Int. J. Business Process Integration and Management, Vol. 5, No. 1, 2010 3 Copyright © 2010 Inderscience Enterprises Ltd. A declarative language and toolkit for scientific workflow implementation and execution Hasan Jamil*, Aminul Islam and Shahriyar Hossain Department of Computer Science, Wayne State University, 5143 Cass Avenue, Detroit, MI 48202, USA E-mail: jamil@cs.wayne.edu E-mail: aminul@wayne.edu E-mail: shah_h@wayne.edu *Corresponding author Abstract: Scientific workflow design is usually complex and demands access to and integration of numerous non-conventional resources. Geographical distribution and semantic heterogeneity of these resources add to this complexity. The cost effectiveness of such workflow design, thus, depends upon the lifespan of the application and its anticipated use. Shorter application lifespan usually entails prohibitive development costs. In this paper, we present an alternative platform for declarative workflow design using BioFlow in such environments. BioFlow is being developed as the query language for a scientific data management system called LifeDB that aims to support on-the-fly data integration and workflow support for life sciences applications. We argue that a declarative and ad hoc workflow design using BioFlow is more efficient and cost effective compared to traditional approaches using systems such as Taverna or Kepler. To demonstrate the advantages of BioFlow, we compare a canonical microarray data analysis workflow application design approach using BioFlow with Taverna and a gene regulation application using BioFlow and Kepler. We show that BioFlow supports ad hoc and modular application design at a throw away cost and produces a superior maintainable application that can adapt to changes in the source without significant effort compared to both Taverna and Kepler. Keywords: BioFlow; declarative language; scientific workflow; Taverna; Kepler. Reference to this paper should be made as follows: Jamil, H., Islam, A. and Hossain, S. (2010) ‘A declarative language and toolkit for scientific workflow implementation and execution’, Int. J. Business Process Integration and Management, Vol. 5, No. 1, pp.3–17. Biographical notes: Hasan Jamil is a member of the Faculty in the Department of Computer Science, Wayne State University. He obtained his PhD in Computer Science from Concordia University, Canada, and his MS and BS in Applied Physics and Electronics from the University of Dhaka, Bangladesh. His current research interests are in the areas of databases, bioinformatics and knowledge representation. He leads the Integration Informatics Laboratory at Wayne State University. Aminul Islam is a PhD student in the Department of Computer Science, Wayne State University. He obtained his BS in Computer Science and Engineering degree from Bangladesh University of Engineering and Technology and MS in Computer Science from Wayne State University. While his research interest is in the general area of bioinformatics, he is currently focusing on microarray data management and analysis. Shahriyar Hossain is a PhD student in the Department of Computer Science, Wayne State University. He obtained his Bachelor in Computer Science and Engineering degree from Bangladesh University of Engineering and Technology. His major research focus is in intelligent querying of life sciences databases and user interfaces for scientific applications. 1 Introduction Application design in life sciences is a challenging exercise due to its inherently complex and ad hoc investigative nature. The challenge is further confounded by the distributed and heterogeneous nature of the resources used – tools and database, exponentially increasing volume of data made available on a daily basis, the relatively short life time of the resources and the rapid propagation of latent errors. Nonetheless, researchers race against time to find a way to make use of the available resources to carry out their investigation to the best of their abilities. Broadly, there are three types of application development approaches. In the first category, researchers