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Simon & Freire Receive NSF CAREER Awards

April 8, 2008 -- CMOP scientists Holly Simon and Juliana Freire have each received National Science Foundation (NSF) Faculty Early Career Development (CAREER) awards.

The NSF CAREER program was established to recognize the critical roles played by faculty members in integrating research and education. It is the NSF's most prestigious award for junior faculty members and is designed to provide support to help awardees develop careers as outstanding teacher-scholars.

Holly SimonHolly Simon

Dr. Simon, an Assistant Professor in Environmental and Biomolecular Systems at OHSU, has received a 5-year, nearly $800,000 NSF CAREER award to study little-understood members of the domain Archaea in riverine sediments. These organisms, referred to as low-to-medium temperature (or nonthermophilic) crenarchaeaotes, were discovered only recently, and very little is known about their ecological function. They are ubiquitous across diverse ecosystems and are very abundant in certain habitats. In fact, they have recently been discovered to be the most abundant archaea in the ocean and appear to play major roles in global biogeochemical cycles.

Dr. Simon notes that only one member of this group—the marine-based Nitrosopumilus maritimus—has been successfully cultured in the laboratory. This strain, isolated by David Stahl's group at the University of Washington, oxidizes ammonia in the presence of oxygen to provide energy for carbon fixation. That reaction is the first and generally the rate-limiting step in the nitrification process—a process that has previously been believed to be carried out exclusively by bacteria and which is a fundamental part of the nitrogen cycle.

The physiological roles of these archaea have proven to be very difficult to study. Part of the difficulty is the time it takes for them to become enriched in laboratory culture: 6 months, in some cases, as opposed to the rapid overnight growth of well-studied bacteria like E. coli. Dr. Simon's NSF proposal was based, in part, on her work growing soil crenarchaeotes in the laboratory. Although she has not yet isolated individual strains of these archaea, she has developed protocols that reproducibly led to the enrichment of members of one highly related cluster of strains. She is using a combination of techniques, including genomics, to investigate the ecological roles of these organisms in soil and in association with plant roots.

The NSF CAREER grant will allow Dr. Simon to extend her research on this important group of archaea into the Columbia River ecosystem with a project that synergizes with her work in CMOP. Preliminary research from Simon's laboratory indicates that Columbia River sediments contain abundant numbers of crenarchaeotes with the genetic capability to carry out ammonia oxidation. Further studies to be supported by the CAREER project will help Simon's group determine the importance of these sediment-dwelling archaea in the nitrification process and will support the investigation of other metabolic processes carried out by the organisms. The research will be done in collaboration with Dr. James Nurmi, CMOP staff scientist, and Dr. Paul Tratnyek, a Professor of Environmental and Biomolecular Systems and CMOP scientist. Drs. Nurmi and Tratnyek will use novel techniques to dissect the chemical microenvironment occupied by riverine microbial communities, which, in conjunction with the sensitive molecular microbial ecology techniques practiced in the Simon laboratory, will provide clues to the different ecological niches that the archaea occupy in the Columbia River ecosystem. Armed with this information and her prior experience, Dr. Simon expects to isolate novel strains of Columbia River sediment-dwelling archaea in laboratory culture, which will allow more thorough investigations of their physiological properties and will eventually lead to a better understanding of their importance in global elemental cycling.

Juliana FreireJuliana Freire

Dr. Freire, a CMOP scientist and Assistant Professor in the School of Computing at the University of Utah, has also recently received a 5-year, $500,000 NSF CAREER award to create computational infrastructure that can capture and manage the provenance of scientific artifacts, including data products (e.g., visualizations), simulation, and analysis workflows. Specifically with this NSF CAREER award, Dr. Freire intends to develop algorithms to help scientists manage large quantities of scientific data and workflows, and to query their provenance.

Dr. Freire's motivation for this research came from examining, together with Dr. Antonio Baptista (CMOP Director), the cyberinfrastructure needs of coastal-margin observatories – in particular, the challenges that CMOP (and other) scientists face in managing and analyzing data collected from sensors and derived from simulations of ocean processes. Some of these issues have been addressed in another NSF award, the goal of which was to develop new tools for streamlining the creation, execution, and sharing of complex visualizations. As part of that project, Dr. Freire's group developed VisTrails (, an open-source scientific workflow and provenance management system. Since its beta release in January 2007, VisTrails has been downloaded over 3,000 times.

Dr. Freire's CAREER project will take a broader look at the problem of provenance management for computational tasks. Dr. Freire notes that computing has been an enormous accelerator to science and to the collection and analysis of data. However, to analyze and understand scientific data, complex computational processes (workflows) must be assembled, often requiring the combination of loosely coupled resources, specialized libraries, and web services. The goal of this project is to produce new algorithms and techniques for exploring and re-using useful knowledge embedded in workflow specifications and in the provenance of the data that scientists manipulate. Her CAREER project addresses key limitations in existing workflow systems. First, this project will develop a set of usable tools to enable casual users (who do not necessarily have programming expertise) to perform exploratory tasks and to solve problems through workflows. Such tools include intuitive user interfaces to manipulate collections of workflow and to query workflows by example. Second, this project will build a scalable provenance management infrastructure to support the efficient execution of these operations. The algorithms and techniques developed in this project will be integrated into VisTrails, and they will also be deployed as part of the cyberinfrastructure of CMOP.

The NSF award also provides support for Drs. Simon and Freire to extend the impact of their research into education. Dr. Simon will develop a new interdisciplinary graduate degree program and curriculum, guide research experiences in genomics for undergraduate students, and mentor high school researchers. The undergraduate genomics program is being developed with Associate Professor Jon Schnorr of Pacific University. In total, Dr. Simon's project will support one doctoral student, up to 10 undergraduate students, and as many as 5 high school students from the Portland-based Saturday Academy.

Dr. Freire's educational aims are to design an introductory computer science course and workbook, the focus of which will be on problem-solving and not on programming. In recent years, low enrollments of students (especially women) in computer science have been attributed in part to the misconception that computer science is just programming. This misconception is reinforced in many undergraduate courses that emphasize programming. The provenance infrastructure and tools to be developed in Dr. Freire's NSF CAREER research will serve as a platform where students can learn computer science and solve computational problems, before learning programming. In addition, Dr. Freire's project will involve 2 doctoral students from the University of Utah.