SlideShare ist ein Scribd-Unternehmen logo
1 von 18
Downloaden Sie, um offline zu lesen
HPC and Precision Medicine - A New Framework for Alzheimer's and Parkinson's
Joseph Lombardo
Executive Director, UNLV’s National Supercomputing Institute
April 2018
Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of
the National Institutes of Health under grant number 5P20GM109025.
The University of Nevada, Las Vegas and the Cleveland Clinic Lou Ruvo Center for Brain Health have been awarded an $11 million federal grant
from the National Institutes of Health and National Institute of General Medical Sciences to advance the understanding of Alzheimer's and
Parkinson's diseases. In this session, we will present how UNLV's National Supercomputing Institute plays a critical role in this research by fusing
brain imaging, neuropsychological and behavioral studies along with the diagnostic exome sequencing models to increase our knowledge of
dementia-related and age-associated degenerative disorders.
Agenda
• About the NSI @ Switch
• UNLV Supercomputing Boosted Through New Collaboration with Altair
• Computing Challenges
• Spotlight on Alzheimer’s and Parkinson's Research
• Other Research Areas that Benefit from HPC
• Data Flow and Analytics in support of Neurodegenerative Diseases
• Fusing brain imaging, neuropsychological and behavioral studies along with the diagnostic
exome sequencing models
• Questions
About the NSI
Full-service supercomputing facility
Mission for excellence in education and research in
supercomputing and its applications
Provides supercomputing training and services to academic
and research institutions, government and private industry
Supports energy, the environment, medical informatics and
health care
Serves researchers at the University of Nevada Las Vegas
and other statewide, nationwide and global research
NSI @ Switch
• 2014 - UNLV moved its NSCEE
facilities to Switch facility in
Las Vegas
• Hosted on Cherry Creek
system – large Intel system for
scientific and economic R&D
• > 26,000 compute cores
• Intel Xeon E5-2697v2 12C
2.700GHz, Intel Truscale, Intel
Xeon Phi 7120P
• Dedicated Research Network
(DMZ) with 200Gb/s potential
HPC and Precision Medicine: A New Framework for Alzheimer's and Parkinson's
NSI Computing Challenges
Numerous and complex workloads
• Hundreds of projects worldwide
• Highly compute-intensive research
Massive data needs
• Users must access massive data remotely to do their work
Time-sensitive projects
• Many NSI projects have critical governmental and
environmental significance, so timely and reliable performance
is a key requirement
Powerful and reliable infrastructure is mandatory!
Spotlight: Alzheimer’s Research
The need for innovation
• Alzheimer's Disease continue to cause tremendous
family, social, and economic burdens to modern society
• Despite substantial progress, existing treatment
approaches are limited – so new therapeutic approaches
are desperately needed
The NSI project
• NSI works with researchers to compare genomes of Alzheimer's patient with normal patients
• Challenge: Researchers wanted to enhance the statistical power of previous analyses by
including more than 10,000 additional patients (and thus genomic data sets) in the study –
meaning a massive leap in computational requirements
Specific Projects:
• The Relationship between Neuropsychological Testing and MRI, PET and Blood Biomarkers in
Neurodegenerative Disease - Sarah J. Banks, Ph.D
• Establish the relationship between neuropsychological tests results to findings on resting state fMRI in the AD
continuum (mild cognitive impairment [MCI], mild to moderate AD) in comparison with cognitively normal controls
(CNC)
• Freezing of Gait (FOG) in Parkinson's Disease (PD) - Brent Bluett, DO
• Evaluate brain network functional and structural connectivity using multimodal neuroimaging in PD-FOG, in
comparison to PD and healthy participants
• The Role of GABA in Microglial Activation and Neurodegeneration in Alzheimer's Disease -
Jefferson W. Kinney, Ph.D.
• Examination of GABA and immune alterations in a mouse model of AD.
New Data
Excel & Exome
(NeuroPsych data saved as
comma-separated values -CSV
SAM & BAM)
FreeSurfer
(MRI data, which is converted by an
NSI application to CSV format)
Double Entry Lou Ruvo
(Screening & Demographic Interviews –
Double Entry is supported by OpenClinica )
NSI
(National Supercomputing Institute )CSV Data
(comma-separated values)
1. Reformat data + study meta-data
(NSI’s multiple data parsing applications automates the
conversion of data from other applications (Excel) to a format
that OpenClinica’s data import application understands )
2. OpenClinica (OC) data import application
(produces XML)
3. XML - Extensible Markup Language)
(this data gets imported into OC)
OpenClinica
OpenClinica Output
(non-exhaustive)
XML
SPSS
CSV
Note: these formats can be
exported to programs that
store data in tables, such
as Microsoft Excel
CNTN
researcher
1. CNTN Defined Archive
(XML, SPSS, CSV & Data Dictionary
files)
2. Subscriber Defined Download
(same as CNTN Defined Archive with the exception that the
remote user selects specific fields in the record that they need
… CNTN will use the selected choices to determine which data
