From Bio-jETI Process Models to Native Code

Bio-jETI is a framework for model-based, graphical development and execution of bioinformatics analysis processes. With the GeneSys code generation framework we can automatically compile the work¿ow models into native, stand-alone program code. We show via a phylogenetic analysis work¿ow designed by the DNA Data Bank of Japan (DDBJ) how we generate 6 variants of Java code from the corresponding process model realized in Bio-jETI. Performance measurements show that 1) the overall work¿ow execution time is dominated by the remote services it uses, and thus 2)all 6 variants are almost as fast as the handwritten Java of DDBJ. This way, we obtain ef¿cient native code essentially without program- ming. Thus, we demonstrate in this paper that model- based work¿ow development in Bio-jETI offers several advantages over manual implementation – including higher agility, greater transparency and better maintainability – without compromising the runtime performance.

[1]  Tiziana Margaria,et al.  Automatic Generation of the SWS- Challenge Mediator with jABC/ABC , 2009, Semantic Web Services Challenge.

[2]  Tiziana Margaria,et al.  jETI: A Tool for Remote Tool Integration , 2005, TACAS.

[3]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[4]  Bertram Ludäscher,et al.  Kepler: an extensible system for design and execution of scientific workflows , 2004, Proceedings. 16th International Conference on Scientific and Statistical Database Management, 2004..

[5]  Cesare Pautasso,et al.  BioOpera: cluster-aware computing , 2002, Proceedings. IEEE International Conference on Cluster Computing.

[6]  Tiziana Margaria,et al.  Game-Based Model Checking for Reliable Autonomy in Space , 2011, J. Aerosp. Comput. Inf. Commun..

[7]  Matthew R. Pocock,et al.  Taverna: a tool for the composition and enactment of bioinformatics workflows , 2004, Bioinform..

[8]  Tiziana Margaria,et al.  Genesys: service-oriented construction of property conform code generators , 2008, Innovations in Systems and Software Engineering.

[9]  Tiziana Margaria,et al.  Model-Driven Development with the jABC , 2006, Haifa Verification Conference.

[10]  Arun Krishnan,et al.  Wildfire: distributed, Grid-enabled workflow construction and execution , 2004, BMC Bioinformatics.

[11]  Tiziana Margaria,et al.  Model-based design of distributed collaborative bioinformatics processes in the jABC , 2006, 11th IEEE International Conference on Engineering of Complex Computer Systems (ICECCS'06).

[12]  Ian J. Taylor,et al.  The Triana Workflow Environment: Architecture and Applications , 2007, Workflows for e-Science, Scientific Workflows for Grids.

[13]  Tiziana Margaria,et al.  Lightweight coarse-grained coordination: a scalable system-level approach , 2004, International Journal on Software Tools for Technology Transfer.

[14]  Alexander Sczyrba,et al.  GeneFisher-P: variations of GeneFisher as processes in Bio-jETI , 2008, BMC Bioinformatics.

[15]  Tiziana Margaria,et al.  Biological LC/MS Preprocessing and Analysis with jABC, jETI and xcms , 2006, Second International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (isola 2006).

[16]  Cesare Pautasso,et al.  A Flexible System for Visual Service Composition , 2004 .

[17]  Tiziana Margaria,et al.  Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes , 2008, BMC Bioinformatics.

[18]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[19]  Tiziana Margaria,et al.  Model-based design of distributed collaborative bioinformatics processes in the jABC , 2006 .

[20]  Tiziana Margaria,et al.  Service-Oriented Design: The Roots , 2005, ICSOC.

[21]  Tiziana Margaria,et al.  Service Engineering: Linking Business and IT , 2006, Computer.

[22]  Tiziana Margaria,et al.  Seven Variations of an Alignment Workflow - An Illustration of Agile Process Design and Management in Bio-jETI , 2008, ISBRA.