E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes

BioSystems

Volumn 103, Issue 2, 2011, Pages 115-124

  Šafránek, David ^a   Červený, Jan ^b,c   Klement, Matěj ^a   Pospíšilová, Jana ^a   Brim, Luboš ^a   Lazár, Dušan ^d   Nedbal, Ladislav ^b,c  

^a MASARYK UNIVERSITY   (Czech Republic)

^b INSTITUTE OF LANDSCAPE ECOLOGY   (Czech Republic)

^c Kolá kova 39   (Czech Republic)

^d PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

Biomodels repository; Computational models; Photosynthesis; Systems biology; Web platform

Indexed keywords

NUMERICAL MODEL; PHOTOSYNTHESIS; SOFTWARE; VISUALIZATION;

ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; E PHOTOSYNTHESIS; KINETICS; NONHUMAN; PHOTOSYNTHESIS; SYSTEMS BIOLOGY; WEB BROWSER;

EID: 78751703494     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2010.10.013     Document Type: Article

References (33)

1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. Nat. Genet. 2000, 25(1):25-29.
2. Barnat J., Brim L., Safranek D. High-performance analysis of biological systems dynamics with the DiVinE model checker. Brief. Bioinform. 2010, 11(3):301-312.
3. Baumert H.Z., Petzoldt T. The role of temperature, cellular quota and nutrient concentrations for photosynthesis, growth and light-dark acclimation in phytoplankton. Limnol. Ecol. Manage. Inland Waters 2008, 38(3-4):313-326.
4. Beard D.A., Britten R., Cooling M.T., Garny A., Halstead M.D.B., Hunter P.J., Lawson J., Lloyd C.M., Marsh J., Miller A., Nickerson D.P., Nielsen P.M.F., Nomura T., Subramanium S., Wimalaratne S.M., Yu T. CellML metadata standards, associated tools and repositories. Philos. Trans. Roy. Soc. A: Math. Phys. Eng. Sci. 2009, 367(1895):1845-1867.
5. Brennan L., Owende P. Biofuels from microalgae - a review of technologies for production, processing, and extractions of biofuels and co-products. Renew. Sust. Energy Rev. 2010, 14(2):557-577.
6. Eaton J.W. GNU Octave Manualed 2002, Network Theory Limited.
7. Hindmarsh A.C. LSODE and LSODI, two new initial value ordinary differnetial equation solvers. SIGNUM Newsl. 1980, 15(4):10-11.
8. Hindmarsh A.C. ODEPACK, a Systematized Collection of ODE Solvers. IMACS Transactions on Scientific Computation 1983, vol. 1:55-64. North-Holland, Amsterdam.
9. Holzwarth A.R., Müller M.G., Reus M., Nowaczyk M., Sander J., Rögner M. Kinetics and mechanism of electron transfer in intact photosystem II and in the isolated reaction center: pheophytin is the primary electron acceptor. Proc. Natl. Acad. Sci. U.S.A. 2006, 103(18):6895-6900.
10. Hucka M., Finney A., Sauro H., Bolouri H., Doyle J., Kitano H., Arkin A., Bornstein B., Bray D., Cornish-Bowden A., Cuellar A., Dronov S., Gilles E., Ginkel M., Gor V., Goryanin I., Hedley W., Hodgman T., Hofmeyr J.-H., Hunter P., Juty N., Kasberger J., Kremling A., Kummer U., Le Novére N., Loew L., Lucio D., Mendes P., Minch E., Mjolsness E., Nakayama Y., Nelson M., Nielsen P., Sakurada T., Schaff J., Shapiro B., Shimizu T., Spence H., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531.
11. Hucka M., Schaff J. Trends and tools for modeling in modern biology. Photosynthesis in Silico: Understanding Complexity from Molecules to Ecosystems. 2009, 3-15. Springer, Netherlands, Dordrecht. A. Laisk, L. Nedbal, Govindjee (Eds.).
12. Chisti Y. Biodiesel from microalgae beats bioethanol. Trends Biotechnol. 2008, 26(3):126-131.
13. Jansson C., Northen T. Calcifying cyanobacteria - the potential of biomineralization for carbon capture and storage. Curr. Opin. Biotechnol. 2010, 21(3):365-371.
14. Jiao N., Herndl G.J., Hansell D.A., Benner R., Kattner G., Wilhelm S.W., Kirchman D.L., Weinbauer M.G., Luo T., Chen F., Azam F. Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean. Nat. Rev. Microbiol. 2010, 8(8):593-599.
