We present G-PIPE, a graphic pipeline generator for PISE that allows the definition of pipelines, parameterization of its component methods, and storage of metadata in XML formats. Our implementation goes beyond macro capacities currently in PISE. As the entire analysis protocol is defined in XML, a complete bioinformatic experiment (linked sets of methods, parameters and results) can be reproduced or shared among users. We also discuss the role of ontologies as as guidance systems in order to provide users with the possibility to define abstract work-flows, and execute them. A relevant baseline ontology is presented. Availability: http://if-web.imb.uq.edu.a
