MOTIVATION: The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13C-labeling experiments. 13C-MFA workflows orchestrate several, mainly human-in-the-loop, software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting and understanding isotopic data from carbon labeling experiments. RESULTS: Graphical modeling, interactive model exploration and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13C-MFA. Almost 30 modules (plug-ins) have been implemented for the Omix visualization software. Several advanced graphical workflows and ergonomic user interfaces support major domain-specific modeling and proofreading tasks. With that, the graphical suite is a productivity enhancing tool and an original educational training instrument supporting the adoption of 13C-MFA applications in all life science fields. AVAILABILITY: The Omix Light Edition is freely available at http://www.omix-visualization.com CONTACT: k.noeh@fz-juelich.de, p.droste@omix-visualization.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The precise quantification of intracellular metabolic flow rates is of fundamental importance in bio(techno)logy and medical research. The gold standard in the field is metabolic flux analysis (MFA) with 13C-labeling experiments. 13C-MFA workflows orchestrate several, mainly human-in-the-loop, software applications, integrating them with plenty of heterogeneous information. In practice, this had posed a major practical barrier for evaluating, interpreting and understanding isotopic data from carbon labeling experiments. RESULTS: Graphical modeling, interactive model exploration and visual data analysis are the key to overcome this limitation. We have developed a first-of-its-kind graphical tool suite providing scientists with an integrated software framework for all aspects of 13C-MFA. Almost 30 modules (plug-ins) have been implemented for the Omix visualization software. Several advanced graphical workflows and ergonomic user interfaces support major domain-specific modeling and proofreading tasks. With that, the graphical suite is a productivity enhancing tool and an original educational training instrument supporting the adoption of 13C-MFA applications in all life science fields. AVAILABILITY: The Omix Light Edition is freely available at http://www.omix-visualization.com CONTACT: k.noeh@fz-juelich.de, p.droste@omix-visualization.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Min Yuan; Daniel M Kremer; He Huang; Susanne B Breitkopf; Issam Ben-Sahra; Brendan D Manning; Costas A Lyssiotis; John M Asara Journal: Nat Protoc Date: 2019-02 Impact factor: 13.491