A taxonomy and survey of grid resource management systems for distributed computing
Software—Practice & Experience
Structural Genomic Workflows Supported by Web Services
DEXA '03 Proceedings of the 14th International Workshop on Database and Expert Systems Applications
Kepler: An Extensible System for Design and Execution of Scientific Workflows
SSDBM '04 Proceedings of the 16th International Conference on Scientific and Statistical Database Management
K2/Kleisli and GUS: experiments in integrated access to genomic data sources
IBM Systems Journal - Deep computing for the life sciences
A survey of data provenance in e-science
ACM SIGMOD Record
A modeling and executive environment for distributed scientific workflows
SSDBM '03 Proceedings of the 15th International Conference on Scientific and Statistical Database Management
Evaluation of BPEL to Scientific Workflows
CCGRID '06 Proceedings of the Sixth IEEE International Symposium on Cluster Computing and the Grid
Taverna: lessons in creating a workflow environment for the life sciences: Research Articles
Concurrency and Computation: Practice & Experience - Workflow in Grid Systems
Scientific workflow management and the Kepler system: Research Articles
Concurrency and Computation: Practice & Experience - Workflow in Grid Systems
Beyond the data deluge: data integration and bio-ontologies
Journal of Biomedical Informatics - Special issue: Biomedical ontologies
Integrating existing scientific workflow systems: the Kepler/Pegasus example
Proceedings of the 2nd workshop on Workflows in support of large-scale science
Bioinformatics
OrthoSearch: a scientific workflow approach to detect distant homologies on protozoans
Proceedings of the 2008 ACM symposium on Applied computing
IAAI'07 Proceedings of the 19th national conference on Innovative applications of artificial intelligence - Volume 2
A taxonomy of grid monitoring systems
Future Generation Computer Systems
Adapting the electronic laboratory notebook for the semantic era
CTS'05 Proceedings of the 2005 international conference on Collaborative technologies and systems
Towards a model of provenance and user views in scientific workflows
DILS'06 Proceedings of the Third international conference on Data Integration in the Life Sciences
A framework for the design and reuse of grid workflows
SAG'04 Proceedings of the First international conference on Scientific Applications of Grid Computing
EPEW'05/WS-FM'05 Proceedings of the 2005 international conference on European Performance Engineering, and Web Services and Formal Methods, international conference on Formal Techniques for Computer Systems and Business Processes
Managing rapidly-evolving scientific workflows
IPAW'06 Proceedings of the 2006 international conference on Provenance and Annotation of Data
A model for user-oriented data provenance in pipelined scientific workflows
IPAW'06 Proceedings of the 2006 international conference on Provenance and Annotation of Data
International Journal of Data Mining and Bioinformatics
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Bioinformatics experiments are typically composed of programs in pipelines manipulating an enormous quantity of data. An interesting approach for managing those experiments is through workflow management systems (WfMS). In this work we discuss WfMS features to support genome homology workflows and present some relevant issues for typical genomic experiments. Our evaluation used Kepler WfMS to manage a real genomic pipeline, named OrthoSearch, originally defined as a Perl script. We show a case study detecting distant homologies on trypanomatids metabolic pathways. Our results reinforce the benefits of WfMS over script languages and point out challenges to WfMS in distributed environments.