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Combining analysis and synthesis in a model of a biological cell

9 years 4 months ago
Combining analysis and synthesis in a model of a biological cell
for ideas, and then abstract away from these ideas to produce algorithmic processes that can create problem solutions in a bottom-up manner. We have previously described a top-down analytical approach, Cell Assembly Kit (CellAK), based on the object-oriented (OO) paradigm and the Unified Modeling Language (UML) and RealTime Object-Oriented Methodology (ROOM) formalisms, for developing models and simulations of cells and other biological entities. In this approach, models consist of a hierarchy of containers (ex: cytosol), active objects with behavior (ex: enzymes, lipid bilayers, transport proteins), and passive small molecules (ex: glucose, pyruvate). In this paper we describe the Substrate Catalyst Link (SCL) bottom-up synthesis approach [17], the concept of autopoiesis on which it is based, and what we have learned in trying to integrate this approach into CellAK. The enhanced CellAK architecture consists of a network of active objects (polymers), each of which has behavior that ca...
Ken Webb, Tony White
Added 30 Jun 2010
Updated 30 Jun 2010
Type Conference
Year 2004
Where SAC
Authors Ken Webb, Tony White
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