is most valuable to the remote research community )
and/or
• FreeSurfer Software Suite: An open source software suite for processing and analyzing (human) brain MRI images.
• Statistical Package for the Social Sciences (SPSS): SPSS is a software package used for logical batched and non-batched statistical analysis.
• Operational Data Model (ODM)-XML: a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data,
along with their associated metadata, administrative data, reference data, and audit information.
• ODM clinical data extraction application: NSI’s software that produces an extract of clinical data from an ODM file produced by OpenClinica and then
writes MRI thickness data for left and right hemispheres to a new file.
• NSI application: Software created by the National Supercomputing Institute (NSI) in support of CNTN.
• Secure Sockets Layer (SSL): is a protocol for encrypting data transferred between two computers.
Data & Software Archives
(freestanding files for download – no access to the
OpenClincal environment is allowed)
Data Management and Statistics Core
Data Flow Summary
(NSI’s ODM clinical data extraction
application is applied here to
create the archive files )
3. Software Archive
Shared Archive
Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption
Firewall SSL Encryption
Remote Researcher
Firewall SSL Encryption
Excel
XML-DD SPSS-DD CSV-DD
XML-DD SPSS-DD CSV-DD
XML-DD SPSS-DD CSV-DD
. . .
. . .
. . .
XML-DD SPSS-DD CSV-DD
• FreeSurfer Software Suite: An open source software suite for processing and analyzing (human) brain MRI images.
• Statistical Package for the Social Sciences (SPSS): SPSS is a software package used for logical batched and non-batched statistical analysis.
• Operational Data Model (ODM)-XML: a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data,
along with their associated metadata, administrative data, reference data, and audit information.
• ODM clinical data extraction application: NSI’s software that produces an extract of clinical data from an ODM file produced by OpenClinica and then
writes MRI thickness data for left and right hemispheres to a new file.
• NSI application: Software created by the National Supercomputing Institute (NSI) in support of CNTN.
• Secure Sockets Layer (SSL): is a protocol for encrypting data transferred between two computers.
Data Management and Statistics Core
Data Flow Summary
New Data
Excel & Exome
(NeuroPsych data saved as comma-separated values
–CSV
SAM BAM)
FreeSurfer
(MRI data, which is converted by an NSI application to CSV format)
Double Entry Lou Ruvo
(Screening & Demographic Interviews –
Double Entry is supported by OpenClinica )
NSI
(National Supercomputing Institute )
Firewall SSL Encryption Firewall SSL Encryption
Firewall SSL Encryption
Data Management and Statistics Core
Data Flow Summary
New Data
Excel & Exome
(NeuroPsych data saved as comma-
separated values –CSV
SAM BAM
FreeSurfer
(MRI data, which is converted by an NSI application
to CSV format)
Double Entry Lou Ruvo
(Screening & Demographic Interviews –
Double Entry is supported by OpenClinica )
NSI
(National Supercomputing Institute )CSV Data
(comma-separated values)
1. Reformat data + study meta-data
(NSI’s multiple data parsing applications automates the
conversion of data from other applications (Excel) to a format
that OpenClinica’s data import application understands )
2. OpenClinica (OC) data import application
(produces XML)
3. XML - Extensible Markup Language)
(this data gets imported into OC)
OpenClinica
Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption
Data Management and Statistics Core
Data Flow Summary
New Data
Excel & Exome
(NeuroPsych data saved as comma-
separated values –CSV
SAM BAM
FreeSurfer
(MRI data, which is converted by an NSI application
to CSV format)
Double Entry Lou Ruvo
(Screening & Demographic Interviews –
Double Entry is supported by OpenClinica )
NSI
(National Supercomputing Institute )CSV Data
(comma-separated values)
1. Reformat data + study meta-data
(NSI’s multiple data parsing applications automates the
conversion of data from other applications (Excel) to a format
that OpenClinica’s data import application understands )
2. OpenClinica (OC) data import application
(produces XML)
3. XML - Extensible Markup Language)
(this data gets imported into OC)
OpenClinica
OpenClinica Output
(non-exhaustive)
XML
SPSS
CSV
Note: these formats can be exported to
programs that store data in tables, such
as Microsoft Excel
CNTN researcher
Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption
Firewall SSL Encryption
Excel
Data Management and Statistics Core
Data Flow Summary
Shared ArchiveOpenClinica
1. CNTN Defined Archive
(XML, SPSS, CSV & Data Dictionary files)
2. Subscriber Defined Download
(same as CNTN Defined Archive with the exception that the remote user selects specific
fields in the record that they need … CNTN will use the selected choices to determine which
data is most valuable to the remote research community )
and/or
Data & Software Archives
(freestanding files for download – no access to the OpenClincal environment is
allowed)
(NSI’s ODM clinical data extraction application is
applied here to create the archive files )
