Processes 2018, 6,39
To sum it up, we think that FluxVisualizer fulfils the two aims stated in the introduction: (i) use the
biochemist’s own diagram and to replace a tedious manual operation of colouring or/and resizing steps
by hand with a fast automatic process and (ii) automatically deliver a series of pathway representations
of the same metabolic map from a text list of these pathways (EFMs for instance). This is a great time
saver that justifies the time spent presenting the metabolic network in SVG format. We believe that this
simple software, freely available at https://fluxvisualizer.ibgc.cnrs.fr, has its place in the theoretical
toolbox of the experimental biochemist.
Acknowledgments: Supported by the Plan cancer 2014–2019 No BIO 2014 06 and the French Association against
Myopathies. We thank Axel Cattouillart for his technical assistance, Sylvain Prigent for his help in manipulating
other tools, Anne Devin for her criticisms and English review and Oliver Ebenhoeh as TDR’s teacher.
Author Contributions: Tim Daniel Rose developed FluxVisualizer, wrote the manual and participated to the
redaction of the paper. Jean-Pierre Mazat conceived the project and wrote the paper.
Conflicts of Interest: The authors declare no conflict of interest.
References
1.
Gehlenborg, N.; O’Donoghue, S.; Baliga, N.S.; Goesmann, A.; Hibbs, M.A.; Kitano, H.; Kohlbacher, O.;
Neuweger, H.; Schneider, R.; Tenenbaum, D.; et al. Visualization of omics data for systems biology.
Nat. Methods 2010, 7, S56–S68. [CrossRef][PubMed]
2.
O’Donoghue, S.I.; Baldi, B.F.; Maier-Hein, L.; Stenau, E.; Hogan, J.M.; Humphrey, S.; Kaur, S.; McCarthy, D.J.;
Moore, W.J.; Procter, J.B.; et al. Visualization of Biomedical Data. Annu. Rev. Biomed. Data Sci. 2018, in press.
3.
Schellenberger, J.; Park, J.O.; Conrad, T.M.; Palsson, B.Ø. BiGG: A Biochemical Genetic and Genomic
knowledgebase of large scale metabolic reconstructions. BMC Bioinform. 2010, 11, 213. [CrossRef][PubMed]
4.
Maarleveld, T.R.; Khandelwal, R.A.; Olivier, B.G.; Teusink, B.; Bruggeman, F.J. Basic concepts and principles
of stoichiometric modeling of metabolic networks. Biotechnol. J. 2013, 8, 997–1008. [CrossRef][PubMed]
5.
Antoniewicz, M.R. Methods and advances in metabolic flux analysis: A mini-review. J. Ind. Microb. Biotechnol.
2015, 42, 317–325. [CrossRef][PubMed]
6.
Kacser, H.; Burns, J.A. The control of flux. Symp. Soc. Exp. Biol. 1973, 32, 65–104. [CrossRef]
7.
Heinrich, R.; Rapoport, T.A. A linear steady-state treatment of enzymatic chains; its application for the
analysis of the crossover theorem and of the glycolysis of human erythrocytes. Acta Biol. Med. Ger. 1973, 31,
479–494. [PubMed]
8.
Reder, C. Metabolic control theory: A structural approach. J. Theor. Biol. 1988, 135, 175–201. [CrossRef]
9.
Sauro, H. Systems Biology: Introduction to Pathway Modeling; Ambrosius Publishing: Bangalore, India, 2014;
ISBN 978-0-9824773-7-3.
10. Klipp, E.; Liebermeister, W.; Wierling, C.; Kowald, A. Systems Biology: A Textbook, 2nd ed.; Wiley-Blackwell:
Berlin, Germany, 2016; ISBN 978-3-527-33636-4.
11. Ataman, M.; Hernandez Gardiol, D.F.; Fengos, G.; Hatzimanikatis, V. redGEM: Systematic reduction and
analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.
PLoS Comput. Biol. 2017, 13, e1005444. [CrossRef][PubMed]
12. Smith, A.C.; Eyassu, F.; Mazat, J.-P.; Robinson, A.J. MitoCore: A curated constraint-based model for
simulating human central metabolism. BMC Syst. Biol. 2017, 11, 114. [CrossRef][PubMed]
13. Orth, J.; Fleming, R.; Palsson, B. Reconstruction and Use of Microbial Metabolic Networks: The Core
Escherichia coli Metabolic Model as an Educational Guide. EcoSal Plus 2010.[ CrossRef][PubMed]
14. Omix Visualization | Welcome. Available online: https://www.omix-visualization.com/ (accessed on
21 April 2018).
15. Jensen, P.A.; Papin, J.A. MetDraw: Automated visualization of genome-scale metabolic network
reconstructions and high-throughput data. Bioinformatics 2014, 30, 1327–1328. [CrossRef][PubMed]
16. Chazalviel, M.; Frainay, C.; Poupin, N.; Vinson, F.; Merlet, B.; Gloaguen, Y.; Cottret, L.; Jourdan, F.
MetExploreViz: Web component for interactive metabolic network visualization. Bioinformatics 2017, 34,
312–313. [CrossRef][PubMed]
17. König, M.; Holzhütter, H.G. Fluxviz—Cytoscape plug-in for visualization of flux distributions in networks.
Genome Inform. 2010, 24, 96–103. [PubMed]
152
To sum it up, we think that FluxVisualizer fulfils the two aims stated in the introduction: (i) use the
biochemist’s own diagram and to replace a tedious manual operation of colouring or/and resizing steps
by hand with a fast automatic process and (ii) automatically deliver a series of pathway representations
of the same metabolic map from a text list of these pathways (EFMs for instance). This is a great time
saver that justifies the time spent presenting the metabolic network in SVG format. We believe that this
simple software, freely available at https://fluxvisualizer.ibgc.cnrs.fr, has its place in the theoretical
toolbox of the experimental biochemist.
