Grid-Flow: A grid-enabled scientific workflow system with a Petri net-based interface.

摘要

Advances in computer power, network speed, and storage capacity have enabled scientists to explore research issues in their respective domains at scales both finer and greater than ever before. The availability of efficient data collection and analysis tools presents researchers with vast opportunities to process heterogeneous data within a distributed environment. To support the opportunities enabled by available massive computation, a suitable scientific workflow system is needed to help users to manage both data and programs, and to design reusable procedures of scientific experimental tasks. This dissertation describes the design and prototyping of such a scientific workflow infrastructure, the Grid-Flow system, which assists researchers in specifying scientific experiments using a Petri net-based interface. The Grid-Flow infrastructure is designed as a Service-Oriented Architecture (SOA) with multi-layer component models.; The major contributions of Grid-Flow are as follows: (1) a new, light-weight, programmable Grid workflow language, called the Grid-Flow Description Language (GFDL), is provided to describe the workflow process in a Grid environment; (2) a Petri net-based user interface, based on the Generic Modeling Environment (GME), is demonstrated to help users design the workflow process with a Petri net model; and (3) a data and program integration component of the Grid-Flow system is presented to integrate various data and non-interactive programs into the system.; This work furthermore contributes to design methodologies (data/program registration, workflow description and execution, and data/program integration), underlying models of modern scientific workflows (Petri net model and Data/Program Chart), the integration and orchestration of online data and programs within workflow cases, as well as the strategies of wrapping existing programs as web/Grid services in a Grid environment. Two workflow case studies, transmembrane region analysis and protein function and expression, are modeled and implemented by the Grid-Flow system in order to demonstrate the capability and usability of this workflow management system.