Applications

Scientists: Yu S. Huang et al. (Center for Neurobehavioral Genetics, UCLA)

As the second OWM (old world monkey) sequenced (the first is Rhesus macaque), vervets, unlike the great apes who are mostly in near-extinction status, are widely available for biomedical research. (Rhesus is widely available in India but the export restriction imposed by the Indian government makes it less ideal for biomedical research).

Scientists: James Knowles, Ting Chen, Ying Wang, Oleg Evgrafov

The Brain Span project seeks to find when and where in the brain a gene is expressed. This information holds clues to potential causes of disease. A recent study found that forms of a gene associated with schizophrenia are over-expressed in the fetal brain. To make such discoveries about what is abnormal, scientists first need to know what the normal patterns of gene expression are during development.

This workflow combines results from the GNOSIS CNV (Copy Number Variation) detection algorithm and PennCNV detection algorithm (including X-Chromosome detection) to produce a file containing Merged CNVs. It then processes these further to compare the results with a list of Common CNVs, and assesses the overlap of parent and children CNVs. Finally it annotates the results.

Scientists: Ben Berman et al. (USC)

This application splits sequence files into multiple parts and converts them to the appropriate file format. Then it filters out noisy and contaminating sequences to maps them to their genomic locations. From the individual mapping steps, it merges them into a single global map and uses sequence maps to calculate the sequence density at each position in the genome. This application has a footprint of 6GB of data.

Scientists at OSU use Pegasus for mass-spectrometry-based proteomics. Proteomics workflows have been executed on local clusters and cloud resources.

Example proteomic workflow: a) Pegasus workflow template. Square boxes with double lines represent file collections and the ellipses with double boundary represent parallel jobs. b) Implementation of workflow for clustering of five shotgun proteomic data sets. c) Hierarchical cluster analysis of the shotgun proteomic data.

Plant scientists at University of Wisconsin Madison are using Pegasus to generate movies of plant root growth and analyze images collected via time-lapse photography. Another project samples forest locations to characterize the understory vegetation to determine how different plant species are distributed in the woods.

Scientists: George Phillips, UW Madison

George Phillips of the Biochemistry Department at UW Madison has interests in the structure and dynamics of proteins as well as in computational biology.

A climate modeling application has used our tools to reduce the amount of time computations take. Simulations which used to take 2.5 months to run manually, took only 2.5 days to run using our tools.

Scientists: Li Zhang, UW Madision

Li Zhang is faculty in the UW Madison Computer Sciences Department, and has interests in computer vision and graphics. Graduate student Alok Deshpande's project is interdisciplinary research that seeks to realize bio-inspired intelligent micro optical imaging systems.

Scientists: Frank McKenna, Thomas J. Hacker, Linas Mockus, Michael McLennan, Steven Clark

Over the past several years, the US National Science Foundation has been funding the development of collaborative web sites or ‘collaboratories’. Many communities have adopted the HUBzero platform to create collaboratories called ‘hubs’ where they can share ideas, models, experiences, publications, and data in pursuit of research and education.

GADU - the Genome Analysis and Database Update system, has been using Pegasus for the past 2 years to perform high-throughout analysis and annotation of the genomics information that it regularly fuses from multiple public information sources, providing an integrated facility that supports research programs within DOE as well as public visitors to its web portal.

Scientists: Laurent Gizon, Raymond Burston, Yacine Saidi

The Solar Dynamics Observatory (SDO) is NASA's most important solar physics mission of this coming decade. To be launched near the end of 2008, the three primary instruments on board SDO are the Helioseismic and Magnetic Imager (HMI), the Atmospheric Imaging Assembly (AIA) and the Extreme ultraviolet Variability Experiment (EVE). The data will be predominantly used to learn about solar magnetic activity and to probe the internal structure and dynamics of the Sun with helioseismology.

Professor Paul Hanson at the Center for Limnology at UW Madison conducts research in carbon cycling, ecosystem variability, microbes, algae, and even fish.

Scientists: Mark Ellisman, Steven Peltier, Abel Lin (UCSD)

Pegasus is also used in the Telescience project and portal to support 3D reconstruction of electron tomography images. The UCSD scientists plan to continue to rely on our workflow technologies to expand the set of Grid applications they support within their portal environment and to develop new techniques that can provide real-time feedback from the 3D reconstruction to the scientists manipulating the instrument.

Researchers at the Jet Propulsion Laboratory are exploring Pegasus WMS to run ocean forecast ensembles of the California coastal region. These models produce a number of daily forecasts for water temperature, salinity, and other measures.

The main forecast workflow (shown below) consumes about 1.8Gb Data and produces output of about 8.7 MB.

Ocean Scientists: Peggy Li and Yi Chao (JPL, NASA)

Scientists: Duncan Brown (Syracuse), Kent Blackburn (Caltech), Britta Dauderts, Robert Engel (Caltech)

 Laser Interferometer Gravitational Wave Observatory (LIGO)  is a network of gravitational-wave detectors, with observatories in Livingston, LA and Hanford, WA.  The observatories' mission is to detect and measure gravitational waves predicted by general relativity─Einstein's theory of gravity─in which gravity is described as due to the curvature of the fabric of time and spa