LIGO pyCBC Workflow. Image Credit: Samantha Usman, Duncan Brown et al

Advanced LIGO - Laser Interferometer Gravitational Wave Observatory

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 … Read More
biodrugscreen

Structural Protein-Ligand Interactome (SPLINTER)

The Structural Protein-Ligand Interactome (SPLINTER) project predicts the interaction of thousands of small molecules with thousands of proteins. These interactions are predicted using the three-dimensional structure of the bound complex between each pair of protein and compound that is predicted by molecular docking. These docking runs consist of millions of … Read More
acme_0

Accelerated Climate Modeling Energy (ACME)

The Accelerated Climate Modeling for Energy (ACME) project is using coupled models of ocean, land, atmosphere and ice to study the complex interaction between climate change and societal energy requirements. One of the flagship workflows of this effort is the fully-coupled climate model running at high resolution. The ACME climate … Read More
refinement

Spallation Neutron Source (SNS)

The Spallation Neutron Source (SNS) is a DOE research facility at Oak Ridge National Laboratory that provides pulsed neutron beams for scientific and industrial research. SNS uses a particle accelerator to impact a mercury-filled target with short proton pulses to produce neutrons by the process of spallation. A wide variety … Read More
scec

Southern California Earthquake Center - CyberShake and Broadband

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 … Read More
astronomy

Montage

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. Montage workflows mapped by Pegasus to the … Read More
Montage Galatic-Plane

Galactic Plane

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. When taken together with images from existing all sky surveys, these new image surveys contain over 18 … Read More
ashg-brochure-v7

GT-FAR - Genome and Transcriptome Free Analysis of RNA

GT-FAR is a RNA seq pipeline that allows users to do  Alignment, Quantification, Differential Expression, and Variant Calling.  This pipeline has been modeled as a Pegasus workflow. Pegasus enables users to execute the pipeline on wide variety of execution environments ranging from local clusters, grids to computational clouds. With funding … Read More
SoyKB

Soybean Knowledge Base (SoyKB) Pipeline

  With the advances in next generation sequencing (NGS) technology and significant reduction in sequencing costs it is now possible to sequence large sets of crop germplasm and generate whole genome scale structural variations and genotypic data. In depth informatics analysis of the genotypic data can provide better understanding of … Read More
mental_disorders

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 … Read More
epigenomic

Epigenomics

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 … Read More
wflow

Plant Development

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. Edgar Spalding, a Professor of … Read More
light_curve_transit_small_0

Periodograms

The periodogram application processes time-series data collected by NASA’s Kepler mission. The Kepler satellite uses high-precision photometry to search for exoplanets transiting their host stars. In 2009 the Kepler mission began a multi-year transit survey of 170,000 stars near the constellation Cygnus. In 2010 the project released a data set … Read More
NEESHubPegasus

OpenSees Workflows on NEESHub

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. Hubs … Read More
ocean

Ocean Forecast

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 … Read More
16_Water_Temperature_l

Ecosystem Modeling

Professor Paul Hanson at the Center for Limnology at UW Madison conducts research in carbon cycling, ecosystem variability, microbes, algae, and even fish. Limnology is the study of inland water bodies. Large coupled hydrodynamic and biological models have proven to be a powerful tool to help understand the complex dynamics … Read More
dna

DNA Sequencing

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. Epigenomic Workflow (computational jobs are shown as circles, data transfer jobs … Read More
comparison_l

Computer Vision

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. Six types of natural eyes are selected to provide inspirations to meet those … Read More
combined_cnv

Combined CNV Detection

This workflow combines results from the GNOSIS CNV (CopyNumber 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. … Read More
chop_0

Children’s Hospital of Philadelphia Pediatric Genome Analysis

“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 … Read More
RSEQ_Workflow-webpage-3_0

Brain Span

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 … Read More
edm

BioChemistry

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

Association Test

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)
yu

Association Mapping and Population Genetics in Vervets

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 … Read More
proteomics

Proteomics

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 … Read More
page_qc_workflow

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 … Read More
sipht_dag

SIPHT

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. These involve the … Read More
gdcsdo_ml

Solar Dynamics Observatory (SDO)

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). … Read More