Team:Berkeley Software/Kepler

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Automation Assembly and Kepler Integration

Contents

Introduction

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 Center for Hybrid & Embedded Software Systems (CHESS). We are improving protocol automation and also create material for a larger audience as well.



Big Picture

A workflow between Clotho and Kepler

Important to Know

Our big picture has been implemented for 2ab assembly protocol that is used in J.Christopher Anderson's lab. Besides that we have been working on the alternative assembly protocols and parts packaging collaborating with Joint BioEnergy Institute. The latest project has been started in August and is still under implementation.

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:

  1. Reporter #1 - BBa_I13521
  2. Reporter #2 - BBa_I763007
  3. Reporter #3 - BBa_J5526
  4. Reporter #4 - BBa_J3901

Zooming In

1. Start Clotho

Starting Clotho

2. Start Kepler

Starting Kepler

3. Specify devices to assemble

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

Clotho Algorithm Manager with running example.
Reporter #1. View in Spectacles.
Reporter #2. View in Spectacles.
Reporter #3. View in Spectacles.
Reporter #4.View in 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 Spectacles.
In our example we can assume that parts were designed in Spectacles.
In the Clotho's Algorithm Manager, input parts are converted into the efficient assembly graph which is imported into the Kepler workflow as Assembly Info. For our example assembly graph can be represented visually as:
Assembly graph for reporter family construction.

4. Launch tool to connect Clotho & Kepler

RMI Tool

This tool provides the mean to import assembly graph as assembly information (Assembly Info) object into the Kepler environment. Further explanation about the Clotho-Kepler connection on the tutorial page : Clotho-Kepler Connection.

5. Launch Kepler assembly automation assignment workflow

Load the automation workflow file into Kepler, choose the stage number then click the Run icon. Automation Workflow

6. Process Info according to stage number

Tutorial

Kepler Tutorial