Workflows avec SmartTools (par Carine Courbis)

• Towards an Aspect Weaving BPEL engine
• Towards Aspect Weaving Applications

Workflows

• Focus
  • JOLIE: a Java Orchestration Language Intepreter Engine

Workflows control-flow

• http://fr.bonitasoft.com/
• http://www.eclipse.org/jwt/

Workflows scientific data-flow

1. Survey
2. Examining the Challenges of Scientific Workflows. Yolanda Gil, Ewa Deelman, Mark Ellisman, Thomas Fahringer, Geoffrey Fox, Dennis Gannon, Carole Goble, Miron Livny, Luc Moreau and Jim Myers. Computer, 40:24-32, 2007. (BIB)PDF
3. http://charles-guillemot.info/2010/03/11/1%C2%B0-approche-des-workflows/
4. WebLab: a data-centric, knowledge-sharing bioinformatic platform. Liu, Xiaoqiao, Wu, Jianmin, Wang, Jun, Liu, Xiaochuan, Zhao, Shuqi, Li, Zhe, Kong, Lei, Gu, Xiaocheng, Luo, Jingchu and Gao, Ge. Nucleic Acids Research, 37(Web Server issue):W33+, may 2009. (URL) (BIB) PDF
5. Experience in using a process language to define scientific workflow and generate dataset provenance. Osterweil, Leon J., Clarke, Lori A., Ellison, Aaron M., Podorozhny, Rodion, Wise, Alexander, Boose, Emery and Hadley, Julian. In Proceedings of the 16th ACM SIGSOFT International Symposium on Foundations of software engineering, pages 319-329, New York, NY, USA, 2008. (URL) (BIB) PDF
6. A Taxonomy of Workflow Management Systems for Grid Computing. Yu, Jia and Buyya, Rajkumar. Journal of Grid Computing, 3(3-4):29, 2005. (URL) (BIB)PDF
7. Comparing Workflow Specification Languages: A Matter of Views. Abiteboul, Serge, Bourhis, Pierre and Vianu, Victor. In International Conference on Database Theory (ICDT) , Uppsala Suede , 03 2011. (Victor Vianu was supported in part by the NSF under award III-0916515 ). (URL) (BIB)PDF
8. Computational solutions to large-scale data management and analysis. Schadt, Eric E., Linderman, Michael D., Sorenson, Jon, Lee, Lawrence and Nolan, Garry P.. Nat Rev Genet, 11(9):647-657, 09 2010/09//print. (URL) (BIB)PDF

Softwares

• http://en.wikipedia.or/wiki/Bioinformatics_workflow_management_systems
• Galaxy phyton
• Kepler Java basé sur http://ptolemy.eecs.berkeley.edu/ptolemyII/ Actor
• Taverna Java (Osgi)
  • roadmap integration taverna and galaxy
  • TavernaGalaxy conversion workflow
  • Comparaison entre Galaxy et Taverna
• Triana
• MOTEUR
  • Flexible and efficient workflow deployement of data-intensive applications on grids with MOTEUR