OrthoSearch: a scientific workflow approach to detect distant homologies on protozoans


Managing bioinformatics experiments is challenging due to the orchestration and interoperation of tools with semantics. An effective approach for managing those experiments is through workflow management systems (WfMS). We present several WfMS features for supporting genome homology workflows and discuss relevant issues for typical genomic experiments. In our evaluation we used OrthoSearch, a real genomic pipeline originally defined as a Perl script. We modeled it as a scientific workflow and implemented it on Kepler WfMS. 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.

DOI: 10.1145/1363686.1363983

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@inproceedings{Cruz2008OrthoSearchAS, title={OrthoSearch: a scientific workflow approach to detect distant homologies on protozoans}, author={S{\'e}rgio Manuel Serra da Cruz and Vanessa Batista and Alberto M. R. D{\'a}vila and Edno Silva and Frederico Tosta and Clarissa Vilela and Maria Luiza Machado Campos and Rafael R. C. Cuadrat and Diogo A. Tschoeke and Marta Mattoso}, booktitle={SAC}, year={2008} }