Computer Science – Computational Engineering – Finance – and Science
Scientific paper
2009-11-23
EPTCS 11, 2009, pp. 19-33
Computer Science
Computational Engineering, Finance, and Science
Scientific paper
10.4204/EPTCS.11.2
We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction levels; in particular, higher-level (e.g. membrane) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. A BioBeta specification provides a protein signature together a set of protein reactions, in the spirit of the kappa-calculus. Moreover, the specification describes when a protein configuration triggers one of the only two membrane interaction allowed, that is "pinch" and "fuse". In this paper we define the syntax and semantics of BioBeta, analyse its properties, give it an interpretation as biobigraphical reactive systems, and discuss its expressivity by comparing with kappa-calculus and modelling significant examples. Notably, BioBeta has been designed after a bigraphical metamodel for the same purposes. Hence, each instance of the calculus corresponds to a bigraphical reactive system, and vice versa (almost). Therefore, we can inherith the rich theory of bigraphs, such as the automatic construction of labelled transition systems and behavioural congruences.
Bacci Giorgio
Grohmann Davide
Miculan Marino
No associations
LandOfFree
A framework for protein and membrane interactions does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with A framework for protein and membrane interactions, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and A framework for protein and membrane interactions will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-279251