15. Kanehisa M., Goto S., Furumichi M., Tanabe M., Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 2010, 38(Suppl. 1):D355-360.
16. Kohn D., Le Novere N. SED-ML: an XML format for the implementation of the MIASE. Computational Methods in Systems Biology 2008, Springer-Verlag, Rostock, Germany, pp. 176-190.
17. Laisk A., Nedbal L., Govindjee Photosynthesis in Silico: Understanding Complexity from Molecules to Ecosystems 2009, Springer, Dordrecht, Netherlands. first ed.
18. Lal R. Carbon sequestration. Philos. Trans. Roy. Soc. B: Biol. Sci. 2008, 363(1492):815-830.
19. Lazár D., Jablonský J. On the approaches applied in formulation of a kinetic model of photosystem II: different approaches lead to different simulations of the chlorophyll a fluorescence transients. J. Theor. Biol. 2009, 257(2):260-269.
20. Lazár D., Schansker G. Models of chlorophyll a fluorescence transients. Photosynthesis in Silico: Understanding Complexity from Molecules to Ecosystems. 2009, 85-123. Springer, Dordrecht, Netherlands. A. Laisk, L. Nedbal, Govindjee (Eds.).
21. Le Novere N., Finney A., Hucka M., Bhalla U.S., Campagne F., Collado-Vides J., Crampin E.J., Halstead M., Klipp E., Mendes P., Nielsen P., Sauro H., Shapiro B., Snoep J.L., Spence H.D., Wanner B.L. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat. Biotechnol. 2005, 23(12):1509-1515.
22. Le Novere N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. BioModels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2006, 34(suppl_1):D689-691.
23. Nedbal L., Červený J., Rascher U., Schmidt H. E-photosynthesis: a comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light. Photosynth. Res. 2007, 93(1):223-234.
24. Nedbal L., Červený J., Schmidt H. Scaling and integration of kinetic models of photosynthesis: towards comprehensive E-photosynthesis. Photosynthesis in Silico: Understanding Complexity from Molecules to Ecosystems 2009, 17-29. Springer, Dordrecht, Netherlands. A. Laisk, L. Nedbal, Govindjee (Eds.).
25. Niinemets Ü., Valladares F. Photosynthetic acclimation to simultaneous and interacting environmental stresses along natural light gradients: optimality and constraints. Plant Biol. (Stuttg.) 2004, 6(03):254-268.
26. Olivier B.G., Snoep J.L. Web-based kinetic modelling using JWS Online. Bioinformatics 2004, 20(13):2143-2144.
27. Orr L., Govindjee Photosynthesis and the Web: 2008. Photosynth. Res. 2007, 91(2):107-131.
28. Rascher U., Nedbal L. Dynamics of photosynthesis in fluctuating light. Curr. Opin. Plant Biol. 2006, 9(6):671-678.
29. Raven J.A., Cockell C.S., De La Rocha C.L. The evolution of inorganic carbon concentrating mechanisms in photosynthesis. Philos. Trans. Roy. Soc. B: Biol. Sci. 2008, 363(1504):2641-2650.
30. Riding R. An atmospheric stimulus for cyanobacterial-bioinduced calcification ca 350 million years ago?. Palaios 2009, 24(10):685-696.
31. Rizk A., Batt G., Fages F., Soliman S. On a continuous degree of satisfaction of temporal logic formulae with applications to systems biology. Computational Methods in Systems Biology 2008, 251-268. Springer-Verlag, Berlin Heidelberg. M. Heiner, A. Uhrmacher (Eds.).
32. Vredenberg W.J. System analysis and photoelectrochemical control of chlorophyll fluorescence. terms of trapping models of photosystem II: a challenging view. Chlorophyll a Fluorescence: A Signature of Photosynthesis 2004, 133-172. Springer, Dordrecht, Netherlands. G.C. Papageorgiou, Govindjee (Eds.).
33. Zhu X.-G., Long S.P., Ort D.R. Improving Photosynthetic Efficiency for Greater Yield. Annu. Rev. Plant Biol. 2010, 61(1):235-261.