3. Software Archive
XML-DD SPSS-DD CSV-DD
XML-DD SPSS-DD CSV-DD
XML-DD SPSS-DD CSV-DD
. . .
. . .
. . .
XML-DD SPSS-DD CSV-DD
New Data
Excel & Exome
(NeuroPsych data saved as
comma-separated values -
CSV)
FreeSurfer
(MRI data, which is converted by an
NSI application to CSV format)
Double Entry Lou Ruvo
(Screening & Demographic Interviews –
Double Entry is supported by OpenClinica )
NSI
(National Supercomputing Institute )CSV Data
(comma-separated values)
1. Reformat data + study meta-data
(NSI’s multiple data parsing applications automates the
conversion of data from other applications (Excel) to a format
that OpenClinica’s data import application understands )
2. OpenClinica (OC) data import application
(produces XML)
3. XML - Extensible Markup Language)
(this data gets imported into OC)
OpenClinica
OpenClinica Output
(non-exhaustive)
XML
SPSS
CSV
Note: these formats can be
exported to programs that
store data in tables, such
as Microsoft Excel
CNTN
researcher
1. CNTN Defined Archive
(XML, SPSS, CSV & Data Dictionary files)
2. Subscriber Defined Download
(same as CNTN Defined Archive with the exception that the
remote user selects specific fields in the record that they need
… CNTN will use the selected choices to determine which data
is most valuable to the remote research community )
and/or
• FreeSurfer Software Suite: An open source software suite for processing and analyzing (human) brain MRI images.
• Statistical Package for the Social Sciences (SPSS): SPSS is a software package used for logical batched and non-batched statistical analysis.
• Operational Data Model (ODM)-XML: a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data,
along with their associated metadata, administrative data, reference data, and audit information.
• ODM clinical data extraction application: NSI’s software that produces an extract of clinical data from an ODM file produced by OpenClinica and then
writes MRI thickness data for left and right hemispheres to a new file.
• NSI application: Software created by the National Supercomputing Institute (NSI) in support of CNTN.
• Secure Sockets Layer (SSL): is a protocol for encrypting data transferred between two computers.
Data & Software Archives
(freestanding files for download – no access to the
OpenClincal environment is allowed)
Data Management and Statistics Core
Data Flow Summary
(NSI’s ODM clinical data extraction
application is applied here to
create the archive files )
3. Software Archive
Shared Archive
Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption
Firewall SSL Encryption
Remote Researcher
Firewall SSL Encryption
Excel
XML-DD SPSS-DD CSV-DD
XML-DD SPSS-DD CSV-DD
XML-DD SPSS-DD CSV-DD
. . .
. . .
. . .
XML-DD SPSS-DD CSV-DD
Alzheimer’s Project Results
• Reduced overall runtimes for processing workload
• Decreased processing time by more than 50% using PBS Professional in conjunction with Rocks
and an improved system with shared memory compute node
• 3 hours instead of the 8+ hours to process a genome
• Fast, easy implementation
• Powerful, flexible customization capabilities -- can be easily extended by adding site-
specific processing plugins/hooks
• Improved system manageability and extensibility:
• Lightweight solution
• Very easy to manage
• Not dependent on any specific operating system
Other NSI Research that Benefits from HPC…
Quantum Dynamics of Chemical Reactions
• HPC dramatically improves ability to understand how atoms and molecules interact and the chemical reactions
that occur in different environments
• Researchers use complex theoretical calculations to explore how molecules behave at absolute zero
temperatures and other conditions
Fracking
• Hydraulic fracturing often takes place >1 mile below groundwater supplies
• Mechanical engineers use sophisticated numerical models to more accurately predict prime locations for
extraction and assess possible contamination associated with the process
Magnetically Dominated Jets in Gamma-Ray Burst
• Gamma-ray bursts are the most luminous, and violent, explosions in the universe -- they signify the deaths,
collisions or swallowing up of stars
• Astrophysicists’ computational research advances our understanding of the physical mechanisms behind GRBs
and other high-energy astrophysical phenomena
Acknowledgements – non-exhaustive list more than 50 projects
Personalized and Precision Medicine Research:
• Martin R. Schiller, Executive Director, Nevada Institute of Personalized Medicine
• Professor School of Life Science
• martin.schiller@unlv.edu
Quantum Dynamics of Chemical Reactions:
• Balakrishnan Naduvalath, Professor of Chemistry
• naduvala@unlv.nevada.edu
Fracking:
• Darrell Pepper, Professor of Mechanical Engineering
• darrell.pepper@unlv.edu
Magnetically Dominated Jets in Gamma-Ray Burst:
• Bing Zhang Professor of Astrophysics
• zhang@physics.unlv.edu
Thank you for your attention!
Joseph Lombardo
Executive Director
UNLV’s National Supercomputing Institute
lombardo@nscee.edu
Research reported in this publication was supported by an
Institutional Development Award (IDeA) from the National Institute
of General Medical Sciences of the National Institutes of Health
under grant number 5P20GM109025.
Questions?

