• Eugene
• Spectacles
• Kepler
• Data Model

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.

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.

(director screenshot)
(list of actor screenshots, similar to poster)

Workflow

The assembly automation workflow
(assembly autmoation screenshot)

Cross-Software 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. (RMI Clotho screenshot)
(List of RMI Clotho method)
(screenshot of Clotho - Kepler with arrow)