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#43 E-cyanobacterium
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 platform consists of several dedicated modules all connected to a central module – Biochemical Space (BCS) – that is the backbone of the platform. BCS provides formal description of the biological problem and it is based on the hierarchy of selected biological processes. For each process, there are presented relevant models, chemical entities, and
rules (reactions).
Annotation is an important task in modelling of biological systems. This is how biological knowledge is mapped to the mathematical description. Our platform considers annotation as an inherent and compulsory part of the modelling procedure. The following aspects of annotation are supported:
- BCS creation and maintenance,
- model annotation by mapping to BCS,
- experiment annotation.
BCS is being continuously extended and revised by the consortium. Researchers supplying their models are required to integrate the models within the current BCS. This gives good feedback to BCS maintainers.
Publications:
http://link.springer.com/chapter/10.1007/978-3-319-45177-0_20
http://www.sciencedirect.com/science/article/pii/S1571066116300615
Contact: ecyano@fi.muni.cz
followed up via email
created the following:
http://identifiers.org/ecyano.entity/
http://identifiers.org/ecyano.model/
http://identifiers.org/ecyano.rule/
some refinements to come, so leaving open for now,
cheers
Nick