JOURNAL OF COMPUTERS (JCP)
ISSN : 1796-203X
Volume : 3    Issue : 2    Date : February 2008

Towards Design Space Exploration for Biological Systems
Simon Polstra, Tessa E. Pronk, Andy D.Pimentel, and Timo M. Breit
Page(s): 1-9
Full Text:
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Abstract
For both embedded systems and biological cell systems, design is a feature that defines their
identity. The assembly of different components in designs of both systems can vary widely. Given
the similarities between computers and cellular systems, methods and models of computation
from the domain of computer systems engineering could be applied to model cellular systems. Our
aim is to construct a framework that focuses on understanding the design options and
consequences within a cell, taking an in-silico (forward-) engineering approach rather than the
reverse-engineering approach now used by default in this domain. We take our ideas from the
domain of embedded computer systems. The most important features of our approach, as taken
from this domain, are a variable abstraction level of model components that allows for inclusion of
components of which detailed information is lacking, and a separation of concerns between
function and performance by components in the design. This allows for efficient and flexible
modeling. Also, there is a strict separation between computation within and communication
between components, thus reducing complexity. As a proof-of-principle, we show that we can make
a statement regarding the design of the gene expression machinery of a cell to produce a protein,
using such a method.

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