XSEDE '14, July 13 - 18 2014, Atlanta, GA, USA
Natasha Pavlovikj , Kevin Begcy, Sairam Behera,
Malachy Campbell, Harkamal Walia, Jitender S.Deogun
University of Nebraska-Lincoln
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Introduction
 Gene expression and transcriptome analysis are one of the main focuses of research for a great number of biologists and scientists
 The analysis of this so called “big data” is done by using a complex set of multitude of software tools
 Enhanced demand of powerful computational resources where the data can be stored and analyzed
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Assembly Pipeline
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 Assembly of raw sequence data is a complex multi-stage process composed of preprocessing, assembling, and postprocessing
 Assembly pipeline is used to simplify the entire assembly process by automating steps of the pipeline

blast2cap3
 Multiple approaches used for assembling the filtered reads produce high redundancy of the resulting transcripts
 Overlap-based assembly program CAP3 is used to merge transcripts based on the overlapping region with specified identity
 However, because most of the produced transcripts code for a protein, a protein similarity should be also considered during the merging
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blast2cap3
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 Blast2cap3 is a protein-guided assembly approach that first clusters the transcripts based on similarity to a common protein and then passes each cluster to CAP3
 Blast2cap3 is a Python script written by Vince
Buffalo from Plant Sciences Department, UCD
 The recent use of blast2cap3 on the wheat transcriptome assembly shows that blast2cap3 generates fewer artificially fused sequences and reduces the total number of transcripts by 8-9%

blast2cap3
 The assembled transcripts are aligned with protein datasets closely related to the organism for which the transcripts are generated, and afterwards, transcripts sharing a common protein hit are merged using CAP3
 The current implementation of blast2cap3 supports only serial execution
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Pegasus Workflow
Management System
 The modularity of blast2cap3 allows us to decompose the existing approach on multiple tasks, some of which can be run in parallel
 The protein-guided assembly can be structured into a scientific workflow
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Pegasus Workflow
Management System
 Pegasus WMS is a framework that automatically maps high-level scientific workflows organized as directed acyclic graph (DAG) onto wide range of execution platforms, including clusters, grids, and clouds
 Pegasus uses DAX (directed acyclic graph in
XML) files to specify an abstract workflow
 The abstract workflow contains information and description of all executable files and logical names of the input files used by the workflow
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blast2cap3 with Pegasus
WMS
 Each node represents a workflow task, while each edge represents the dependency between the tasks
 Archive of all required built libraries and tools
(Python, Biopython, CAP3)
 The step of downloading and extracting this archive is defined as a task in the workflow
 Pegasus WMS implementation of blast2cap3 reduces the running time of the current serial implementation of blast2cap3 for more than 95%
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Execution Platforms
 The resources that scientific workflows require can exceed the capabilities of the local computational resources
 Scientific workflows are usually executed on distributed platforms, such as campus clusters, grids or clouds
 Used execution platforms
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Sandhills: University of
Nebraska Campus Cluster
 Sandhills is one of the High Performance
Computing (HPC) Clusters at the University of
Nebraska – Lincoln Holland Computing Center
(HCC)
 Used by faculty and students
 Sandhills was constructed in 2011 and it has
1440 AMD cores housed in a total of 44 nodes
 Every new user account of HCC is required to be associated with a faculty or research group
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OSG: Open Science Grid
 OSG is a national consortium of geographically distributed academic institutions and laboratories that provide hundreds computing and storage resources to the OSG users
 OSG is organized into Virtual Organizations
 OSG does not own any computing or storage resources, but allows users to use the resources contributed by the other members of the OSG and VO’s
 Every new user applies for an OSG certificate
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Amazon EC2: Amazon
Elastic Compute Cloud
 Amazon Elastic Compute Cloud (Amazon EC2) is a large commercial Web-based service provided by Amazon.com
 Users have access to virtual machine (VM) instances where they deploy VM images with customized software and libraries
 Amazon EC2 is a scalable, elastic and flexible platform
 Amazon EC2 users are hourly billed for the number and the type of resources they are using
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Experiments
 Investigate the behavior of the modified Pegasus
WMS implementation of blast2cap3 when the workflow is composed of 30, 110, 210, 610,
1,010, and 2,010 tasks respectively
 Run the workflow multiple times on the different execution platforms in order to detect the different workflow performance as well as the different resource availability over time
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Experiments
 Compare the total workflow running time between different execution platforms
 Examine the number of running versus the number of idle jobs over time for each workflow
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Experimental Data
 Diploid wheat Triticum urartu dataset from NCBI
 The assembled transcripts were generated using
Velvet as a de novo assembler
 These transcripts were aligned with closely related wheat organisms (B arley , Brachypodium ,
Rice , Maize , Sorghum, Arabidopsis)
 “ transcripts.fasta
”, 404 MB big, 236,529 assembled transcripts
 “ alignments.out
”, 155 MB big, 1,717,454 protein hits
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Comparing Running Time on Sandhills,
OSG and Amazon EC2 for Workflows with
Different Number of Tasks
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Comparing the Number of Running Jobs versus the Number of Idle Jobs Over Time for Workflows with Different Task Number
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Comparing the Number of Running Jobs versus the Number of Idle Jobs Over Time for Workflows with Different Task Number
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Comparing the Number of Running Jobs versus the Number of Idle Jobs Over Time for Workflows with Different Task Number
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Comparing the Number of Running Jobs versus the Number of Idle Jobs Over Time for Workflows with Different Task Number
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Comparing the Number of Running Jobs versus the Number of Idle Jobs Over Time for Workflows with Different Task Number
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Comparing the Number of Running Jobs versus the Number of Idle Jobs Over Time for Workflows with Different Task Number
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Cost Comparison of Different Execution
Platforms
 The main and the most important difference between the commercial cloud and the academic distributed resources is the cost
 Sandhills:
 generally free resources
 OSG:
 completely free resources
 Amazon EC2:
 complex pricing model
 50 m1.large spot instance X $0.04 per hour = $122.84
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Conclusion
 Using more than 100 tasks in a workflow significantly reduces the running time for all execution platforms
 The resource allocation on Sandhills and OSG is opportunistic, and its availability changes over time
 The results are almost constant when Amazon
EC2 is used
 Workflow failures were not encountered on
Sandhills and Amazon EC2
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Conclusion
 The predictability of the Amazon EC2 resources leads to better workflow running time when the cloud is used as a platform
 For our blast2cap3 workflow, better running time and better usage of the allocated resources were achieved when Amazon EC2 is used
 Due to the Amazon EC2 cost, the academic distributed systems can be a good alternative
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Acknowledgments
 University of Nebraska Holland Computing
Center
 Open Science Grid
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