Weitere ähnliche Inhalte

Was ist angesagt?

IDs书友会 - 主题1 - Swinburne Next Generation Research
IDs书友会 - 主题1 - Swinburne Next Generation Research IDs书友会 - 主题1 - Swinburne Next Generation Research
IDs书友会 - 主题1 - Swinburne Next Generation Research IDs Club 澳洲互联网俱乐部
 
Opportunistic Persistent Data Storage
Opportunistic Persistent Data StorageOpportunistic Persistent Data Storage
Opportunistic Persistent Data StorageLuke Weerasooriya
 
Data repository for sensor network a data mining approach
Data repository for sensor network  a data mining approachData repository for sensor network  a data mining approach
Data repository for sensor network a data mining approachijdms
 
What is a Data Commons and Why Should You Care?
What is a Data Commons and Why Should You Care? What is a Data Commons and Why Should You Care?
What is a Data Commons and Why Should You Care? Robert Grossman
 
Fabricio Silva: Cloud Computing Technologies for Genomic Big Data Analysis
Fabricio  Silva: Cloud Computing Technologies for Genomic Big Data AnalysisFabricio  Silva: Cloud Computing Technologies for Genomic Big Data Analysis
Fabricio Silva: Cloud Computing Technologies for Genomic Big Data AnalysisFlávio Codeço Coelho
 
Machine Learning in Healthcare: What's Now & What's Next
Machine Learning in Healthcare: What's Now & What's NextMachine Learning in Healthcare: What's Now & What's Next
Machine Learning in Healthcare: What's Now & What's NextPointClear Solutions
 
Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)
Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)
Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)Laurent Lefort
 
Materials Data Facility: Streamlined and automated data sharing, discovery, ...
Materials Data Facility: Streamlined and automated data sharing,  discovery, ...Materials Data Facility: Streamlined and automated data sharing,  discovery, ...
Materials Data Facility: Streamlined and automated data sharing, discovery, ...Ian Foster
 

Was ist angesagt? (8)

IDs书友会 - 主题1 - Swinburne Next Generation Research
IDs书友会 - 主题1 - Swinburne Next Generation Research IDs书友会 - 主题1 - Swinburne Next Generation Research
IDs书友会 - 主题1 - Swinburne Next Generation Research
 
Opportunistic Persistent Data Storage
Opportunistic Persistent Data StorageOpportunistic Persistent Data Storage
Opportunistic Persistent Data Storage
 
Data repository for sensor network a data mining approach
Data repository for sensor network  a data mining approachData repository for sensor network  a data mining approach
Data repository for sensor network a data mining approach
 
What is a Data Commons and Why Should You Care?
What is a Data Commons and Why Should You Care? What is a Data Commons and Why Should You Care?
What is a Data Commons and Why Should You Care?
 
Fabricio Silva: Cloud Computing Technologies for Genomic Big Data Analysis
Fabricio  Silva: Cloud Computing Technologies for Genomic Big Data AnalysisFabricio  Silva: Cloud Computing Technologies for Genomic Big Data Analysis
Fabricio Silva: Cloud Computing Technologies for Genomic Big Data Analysis
 
Machine Learning in Healthcare: What's Now & What's Next
Machine Learning in Healthcare: What's Now & What's NextMachine Learning in Healthcare: What's Now & What's Next
Machine Learning in Healthcare: What's Now & What's Next
 
Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)
Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)
Design and generation of Linked Clinical Data Cube (Semantic Stats 2013)
 
Materials Data Facility: Streamlined and automated data sharing, discovery, ...
Materials Data Facility: Streamlined and automated data sharing,  discovery, ...Materials Data Facility: Streamlined and automated data sharing,  discovery, ...
Materials Data Facility: Streamlined and automated data sharing, discovery, ...
 

