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Kepler design environment helps scientists design models and analysis across a broad range of scientific and engineering disciplines.Kepler Project Website This summer we introduced Kepler into synthetic biology by building a set of new Kepler actors for assembly automation and Clotho connection.

Components

In Kepler, a workflow is built from a collection of process steps that run under the control of a supervisor system.
Those separate steps are called "actors", they are represented as square icons but inside them are codes to define what to run in a step. A step can be an input/output operation, a computational function, or even another workflow. These actors are supervised by the "director", which keep track of when to run each actor.
Some Kepler actors

Assembly Workflows

As described in the Kepler project page, this workflow get assembly information from Clotho's Algorithm Manager, and output files for the liquid handling robot and human instructions.

Actor list

A. OpenClothoConnection: connect Kepler to Clotho with RMI Tool running. If succeeds, this actor output the connection with Clotho RMI methods so the next actors can use.
B. GetAssemblyGraph & GetString: get data from Clotho, such as the algorithm graph or some debugging string. These actors output either genetic Object data or special structure such as the assembly information
C. GraphProcessing: process the assembly information, check & prepare data for further options
D. DialogOption: antibiotic choices, either at runtime or user provides a choice in the parameter before workflow runs

To start designing Kepler workflow, the online manuals provide details instruction: Kepler Documentation

Clotho Connection

One of the key challenge for biology tool development is how to effectively share and cooperate. This year we strengthen the possibility of connection between multiple software. In particular, the Clotho platform from last year and Kepler can connect and send data through the remore interface with Java RMI. This RMI connection will guarantee Clotho and Kepler to talk to any Java software that import the same interface.

In assembly workflow, we made actor that open a Clotho RMI connection and actors that read data from Clotho tools. These actors supports all genetic data objects and has genetic parameters for tool name and object fields, thus they will work with any future Clotho tools, as long as those tool support Clotho API data methods.

This is the configuration of the Kepler actor GetString. This actor can read data from tools in Clotho and send out a String object to output ports. In the image, we want to read data from the tool AlgorithmManager, if there are multiple data fields, we can further specify what data we want with the other two parameters.