title: Detecting distant homologies on protozoans metabolic pathways using scientific workflows.
abstract: 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.
authors.affiliation: Computer Science Department, COPPE, Federal University of Rio de Janeiro (UFRJ), P.O. Box 68511, 21941-972 Rio de Janeiro, RJ, Brazil. serra@cos.ufrj.br
authors.forename: Sérgio Manuel Serra
authors.initials: SM
authors.lastname: da Cruz
authors.forename: Vanessa
authors.initials: V
authors.lastname: Batista
authors.forename: Edno
authors.initials: E
authors.lastname: Silva
authors.forename: Frederico
authors.initials: F
authors.lastname: Tosta
authors.forename: Clarissa
authors.initials: C
authors.lastname: Vilela
authors.forename: Rafael
authors.initials: R
authors.lastname: Cuadrat
authors.forename: Diogo
authors.initials: D
authors.lastname: Tschoeke
authors.forename: Alberto M R
authors.initials: AM
authors.lastname: Dávila
authors.forename: Maria Luiza Machado
authors.initials: ML
authors.lastname: Campos
authors.forename: Marta
authors.initials: M
authors.lastname: Mattoso
mesh_terms: D018503:Genome, Protozoan; D023281:Genomics / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D012586:Science; D017385:Sequence Homology; D057188:Workflow