Ähnlich wie HPC and Precision Medicine: A New Framework for Alzheimer's and Parkinson's

Bionimbus Cambridge Workshop (3-28-11, v7)
Bionimbus Cambridge Workshop (3-28-11, v7)Bionimbus Cambridge Workshop (3-28-11, v7)
Bionimbus Cambridge Workshop (3-28-11, v7)Robert Grossman
 
iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...
iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...
iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...Bonnie Hurwitz
 
Continuous modeling - automating model building on high-performance e-Infrast...
Continuous modeling - automating model building on high-performance e-Infrast...Continuous modeling - automating model building on high-performance e-Infrast...
Continuous modeling - automating model building on high-performance e-Infrast...Ola Spjuth
 
Data-intensive applications on cloud computing resources: Applications in lif...
Data-intensive applications on cloud computing resources: Applications in lif...Data-intensive applications on cloud computing resources: Applications in lif...
Data-intensive applications on cloud computing resources: Applications in lif...Ola Spjuth
 
Cao report 2007-2012
Cao report 2007-2012Cao report 2007-2012
Cao report 2007-2012Elif Ceylan
 
Data-intensive bioinformatics on HPC and Cloud
Data-intensive bioinformatics on HPC and CloudData-intensive bioinformatics on HPC and Cloud
Data-intensive bioinformatics on HPC and CloudOla Spjuth
 
A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...
A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...
A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...Larry Smarr
 
Data Harmonization for a Molecularly Driven Health System
Data Harmonization for a Molecularly Driven Health SystemData Harmonization for a Molecularly Driven Health System
Data Harmonization for a Molecularly Driven Health SystemWarren Kibbe
 
Neo4j for Discovering Drugs and Biomarkers
Neo4j for Discovering Drugs and BiomarkersNeo4j for Discovering Drugs and Biomarkers
Neo4j for Discovering Drugs and BiomarkersNeo4j
 
The XNAT imaging informatics platform
The XNAT imaging informatics platformThe XNAT imaging informatics platform
The XNAT imaging informatics platformimgcommcall
 
An Overview of VIEW
An Overview of VIEWAn Overview of VIEW
An Overview of VIEWShiyong Lu
 
Utilization of hpc in cancer research 2008 ric
Utilization of hpc in cancer research 2008 ricUtilization of hpc in cancer research 2008 ric
Utilization of hpc in cancer research 2008 ricBIT002
 
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...Spark Summit
 
IEEE_BigData2014-Lee.pdf
IEEE_BigData2014-Lee.pdfIEEE_BigData2014-Lee.pdf
IEEE_BigData2014-Lee.pdfssuserff37aa
 
Computation and Knowledge
Computation and KnowledgeComputation and Knowledge
Computation and KnowledgeIan Foster
 
Patient-Like-Mine
Patient-Like-MinePatient-Like-Mine
Patient-Like-MineSimon Yates
 
NERSC, AI and the Superfacility, Debbie Bard
NERSC, AI and the Superfacility, Debbie BardNERSC, AI and the Superfacility, Debbie Bard
NERSC, AI and the Superfacility, Debbie BardPacificResearchPlatform
 
White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...
White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...
White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...EMC
 

Ähnlich wie HPC and Precision Medicine: A New Framework for Alzheimer's and Parkinson's (20)

SomeSlides
SomeSlidesSomeSlides
SomeSlides
 
Bionimbus Cambridge Workshop (3-28-11, v7)
Bionimbus Cambridge Workshop (3-28-11, v7)Bionimbus Cambridge Workshop (3-28-11, v7)
Bionimbus Cambridge Workshop (3-28-11, v7)
 
iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...
iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...
iMicrobe and iVirus: Extending the iPlant cyberinfrastructure from plants to ...
 
Continuous modeling - automating model building on high-performance e-Infrast...
Continuous modeling - automating model building on high-performance e-Infrast...Continuous modeling - automating model building on high-performance e-Infrast...
Continuous modeling - automating model building on high-performance e-Infrast...
 
Data-intensive applications on cloud computing resources: Applications in lif...
Data-intensive applications on cloud computing resources: Applications in lif...Data-intensive applications on cloud computing resources: Applications in lif...
Data-intensive applications on cloud computing resources: Applications in lif...
 
Cao report 2007-2012
Cao report 2007-2012Cao report 2007-2012
Cao report 2007-2012
 
Data-intensive bioinformatics on HPC and Cloud
Data-intensive bioinformatics on HPC and CloudData-intensive bioinformatics on HPC and Cloud
Data-intensive bioinformatics on HPC and Cloud
 
A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...
A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...
A National Big Data Cyberinfrastructure Supporting Computational Biomedical R...
 
