Comprehensive Modelling Platform for Cyanobacteria

E-cyanobacterium.org is an online platform providing tools for public sharing, annotation, analysis, and visualization of dynamical models and wet-lab experiments related to cyanobacteria. The platform is unique in integrating abstract mathematical models with a precise consortium-agreed biochemical description provided in a rule-based formalism. The general aim is to stimulate collaboration between experimental and computational systems biologists to achieve better understanding of cyanobacteria.

An existing resource to inspire further expansion of cyanobacteria modelling are the established web repositories of curated and well-annotated models traversing already through many branches of biology. Unfortunately, cyanobacteria models are strongly under-represented in these repositories, probably because of the natural differences that exist between common bacteria and phototrophic bacteria. There exist several online tools presenting biological networks or genome knowledge. However, due to enormous complexity of biological processes, it is a challenge to develop tools presenting biological networks alongside with executable or mathematical models. Focusing on domain-specific organisms allows us to integrate the knowledge and present it in a concise and understandable form. This has been already proven on examples of well-known model organisms such as E. coli or C. elegans. Nevertheless, these resources do not couple the presented knowledge with modelling. E-cyanobacterium.org is an online platform for modelling of cyanobacteria processes. As an instance of Comprehensive Modelling Platform, it integrates several dedicated tools and is distinct in the following aspects:

  • formal rule-based representation of biochemical interactions facilitated by cyanobacteria biochemical entities,
  • repository of kinetic models providing basic analysis tools online (simulation, custom data sets, basic static analysis)
  • integration of models within the rule-based description and export to SBML
  • storage, maintenance and presentation of experimental data;
  • content visualisation (graphical presentation of models, biochemical space and modelling/experimental data).
E-cyanobacterium.org provides support for modelling and analysis of biological systems. The most important fact is that all these parts are integrated within common knowledge-base - Biochemical Space. Therefore it is possible to reveal non-trivial relations between biochemical substances and models. The general platform features are:
  • annotation - relation of biological knowledge to the mathematical description,
  • visualisation - provided in terms of schemas showing the process hierarchy and plotting of measured or computed experimental data,
  • simulation - for every implemented model it is possible to execute simulations in particular experimental settings,
  • static analysis - analysis avoiding combinatorial explosion unavoidable in case of dynamic analysis.