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E-cyanobacterium.org is a web-based platform for public sharing, annotation, analysis, and visualisation of dynamical models and wet-lab experiments related to cyanobacteria. It allows models to be represented at different levels of abstraction — as biochemical reaction networks or ordinary differential equations. The platform is unique in providing concise mapping of mathematical models to the formalised consortium-agreed biochemical description. The main goal of the platform is to connect the world of biological knowledge with benefits of mathematical description of dynamic processes. |
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| Model repository is a collection of mathematical models describing particular parts of biological processes. Each model component (i.e. reactant or reaction) is related to Biochemical Space. The model then includes complete biological annotation of all reactants and reactions. Simulations, static analysis, and SBML export are available. | Biochemical Space is constructed from hierarchy of entities and rules visualised in graphical schemes. It forms the backbone of the platform – the process tree. Each scheme represents chosen biological process of cyanobacteria. For each process, appropriate biochemical entities, rules, and models are attached. | Experiments repository is a tool for storage and presentation of time-series data from wet-lab experiments. Every experiment is well-grounded by precise description (device, medium, organism, etc.) and appropriate annotations. Experiment's variables might be related to Biochemical Space. Moreover, it is possible to visualise the data in a chart. |
The experimental platform supplying data for this website has been partially supported by the Czech research infrastructure for systems biology C4SYS (project no LM2015055).
The platform development was partially supported within the activities of EC OP project financed from EU with the support of MEYS CR: Local Team and International Consortium for Computational Modelling of a Cyanobacterial Cell, Reg. No. CZ.1.07/2.3.00/20.0256)
M. Trojak, D. Safranek, J. Hrabec, J. Salagovic, F. Romanovska, J. Cerveny: E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In: Computational Methods in Systems Biology, CMSB 2016, Vol. 9859 of LNCS, pp. 316-322. Springer, 2016. DOI