Data Harmonization for a Molecularly Driven Health System
Data Harmonization for a Molecularly Driven Health SystemData Harmonization for a Molecularly Driven Health System
Data Harmonization for a Molecularly Driven Health System
 
Neo4j for Discovering Drugs and Biomarkers
Neo4j for Discovering Drugs and BiomarkersNeo4j for Discovering Drugs and Biomarkers
Neo4j for Discovering Drugs and Biomarkers
 
The XNAT imaging informatics platform
The XNAT imaging informatics platformThe XNAT imaging informatics platform
The XNAT imaging informatics platform
 
An Overview of VIEW
An Overview of VIEWAn Overview of VIEW
An Overview of VIEW
 
Utilization of hpc in cancer research 2008 ric
Utilization of hpc in cancer research 2008 ricUtilization of hpc in cancer research 2008 ric
Utilization of hpc in cancer research 2008 ric
 
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
Escaping Flatland: Interactive High-Dimensional Data Analysis in Drug Discove...
 
IEEE_BigData2014-Lee.pdf
IEEE_BigData2014-Lee.pdfIEEE_BigData2014-Lee.pdf
IEEE_BigData2014-Lee.pdf
 
Computation and Knowledge
Computation and KnowledgeComputation and Knowledge
Computation and Knowledge
 
Patient-Like-Mine
Patient-Like-MinePatient-Like-Mine
Patient-Like-Mine
 
NERSC, AI and the Superfacility, Debbie Bard
NERSC, AI and the Superfacility, Debbie BardNERSC, AI and the Superfacility, Debbie Bard
NERSC, AI and the Superfacility, Debbie Bard
 
Big Data
Big Data Big Data
Big Data
 
White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...
White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...
White Paper: Life Sciences at RENCI, Big Data IT to Manage, Decipher and Info...
 

Mehr von inside-BigData.com

Preparing to program Aurora at Exascale - Early experiences and future direct...
Preparing to program Aurora at Exascale - Early experiences and future direct...Preparing to program Aurora at Exascale - Early experiences and future direct...
Preparing to program Aurora at Exascale - Early experiences and future direct...inside-BigData.com
 
Transforming Private 5G Networks
Transforming Private 5G NetworksTransforming Private 5G Networks
Transforming Private 5G Networksinside-BigData.com
 
The Incorporation of Machine Learning into Scientific Simulations at Lawrence...
The Incorporation of Machine Learning into Scientific Simulations at Lawrence...The Incorporation of Machine Learning into Scientific Simulations at Lawrence...
The Incorporation of Machine Learning into Scientific Simulations at Lawrence...inside-BigData.com
 
How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...
How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...
How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...inside-BigData.com
 
Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...
Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...
Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...inside-BigData.com
 
HPC Impact: EDA Telemetry Neural Networks
HPC Impact: EDA Telemetry Neural NetworksHPC Impact: EDA Telemetry Neural Networks
HPC Impact: EDA Telemetry Neural Networksinside-BigData.com
 
Biohybrid Robotic Jellyfish for Future Applications in Ocean Monitoring
Biohybrid Robotic Jellyfish for Future Applications in Ocean MonitoringBiohybrid Robotic Jellyfish for Future Applications in Ocean Monitoring
Biohybrid Robotic Jellyfish for Future Applications in Ocean Monitoringinside-BigData.com
 
Machine Learning for Weather Forecasts
Machine Learning for Weather ForecastsMachine Learning for Weather Forecasts
Machine Learning for Weather Forecastsinside-BigData.com
 
HPC AI Advisory Council Update
HPC AI Advisory Council UpdateHPC AI Advisory Council Update
HPC AI Advisory Council Updateinside-BigData.com
 
Fugaku Supercomputer joins fight against COVID-19
Fugaku Supercomputer joins fight against COVID-19Fugaku Supercomputer joins fight against COVID-19
Fugaku Supercomputer joins fight against COVID-19inside-BigData.com
 
Energy Efficient Computing using Dynamic Tuning
Energy Efficient Computing using Dynamic TuningEnergy Efficient Computing using Dynamic Tuning
Energy Efficient Computing using Dynamic Tuninginside-BigData.com
 
HPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD
HPC at Scale Enabled by DDN A3i and NVIDIA SuperPODHPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD
HPC at Scale Enabled by DDN A3i and NVIDIA SuperPODinside-BigData.com
 
Versal Premium ACAP for Network and Cloud Acceleration
Versal Premium ACAP for Network and Cloud AccelerationVersal Premium ACAP for Network and Cloud Acceleration
Versal Premium ACAP for Network and Cloud Accelerationinside-BigData.com
 
