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Evolutionary Biologists have long struggled with the challenge of developinganalysis workflows in a flexible manner, thus facilitating the reuse ofphylogenetic knowledge. An evolutionary biology workflow can be viewed as aplan which composes web services that can retrieve, manipulate, and producephylogenetic trees. The Phylotastic project was launched two years ago as acollaboration between evolutionary biologists and computer scientists, with thegoal of developing an open architecture to facilitate the creation of suchanalysis workflows. While composition of web services is a problem that hasbeen extensively explored in the literature, including within the logicprogramming domain, the incarnation of the problem in Phylotastic provides anumber of additional challenges. Along with the need to integrate preferencesand formal ontologies in the description of the desired workflow, evolutionarybiologists tend to construct workflows in an incremental manner, bysuccessively refining the workflow, by indicating desired changes (e.g.,exclusion of certain services, modifications of the desired output). This leadsto the need of successive iterations of incremental replanning, to develop anew workflow that integrates the requested changes while minimizing the changesto the original workflow. This paper illustrates how Phylotastic has addressedthe challenges of creating and refining phylogenetic analysis workflows usinglogic programming technology and how such solutions have been used within thegeneral framework of the Phylotastic project. Under consideration in Theory andPractice of Logic Programming (TPLP).

Phylotastic: An Experiment in Creating, Manipulating, and Evolving Phylogenetic Biology Workflows Using Logic Programming