Team:BU Wellesley Software/Puppetshow
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<h1>Computational Team</h1> | <h1>Computational Team</h1> | ||
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+ | Our solution comprises a five-layer stack as illustrated in Figure~\ref{puphal}. Using the Clotho | ||
+ | platform \cite{densmore-tapia-2009}, we develop two applications for specifying and executing | ||
+ | biological protocols. The Assembly Planner \cite{densmore-nar-2010} is the end-point of an | ||
+ | end-to-end design workflow \cite{beal-iwbda-2011} that produces an assembly plan for synthetic | ||
+ | biological devices, with each assembly step annotated with the name of a biological protocol. Each | ||
+ | such protocol itself may be fully specified using another Clotho application called PuppetShow, which | ||
+ | provides an environment for writing, testing, debugging, and executing biological protocols. | ||
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+ | The protocols are written in a new high-level language called Puppeteer. The Language layer | ||
+ | comprises the Puppeteer interpreter and linker. A protocol specified in Puppeteer may contain | ||
+ | Puppeteer instructions as well as references to previously created Puppeteer programs available in a | ||
+ | library. The Language layer expands and translates a Puppeteer protocol to a sequence of low-level | ||
+ | commands expressed in a Common Robot Instruction Set (CRIS). CRIS provides a standardized | ||
+ | instruction set that high level biological protocol languages like Puppeteer may assume to be | ||
+ | supported by any robot. Any high-level language may produce CRIS programs and any robot vendor may | ||
+ | support a superset of CRIS: this decouples robot hardware details from biological protocol and | ||
+ | specification details and supports our goal of portability and protocol library reuse. The Hardware | ||
+ | Layer---the external control and I/O interface of a robot---is wrapped under a Hardware Abstraction | ||
+ | Layer (HAL). Vendor-provided software for programming the robot may be proprietary and is used to | ||
+ | control the robot. An interface to it is provided by a software bridge, which maps protocols | ||
+ | expressed in CRIS to sequences of native robot instructions. | ||
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+ | The Resource Management layer maintains resource state information and provides a standardizable | ||
+ | high-level interface for initializing, requesting, naming, aggregating, and accessing resources to | ||
+ | the Language layer, analogous to a ``system call'' suite. This interface supports our goal of | ||
+ | removing the minutiae of resource management from the protocol specification language. | ||
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<img style="float:right; width:380px; height:450px" src="http://wiki.bu.edu/wiki/ece-cidar/images/f/fd/Puphal.jpg"/> | <img style="float:right; width:380px; height:450px" src="http://wiki.bu.edu/wiki/ece-cidar/images/f/fd/Puphal.jpg"/> |
Revision as of 21:32, 10 September 2011