Planning and Workflow Management for a Virtual Laboratory for Structural Biology

Purdue University, West Lafayette IN

Investigators

Abstract

We propose to create an infrastructure, a Virtual Laboratory, to support sharing of knowledge in structural biology, to plan an experiment, and to facilitate a rigorous process of scientific discovery. We call it a virtual laboratory because it will allow an individual sitting in front of a computer connected to the Internet, to control an experiment, to follow the most relevant aspects of an experiment conducted in the past by a well established group, or to get advice at a critical junction. The process of discovery in structural biology, and other natural sciences like physics or chemistry is fairly complex, it involves some tedious and time consuming activities, sharing of knowledge, analysis of the results, backtracking. The virtual laboratory will allow structural biologists to reduce the time to obtain the results, improve the quality of the results, and restructure the human involvement by allowing a scientist to concentrate on the experiment and the discovery process. To reduce the time to obtain results we need efficient components, fully integrated experiment, simulation, and modeling environments, and some form of knowledge sharing and management. To improve the quality of the solution we need to fully integrate sensors in the feedback loop and to use optimal model parameters. Last, but not least, we need to automate simple tasks like data migration, format conversion, and selection of optimal running condition for each computational task. The high level of sophistication necessary to obtain quality results in this field motivates our effort. Some components of the infrastructure are specific to structural biology e.g. the interfaces for building the knowledge base, but the basic mechanisms e.g., the planning and the workflow enactment engines, are general and can be used for other classes of problems with similar characteristics. In this grant application we propose to develop agents for 3D structure determination using cryo TEM methods and to design an integrated workflow enactment engine based upon a Petri Net model with a planning engine and a knowledge management system. All our programs are distributed under open source licenses from our Web site: http://bond.cs.purdue.edu. The project will contribute to education and support knowledge sharing in structural biology laboratories.