glutamicum model (51 reactions, 36 metabolites) (single labeling experiment), ∼30-70 h for CIs (Monte Carlo method) , ( ) .

Techniques: Labeling

Journal: Microbial Cell Factories

Article Title: OpenFLUX2: 13 C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments

doi: 10.1186/s12934-014-0152-x

Figure Lengend Snippet: Workflow of OpenFLUX2. Green boxes represent the two main components of OpenFLUX(2): PARSER for automatic stoichiometric and isotopomer model generation and the MATLAB-based box for the 13 C-MFA of the generated model. A gray background indicates options offered by OpenFLUX(2). A yellow background indicates options added during OpenFLUX2 development.

Article Snippet: Statistically acceptable solution (corresponding to the value 9.65 of Ξ( θ ) function (for the group of 27 from 100 performed trials) that was smaller even the lower threshold, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $$ \left({\chi}_{0.025}^2(30)=16.79\right) $$ \end{document} χ 0.025 2 30 = 16.79 ) at the 95% confidence level, with Ν(0, 1) distributed weighted residuals, was found using OpenFLUX2 (Table (Exp_3.6) ).

Techniques: Generated

Journal: Microbial Cell Factories

Article Title: OpenFLUX2: 13 C-MFA modeling software package adjusted for the comprehensive analysis of single and parallel labeling experiments

doi: 10.1186/s12934-014-0152-x

Figure Lengend Snippet: Experimental design studies for the identification of mixtures of [1- 13 C]/[U- 12 C]/[U- 13 C]-glucose isotopomers for “general” optimization or for the best resolution (“partial” optimization) of θ 31 , θ 14 , θ 22 fluxes (I) , results of these flux estimations (II) obtained through 13 C-MFA of the simulated SLEs ( A – F ) or PLEs ( G ) with the mentioned mixed tracers: A − SLE, 0/50/50, %% (partially optimized for θ 12 ); B − SLE, 10/44/46, %% (partially optimized for θ 22 ); C − SLE, 13/0/87, %% (partially optimized for θ 31 ); D − SLE, 66/0/34, %% (partially optimized for θ 14 ); E − SLE, 89/0/11, %% (partially optimized for θ 10 ); F −78/0/22, %% (generally optimized); G − PLE consisting of five LEs using the same tracers as in A – E for each experiment (red 68% CI boxes); (III) the normalized flux precision function values for the confidence level of γ = 0.95 computed for these (A – G) experiments. Green 68% CI boxes in (II) indicate flux estimation resulted from 13 C-MFA of SLE optimized for best resolution of this flux. The results of the experimental design studies computed by OpenFLUX2 were visualized in the form of a ternary plot generated by commercially available OriginPro 9.1 (Originlab Corp., Northampton, MA, USA) software.

Article Snippet: Statistically acceptable solution (corresponding to the value 9.65 of Ξ( θ ) function (for the group of 27 from 100 performed trials) that was smaller even the lower threshold, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document} $$ \left({\chi}_{0.025}^2(30)=16.79\right) $$ \end{document} χ 0.025 2 30 = 16.79 ) at the 95% confidence level, with Ν(0, 1) distributed weighted residuals, was found using OpenFLUX2 (Table (Exp_3.6) ).

Techniques: Generated, Software