Davidson, Susan B
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Publication A Model for User-Oriented Data Provenance in Pipelined Scientific Workflows(2006-05-03) Bowers, Shawn; McPhillips, Timothy; Ludascher, Bertram; Cohen, Shirley; Davidson, Susan B.Integrated provenance support promises to be a chief advantage of scientific workflow systems over script-based alternatives. While it is often recognized that information gathered during scientific workflow execution can be used automatically to increase fault tolerance (via checkpointing) and to optimize performance (by reusing intermediate data products in future runs), it is perhaps more significant that provenance information may also be used by scientists to reproduce results from earlier runs, to explain unexpected results, and to prepare results for publication. Current workflow systems offer little or no direct support for these "scientist-oriented" queries of provenance information. Indeed the use of advanced execution models in scientific workflows (e.g., process networks, which exhibit pipeline parallelism over streaming data) and failure to record certain fundamental events such as state resets of processes, can render existing provenance schemas useless for scientific applications of provenance. We develop a simple provenance model that is capable of supporting a wide range of scientific use cases even for complex models of computation such as process networks. Our approach reduces these use cases to database queries over event logs, and is capable of reconstructing complete data and invocation dependency graphs for a workflow run.Publication Path-based systems to guide scientists in the maze of biological data sources(2006-08-24) Cohen-Boulakia, Sarah; Davidson, Susan B.; Froidevaux, Christine; Lacroix, Zoe; Vidal, Maria-EstherFueled by novel technologies capable of producing massive amounts of data for a single experiment, scientists are faced with an explosion of information which must be rapidly analyzed and combined with other data to form hypotheses and create knowledge. Today, numerous biological questions can be answered without entering a wet lab. Scientific protocols designed to answer these questions can be run entirely on a computer. Biological resources are often complementary, focused on different objects and reflecting various experts' points of view. Exploiting the richness and diversity of these resources is crucial for scientists. However, with the increase of resources, scientists have to face the problem of selecting sources and tools when interpreting their data. In this paper, we analyze the way in which biologists express and implement scientific protocols, and we identify the requirements for a system which can guide scientists in constructing protocols to answer new biological questions. We present two such systems, BioNavigation and BioGuide dedicated to help scientists select resources by following suitable paths within the growing network of interconnected biological resources.Publication BioGuideSRS: Querying Multiple Sources with a user-centric perspective(2007-01-01) Cohen-Boulakia, Sarah; Biton, Olivier; Davidson, Susan B; Froidevaux, ChristineSummary: Biologists are frequently faced with the problem of integrating information from multiple heterogeneous sources with their own experimental data. Given the large number of public sources, it is difficult to choose which sources to integrate without assistance. When doing this manually, biologists differ in their preferences concerning the sources to be queried as well as the strategies, i.e. the querying process they follow for navigating through the sources. In response to these findings, we have developed BioGuide to assist scientists search for relevant data within external sources while taking their preferences and strategies into account. In this paper, we present BioGuideSRS, a user-friendly system which automatically retrieves instances of data by using BioGuide on top of the SRS system. BioGuideSRS is an Applet that can be run from its web page on any system with Java 5.0. Availability: http://www.bioguide-project.net