Revision as of 23:55, 17 October 2009

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Automation Assembly and Kepler Integration

Two of the key requirements for introducing automation into the biological design process are reproducibility of specific protocols and formally capturing these protocols. Often these are very complicated, take considerable time to develop and “debug”, and are lab/equipment specific. A highly modular, expressive, and extensible framework to capture and design these workflows would be useful. Our project integrated the Kepler workflow design environment with the existing Clotho platform, in order to formally capture a number of specific design protocols related to composite part assembly.
Kepler is a multi-university design effort focusing on scientific workflows, and is used by a wide variety of projects in different fields. This work is done in conjunction with the [http://chess.eecs.berkeley.edu/ Center for Hybrid & Embedded Software Systems (CHESS)]. We are improving protocol automation and also create material for a larger audience as well.

Big Picture

Physical Assembly Running Example

As we are going through steps in the workflow, we will show the construction of a family of reporters which consists of four devices:

[http://partsregistry.org/wiki/index.php?title=Part:BBa_I13521 Reporter #1 - BBa_I13521]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_I763007 Reporter #2 - BBa_I763007]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_J5526 Reporter #3 - BBa_J5526]
[http://partsregistry.org/wiki/index.php?title=Part:BBa_J3901 Reporter #4 - BBa_J3901]

Zooming In

1. Start Clotho

2. Start Kepler

3. Specify Devices to Assemble

This action is done in Clotho's Algorithm Manager - a tool constructed by Berkeley_Software iGEM team 2008.

Devices are specified in a string format where basic parts are separated by dots to represent the overall goal part. Each goal part is entered on a separate line. This can be done either manually, or imported from a file, or imported from Spectacles.
In our example we can assume that parts were designed in Spectacles: Reporter #1 Reporter #2 Reporter #3 Reporter #4

4. Launch tool to connect Clotho & Kepler

Further explanation about the Clotho-Kepler connection on the tutorial page : Clotho-Kepler Connection

Tutorial

Kepler Tutorial

@@ Line 21: / Line 21: @@
 ==Physical Assembly Running Example==
 As we are going through steps in the workflow, we will show the construction of a family of reporters which consists of four devices:
+# [http://partsregistry.org/wiki/index.php?title=Part:BBa_I13521 Reporter #1 - BBa_I13521]
+# [http://partsregistry.org/wiki/index.php?title=Part:BBa_I763007 Reporter #2 - BBa_I763007]
+# [http://partsregistry.org/wiki/index.php?title=Part:BBa_J5526 Reporter #3 - BBa_J5526]
+# [http://partsregistry.org/wiki/index.php?title=Part:BBa_J3901 Reporter #4 - BBa_J3901]
 ==Zooming In==
@@ Line 36: / Line 37: @@
 [[Image:Berkeley_Software2009_ClothoAlgoManager.png|500px|Clotho Algorithm Manager with running example.]]
-Devices are specified in a string format where basic parts are separated by dots to represent the overall goal part. Each goal part is entered on a separate line. This can be done either manually, or imported from a file, or imported from [[Team:Berkeley_Software/Spectacles|Spectacles]].
+Devices are specified in a string format where basic parts are separated by dots to represent the overall goal part. Each goal part is entered on a separate line. This can be done either manually, or imported from a file, or imported from [[Team:Berkeley_Software/Spectacles|Spectacles]].<br>
+In our example we can assume that parts were designed in [[Team:Berkeley_Software/Spectacles|Spectacles]]:
+[[Image:Berkeley_Software2009_Reporter1|Reporter #1]]
+[[Image:Berkeley_Software2009_Reporter1|Reporter #2]]
+[[Image:Berkeley_Software2009_Reporter1|Reporter #3]]
+[[Image:Berkeley_Software2009_Reporter1|Reporter #4]]
 ===4. Launch tool to connect Clotho & Kepler===

Team:Berkeley Software/Kepler

From 2009.igem.org