Zettar: Moving Massive Amounts of Data across Any Distance Efficiently
Zettar: Moving Massive Amounts of Data across Any Distance EfficientlyZettar: Moving Massive Amounts of Data across Any Distance Efficiently
Zettar: Moving Massive Amounts of Data across Any Distance Efficientlyinside-BigData.com
 
Scaling TCO in a Post Moore's Era
Scaling TCO in a Post Moore's EraScaling TCO in a Post Moore's Era
Scaling TCO in a Post Moore's Erainside-BigData.com
 
CUDA-Python and RAPIDS for blazing fast scientific computing
CUDA-Python and RAPIDS for blazing fast scientific computingCUDA-Python and RAPIDS for blazing fast scientific computing
CUDA-Python and RAPIDS for blazing fast scientific computinginside-BigData.com
 
Introducing HPC with a Raspberry Pi Cluster
Introducing HPC with a Raspberry Pi ClusterIntroducing HPC with a Raspberry Pi Cluster
Introducing HPC with a Raspberry Pi Clusterinside-BigData.com
 

Mehr von inside-BigData.com (20)

Major Market Shifts in IT
Major Market Shifts in ITMajor Market Shifts in IT
Major Market Shifts in IT
 
Preparing to program Aurora at Exascale - Early experiences and future direct...
Preparing to program Aurora at Exascale - Early experiences and future direct...Preparing to program Aurora at Exascale - Early experiences and future direct...
Preparing to program Aurora at Exascale - Early experiences and future direct...
 
Transforming Private 5G Networks
Transforming Private 5G NetworksTransforming Private 5G Networks
Transforming Private 5G Networks
 
The Incorporation of Machine Learning into Scientific Simulations at Lawrence...
The Incorporation of Machine Learning into Scientific Simulations at Lawrence...The Incorporation of Machine Learning into Scientific Simulations at Lawrence...
The Incorporation of Machine Learning into Scientific Simulations at Lawrence...
 
How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...
How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...
How to Achieve High-Performance, Scalable and Distributed DNN Training on Mod...
 
Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...
Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...
Evolving Cyberinfrastructure, Democratizing Data, and Scaling AI to Catalyze ...
 
HPC Impact: EDA Telemetry Neural Networks
HPC Impact: EDA Telemetry Neural NetworksHPC Impact: EDA Telemetry Neural Networks
HPC Impact: EDA Telemetry Neural Networks
 
Biohybrid Robotic Jellyfish for Future Applications in Ocean Monitoring
Biohybrid Robotic Jellyfish for Future Applications in Ocean MonitoringBiohybrid Robotic Jellyfish for Future Applications in Ocean Monitoring
Biohybrid Robotic Jellyfish for Future Applications in Ocean Monitoring
 
Machine Learning for Weather Forecasts
Machine Learning for Weather ForecastsMachine Learning for Weather Forecasts
Machine Learning for Weather Forecasts
 
HPC AI Advisory Council Update
HPC AI Advisory Council UpdateHPC AI Advisory Council Update
HPC AI Advisory Council Update
 
Fugaku Supercomputer joins fight against COVID-19
Fugaku Supercomputer joins fight against COVID-19Fugaku Supercomputer joins fight against COVID-19
Fugaku Supercomputer joins fight against COVID-19
 
Energy Efficient Computing using Dynamic Tuning
Energy Efficient Computing using Dynamic TuningEnergy Efficient Computing using Dynamic Tuning
Energy Efficient Computing using Dynamic Tuning
 
HPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD
HPC at Scale Enabled by DDN A3i and NVIDIA SuperPODHPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD
HPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD
 
State of ARM-based HPC
State of ARM-based HPCState of ARM-based HPC
State of ARM-based HPC
 
Versal Premium ACAP for Network and Cloud Acceleration
Versal Premium ACAP for Network and Cloud AccelerationVersal Premium ACAP for Network and Cloud Acceleration
Versal Premium ACAP for Network and Cloud Acceleration
 
Zettar: Moving Massive Amounts of Data across Any Distance Efficiently
Zettar: Moving Massive Amounts of Data across Any Distance EfficientlyZettar: Moving Massive Amounts of Data across Any Distance Efficiently
Zettar: Moving Massive Amounts of Data across Any Distance Efficiently
 
Scaling TCO in a Post Moore's Era
Scaling TCO in a Post Moore's EraScaling TCO in a Post Moore's Era
Scaling TCO in a Post Moore's Era
 
