Formal Biochemical Space with Semantics in Kappa and BNGL
| Authors | |
|---|---|
| Year of publication | 2016 |
| Type | Article in Proceedings |
| Conference | The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015 |
| MU Faculty or unit | |
| Citation | |
| Doi | http://dx.doi.org/10.1016/j.entcs.2016.09.017 |
| Field | Informatics |
| Keywords | Kappa; Biochemical space; CMP; cyanobacteria processes |
| Description | Biochemical Space (BCS) has been introduced as a semi-formal notation for reaction networks of biological processes. It provides a concise mapping of mathematical models to their biological description established at a desired level of abstraction. In this paper, we first turn BCS into a completely formal language with rigorously defined semantics by means of a simplified Kappa calculus. On the practical end, we support BCS with translation to BNGL, a well-known practically used rule-based language. Finally, we show the current status of BCS defined for cyanobacteria processes. |
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