Acknowledgments: Supported by the Plan cancer 2014–2019 No BIO 2014 06 and the French Association against
Myopathies. We thank Axel Cattouillart for his technical assistance, Sylvain Prigent for his help in manipulating
other tools, Anne Devin for her criticisms and English review and Oliver Ebenhoeh as TDR’s teacher.
Author Contributions: Tim Daniel Rose developed FluxVisualizer, wrote the manual and participated to the
redaction of the paper. Jean-Pierre Mazat conceived the project and wrote the paper.
Conflicts of Interest: The authors declare no conflict of interest.
References
1.
Gehlenborg, N.; O’Donoghue, S.; Baliga, N.S.; Goesmann, A.; Hibbs, M.A.; Kitano, H.; Kohlbacher, O.;
Neuweger, H.; Schneider, R.; Tenenbaum, D.; et al. Visualization of omics data for systems biology.
Nat. Methods 2010, 7, S56–S68. [CrossRef][PubMed]
2.
O’Donoghue, S.I.; Baldi, B.F.; Maier-Hein, L.; Stenau, E.; Hogan, J.M.; Humphrey, S.; Kaur, S.; McCarthy, D.J.;
Moore, W.J.; Procter, J.B.; et al. Visualization of Biomedical Data. Annu. Rev. Biomed. Data Sci. 2018, in press.
3.
Schellenberger, J.; Park, J.O.; Conrad, T.M.; Palsson, B.Ø. BiGG: A Biochemical Genetic and Genomic
knowledgebase of large scale metabolic reconstructions. BMC Bioinform. 2010, 11, 213. [CrossRef][PubMed]
4.
Maarleveld, T.R.; Khandelwal, R.A.; Olivier, B.G.; Teusink, B.; Bruggeman, F.J. Basic concepts and principles
of stoichiometric modeling of metabolic networks. Biotechnol. J. 2013, 8, 997–1008. [CrossRef][PubMed]
5.
Antoniewicz, M.R. Methods and advances in metabolic flux analysis: A mini-review. J. Ind. Microb. Biotechnol.
2015, 42, 317–325. [CrossRef][PubMed]
6.
Kacser, H.; Burns, J.A. The control of flux. Symp. Soc. Exp. Biol. 1973, 32, 65–104. [CrossRef]
7.
Heinrich, R.; Rapoport, T.A. A linear steady-state treatment of enzymatic chains; its application for the
analysis of the crossover theorem and of the glycolysis of human erythrocytes. Acta Biol. Med. Ger. 1973, 31,
479–494. [PubMed]
8.
Reder, C. Metabolic control theory: A structural approach. J. Theor. Biol. 1988, 135, 175–201. [CrossRef]
9.
Sauro, H. Systems Biology: Introduction to Pathway Modeling; Ambrosius Publishing: Bangalore, India, 2014;
ISBN 978-0-9824773-7-3.
10. Klipp, E.; Liebermeister, W.; Wierling, C.; Kowald, A. Systems Biology: A Textbook, 2nd ed.; Wiley-Blackwell:
Berlin, Germany, 2016; ISBN 978-3-527-33636-4.
11. Ataman, M.; Hernandez Gardiol, D.F.; Fengos, G.; Hatzimanikatis, V. redGEM: Systematic reduction and
analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models.
PLoS Comput. Biol. 2017, 13, e1005444. [CrossRef][PubMed]
12. Smith, A.C.; Eyassu, F.; Mazat, J.-P.; Robinson, A.J. MitoCore: A curated constraint-based model for
simulating human central metabolism. BMC Syst. Biol. 2017, 11, 114. [CrossRef][PubMed]
13. Orth, J.; Fleming, R.; Palsson, B. Reconstruction and Use of Microbial Metabolic Networks: The Core
Escherichia coli Metabolic Model as an Educational Guide. EcoSal Plus 2010.[ CrossRef][PubMed]
14. Omix Visualization | Welcome. Available online: https://www.omix-visualization.com/ (accessed on
21 April 2018).
15. Jensen, P.A.; Papin, J.A. MetDraw: Automated visualization of genome-scale metabolic network
reconstructions and high-throughput data. Bioinformatics 2014, 30, 1327–1328. [CrossRef][PubMed]
16. Chazalviel, M.; Frainay, C.; Poupin, N.; Vinson, F.; Merlet, B.; Gloaguen, Y.; Cottret, L.; Jourdan, F.
MetExploreViz: Web component for interactive metabolic network visualization. Bioinformatics 2017, 34,
312–313. [CrossRef][PubMed]
17. König, M.; Holzhütter, H.G. Fluxviz—Cytoscape plug-in for visualization of flux distributions in networks.
Genome Inform. 2010, 24, 96–103. [PubMed]
152