About project

supporting "Photosynthesis in silico" book of the Springer Series "Advances in Photosynthesis and Respiration"

Mathematical models are essential to understand dynamic behavior of complex biological systems. Photosynthesis as it occurs in a natural environment reflects not only the primary biophysical and biochemical reactions but also a network of regulatory interactions that act across timescales and spatial boundaries. Modeling such a tightly regulated biosystem is feasible when the model is reduced to describe only a rather particular experimental situation such as fluorescence response to a single turnover light flash or the dynamics around the steady-state of Calvin Benson cycle. Then, the external regulatory interactions can be considered negligible or not changing so that the investigated dynamics can be predicted by modeling the system with only few key components that are relevant for the given time and complexity scale. Such an empiric dimensionality reduction has been successfully applied in photosynthesis research, leading to a mosaic of partial models that map along the Z-scheme of light reactions as well as covering parts of carbon metabolism. The validity ranges of the partial models are frequently not overlapping, leaving gaps in the photosynthesis modeling space. Filling the gaps and, even more important, modeling of regulatory interactions between modeled entities are hampered by incompatibility of the partial models that focus on different time scales or that are restricted to particular experimental situations. This led us to propose the Comprehensive Modeling Space, CMS where the partial photosynthesis models would be shared by means of the Systems Biology Mark-Up Language, SBML (http://sbml.org), which is the de-facto standard for the formal representation of biochemical models. The model validity is defined by a customized extension of the biology-wide standard of Minimum Information Requested in the Annotation of Biochemical Models, MIRIAM. The hierarchy and connectivity of the partial models within the Comprehensive Modeling Space is determined by rigorous dimensionality reduction techniques.

The project will start in 2009/2010 by translation of selected partial models from the "Photosynthesis in silico" book to Systems Biology Mark-Up Language format. The on-line simulation of photosynthetic dynamics will be possible. More info can be obtained from the project administrator (admin(at)e-photosynthesis.org).

To refer the e-photosynthesis website please cite the following publication:

J. Cerveny, M. Klement, J. Pospisilova, L. Brim, D. Lazar, and L. Nedbal. E-photosynthesis: web-based platform for modeling of complex photosynthetic processes. Biosystems. 2011 Feb;103(2):115-24. DOI