Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
4950076 | Electronic Notes in Theoretical Computer Science | 2016 | 23 Pages |
Abstract
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.
Related Topics
Physical Sciences and Engineering
Computer Science
Computational Theory and Mathematics
Authors
T. DÄd, D. Å afránek, M. Troják, M. Klement, J. Å alagoviÄ, L. Brim,