Comprehensive Modelling Platform for Photosynthesis
Mathematical models are essential to understand dynamic behaviour 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. E-photosynthesis.org is a web-based instance of Comprehensive Modelling Platform tailored for modelling and analysis of photosynthetic processes.
Modelling such a tightly regulated bio-system as photosynthesis 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 modelling 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 modelling space. Filling the gaps and, even more important, modelling of regulatory interactions between modelled entities are hampered by incompatibility of the partial models that focus on different time scales or that are restricted to particular experimental situations.
The platformcurrently offers the following services available on-line:
- model repository customized for specific needs of photosynthesis research
- MIRIAM-compatible annotation database and ontology of photosynthesis-related terms
- graphical environment visualizing the models in a modular and hierarchical manner
- model examination module prepared for further deployment to high-performance platforms
online version: http://www.e-photosynthesis.org/