In Services: Data Management for In Silico Workflows

Scientific workflows are emerging as a suitable practice to support bio informatics experiments. Specially, in distributed environments, where workflow steps are located at different sites, workflows can create an independent and interoperable environment between the scientific applications and databases, when combined with the Web services technology. Web services have been useful as legacy code wrappers, in order to facilitate distributed workflow definition and orchestration. However, there is an increasing need to address workflow intermediate data management. This work presents the In Services system that provides support for bio informatics workflows redefinition. This redefinition enables the user to include specific data management services, according to his needs. These services are able to filter, store and retrieve data that are generated in each workflow execution step

[1]  Akinori Sarai,et al.  The Diamond STING server , 2005, Nucleic Acids Res..

[2]  Val Tannen,et al.  K2/Kleisli and GUS: Experiments in integrated access to genomic data sources , 2001, IBM Syst. J..

[3]  Sourav S. Bhowmick,et al.  The gRNA: A Highly Programmable Infrastructure for Prototyping, Developing and Deploying Genomics-Centric Applications , 2002, VLDB.

[4]  Calton Pu,et al.  A modeling and execution environment for distributed scientific workflows , 2003, 15th International Conference on Scientific and Statistical Database Management, 2003..

[5]  Marta Mattoso,et al.  An Environment to Define and Execute In-Silico Workflows Using Web Services , 2005, DILS.

[6]  André Yoshiaki Kashiwabara,et al.  EGene: a configurable pipeline generation system for automated sequence analysis , 2005, Bioinform..

[7]  Sandeepan Banerjee.  A Database Platform for Bioinformatics , 2000, VLDB.

[8]  Nathan Goodman,et al.  The LabBase system for data management in large scale biology research laboratories , 1998, Bioinform..

[9]  Edward A. Lee,et al.  Scientific workflow management and the Kepler system , 2006, Concurr. Comput. Pract. Exp..

[10]  Abdelkader Hameurlain,et al.  Proceedings of the 13th International Conference on Database and Expert Systems Applications , 1995 .

[11]  Matjaz B. Juric,et al.  Business process execution language for web services , 2004 .

[12]  C. Goble,et al.  The {my}Grid Project: Services, Architecture and Demonstrator , 2003 .

[13]  Roberto Chinnici,et al.  Web Services Description Language (WSDL) Version 2.0 Part 1: Core Language , 2007 .

[14]  Mark D. Wilkinson,et al.  BioMOBY: An Open Source Biological Web Services Proposal , 2002, Briefings Bioinform..

[15]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.