Scientists: Bruce Berriman, John Good (IPAC)
A collaboration with NASA/IPAC Infrared Science Archive (http://irsa.ipac.caltech.edu). The imaging capabilities of the Spitzer Space Telescope have enabled for the first time surveys of the plane of our Galaxy across the infrared spectrum.Read more...
Scientists: Bruce Berriman, John Good (IPAC)
Caltech astronomers are using Pegasus to generate science-grade mosaics of the sky (Montage project http://montage.ipac.caltech.edu/). Montage delivers science-grade mosaics of the sky. Our technologies were used to transform a single-processor Montage code into a complex workflow and parallelized computations to process larger-scale images.Read more...
|Association Mapping and Population Genetics in Vervets||
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).Read more...
This application uses the Cochran-Mantel-Haenszel (CMH) association statistic to do an association test conditional on the matching done in the population stratification step. The clustering uses Plink's Inheritance-by-Structure (IBS) clustering.
Scientists:Christopher Mason, Stephan Sanders, and Matthew State (Yale)Read more...
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.Read more...
|Children’s Hospital of Philadelphia Pediatric Genome Analysis||
Scientists: Mahdi Sarmady, Juan Perin
"The Center for Biomedical Informatics at the Children’s hospital of Philadelphia is the home for the development of innovative solutions to healthcare's immediate and long-term informatics needs. CBMi provides informatics-focused services, applications, and educational programs to Children's Hospital clinicians and researchers and seek to transform their craft with high-impact, low-cost solutions. One of the CBMi’s main areas of focus is genomics.Read more...
|Combined CNV Detection||
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.Read more...
The USC Epigenome Center is currently using the Illumina Genetic Analyzer (GA) system to generate high throughput DNA sequence data (up to 8 billion nucleotides per week) to map the epigenetic state of human cells on a genome-wide scale.
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.Read more...
|Genomic Studies of Mental Disorders||
The computational portal developed for the Center for Genomic Studies of Mental Disorders uses Pegasus to manage workflows for genetic population studies. This portal uses the Wings (url) workflow composition system and Pegasus to enable scientists to launch an analysis based on the available workflow template. Below is a screenshot of the portal Workflow Gallery.
Scientists: Chris Mason, Cornell Medical School; Yolanda Gil, ISI
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.Read more...
|Quality Control of Population Studies||
This workflow aims to indicate discrepancy in the data coming from different group and checks of concordance on the genotype calls against HapMap genotypes. Initially, it was a big R scripts which computed all the steps at once, sequentially. We have split the code into different steps/tasks to represent them as workflow. As a result, we manage to execute the whole workflow within 30 min on a small cluster compare to the 4 hours of the initial sequential version.Read more...
SeqWare (http://sourceforge.net/projects/seqware/) is an open source software developed at UCLA. It is used to support massively parallel sequencing technologies and provides a number of different functionality including a LIMS, computational pipelines (supported by Pegasus), and a metadata component . This software was recently used to sequence the U87MG cancer cell line
Scientists: Brian O"Connor and Jordan Mendler, UCLARead more...
Scientists: Jonathan Livny (Harvard)
This application is conducting a wide search for small untranslated RNAs (sRNAs) that regulate several processes such as secretion or virulence in bacteria. The kingdom-wide prediction and annotation of sRNA encoding genes involves a variety of individual programs that are executed in the proper order using PEGASUS.Read more...
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.Read more...
|Vegetation and Landscape Ecology||
Don Waller, a Professor of Botany and Environmental Studies at UW Madison, and his graduate student Erika Mudrak investigate spatial patterns in vegetation and tracking change in landscape ecology across spatial and temporal scales.Read more...
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.Read more...
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.Read more...
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.Read more...
|OpenSees Workflows on NEESHub||
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.Read more...
|Southern California Earthquake Center - CyberShake and Broadband||
Scientists: Thomas H. Jordan, Scott Callaghan, Philip Maechling, Kevin Milner, Robert Graves, Edward Field, David Okaya
Southern California Earthquake Center (SCEC) is a community of over 600 scientists, students, and others at over 60 institutions worldwide, headquartered at the University of Southern California. SCEC is funded by the National Science Foundation and the U.S. Geological Survey to develop a comprehensive understanding of earthquakes in Southern California and elsewhere, and to communicate useful knowledge for reducing earthquake risk.Read more...
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.Read more...
|Solar Dynamics Observatory (SDO)||
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.Read more...
Professor Paul Hanson at the Center for Limnology at UW Madison conducts research in carbon cycling, ecosystem variability, microbes, algae, and even fish.Read more...
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.Read more...
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)Read more...
|Laser Interferometer Gravitational Wave Observatory (LIGO)||
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 spaRead more...
Scientists: Juan de Pablo, UW Madison
Juan de Pablo and the Molecular Thermodynamics and Statistical Mechanics Research Group at the University of Wisconsin use the computational resources provided by the CHTC (http://chtc.cs.wisc.edu/) and Pegasus WMS to predict the motions of macroscopic objects through simulations of what their microscopic particles are doing. For more information, visit the research group's website.Read more...