Conference proceeding
Cells Are Plausible Targets for High-Level Spatial Languages
SASOW 2008: SECOND IEEE INTERNATIONAL CONFERENCE ON SELF-ADAPTIVE AND SELF-ORGANIZING SYSTEMS WORKSHOPS, PROCEEDINGS, pp.284-291
01/01/2008
DOI: 10.1109/SASOW.2008.14
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[1].
Details
- Title: Subtitle
- Cells Are Plausible Targets for High-Level Spatial Languages
- Creators
- Jacob Beal - MIT CSAIL, Cambridge, MA 02139 USAJonathan Bachrach - MIT CSAIL, Cambridge, MA 02139 USA
- Contributors
- G D Serugendo (Editor)
- Resource Type
- Conference proceeding
- Publication Details
- SASOW 2008: SECOND IEEE INTERNATIONAL CONFERENCE ON SELF-ADAPTIVE AND SELF-ORGANIZING SYSTEMS WORKSHOPS, PROCEEDINGS, pp.284-291
- Publisher
- IEEE
- DOI
- 10.1109/SASOW.2008.14
- Number of pages
- 8
- Language
- English
- Date published
- 01/01/2008
- Academic Unit
- Electrical and Computer Engineering
- Record Identifier
- 9984627200002771
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