DocumentCode :
2981534
Title :
Cells Are Plausible Targets for High-Level Spatial Languages
Author :
Beal, Jacob ; Bachrach, Jonathan
Author_Institution :
MIT CSAIL, Cambridge, MA
fYear :
2008
fDate :
20-24 Oct. 2008
Firstpage :
284
Lastpage :
291
Abstract :
High level languages greatly increase the power of a programmer at the cost of programs that consume more resources than those written at a lower level of abstraction. This inefficiency is a major concern for the programming of biological systems: although advances in synthetic biology are beginning to allow bacteria to be programmed at an "assembly language\´\´ level, metabolic and chemical constraints currently place tight limits on the computational resources available. We find, however, that the semantics of the Proto spatial computing language appear to be a good match for engineered genetic regulatory networks, and particularly for describing the spatial differentiation necessary to construct tissues or organs. In this paper, we propose a mapping between Proto programs and standardized biological parts. We then demonstrate the plausibility of this mapping by applying it to a band detection program, finding that standard code optimization techniques can transform the inefficient program produced by the initial mapping into an efficient design equivalent to the Weiss laboratory\´s hand-designed band detector.
Keywords :
assembly language; biology computing; high level languages; optimisation; Proto programs; Proto spatial computing language; assembly language; band detection program; biological systems; code optimization techniques; genetic regulatory networks; synthetic biology; Assembly systems; Biological systems; Biology computing; Chemicals; Computer networks; Costs; High level languages; Microorganisms; Programming profession; Synthetic biology; amorphous computing; spatial computing; synthetic biology;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Self-Adaptive and Self-Organizing Systems Workshops, 2008. SASOW 2008. Second IEEE International Conference on
Conference_Location :
Venice
Print_ISBN :
978-0-7695-3553-1
Electronic_ISBN :
978-0-7695-3553-1
Type :
conf
DOI :
10.1109/SASOW.2008.14
Filename :
4800692
Link To Document :
بازگشت