CUDA-Python and RAPIDS for blazing fast scientific computing
CUDA-Python and RAPIDS for blazing fast scientific computingCUDA-Python and RAPIDS for blazing fast scientific computing
CUDA-Python and RAPIDS for blazing fast scientific computing
 
Introducing HPC with a Raspberry Pi Cluster
Introducing HPC with a Raspberry Pi ClusterIntroducing HPC with a Raspberry Pi Cluster
Introducing HPC with a Raspberry Pi Cluster
 
Overview of HPC Interconnects
Overview of HPC InterconnectsOverview of HPC Interconnects
Overview of HPC Interconnects
 

Kürzlich hochgeladen

UiPath Solutions Management Preview - Northern CA Chapter - March 22.pdf
UiPath Solutions Management Preview - Northern CA Chapter - March 22.pdfUiPath Solutions Management Preview - Northern CA Chapter - March 22.pdf
UiPath Solutions Management Preview - Northern CA Chapter - March 22.pdfDianaGray10
 
UiPath Studio Web workshop series - Day 8
UiPath Studio Web workshop series - Day 8UiPath Studio Web workshop series - Day 8
UiPath Studio Web workshop series - Day 8DianaGray10
 
Cybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptxCybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptxGDSC PJATK
 
AI Fame Rush Review – Virtual Influencer Creation In Just Minutes
AI Fame Rush Review – Virtual Influencer Creation In Just MinutesAI Fame Rush Review – Virtual Influencer Creation In Just Minutes
AI Fame Rush Review – Virtual Influencer Creation In Just MinutesMd Hossain Ali
 
Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)Commit University
 
Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024D Cloud Solutions
 
9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding Team9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding TeamAdam Moalla
 
UiPath Platform: The Backend Engine Powering Your Automation - Session 1
UiPath Platform: The Backend Engine Powering Your Automation - Session 1UiPath Platform: The Backend Engine Powering Your Automation - Session 1
UiPath Platform: The Backend Engine Powering Your Automation - Session 1DianaGray10
 
Computer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and HazardsComputer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and HazardsSeth Reyes
 
UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7DianaGray10
 
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...Aggregage
 
Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...
Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...
Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...DianaGray10
 
Bird eye's view on Camunda open source ecosystem
Bird eye's view on Camunda open source ecosystemBird eye's view on Camunda open source ecosystem
Bird eye's view on Camunda open source ecosystemAsko Soukka
 
activity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdf
activity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdf
activity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdfJamie (Taka) Wang
 
KubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCost
KubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCostKubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCost
KubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCostMatt Ray
 
Machine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdfMachine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdfAijun Zhang
 
Secure your environment with UiPath and CyberArk technologies - Session 1
Secure your environment with UiPath and CyberArk technologies - Session 1Secure your environment with UiPath and CyberArk technologies - Session 1
Secure your environment with UiPath and CyberArk technologies - Session 1DianaGray10
 
Building Your Own AI Instance (TBLC AI )
Building Your Own AI Instance (TBLC AI )Building Your Own AI Instance (TBLC AI )
Building Your Own AI Instance (TBLC AI )Brian Pichman
 
Linked Data in Production: Moving Beyond Ontologies
Linked Data in Production: Moving Beyond OntologiesLinked Data in Production: Moving Beyond Ontologies
Linked Data in Production: Moving Beyond OntologiesDavid Newbury
 
IaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdf
IaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdfIaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdf
IaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdfDaniel Santiago Silva Capera
 

Kürzlich hochgeladen (20)

UiPath Solutions Management Preview - Northern CA Chapter - March 22.pdf
UiPath Solutions Management Preview - Northern CA Chapter - March 22.pdfUiPath Solutions Management Preview - Northern CA Chapter - March 22.pdf
UiPath Solutions Management Preview - Northern CA Chapter - March 22.pdf
 
UiPath Studio Web workshop series - Day 8
UiPath Studio Web workshop series - Day 8UiPath Studio Web workshop series - Day 8
UiPath Studio Web workshop series - Day 8
 
Cybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptxCybersecurity Workshop #1.pptx
Cybersecurity Workshop #1.pptx
 
AI Fame Rush Review – Virtual Influencer Creation In Just Minutes
AI Fame Rush Review – Virtual Influencer Creation In Just MinutesAI Fame Rush Review – Virtual Influencer Creation In Just Minutes
AI Fame Rush Review – Virtual Influencer Creation In Just Minutes
 
Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)Crea il tuo assistente AI con lo Stregatto (open source python framework)
Crea il tuo assistente AI con lo Stregatto (open source python framework)
 
Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024Artificial Intelligence & SEO Trends for 2024
Artificial Intelligence & SEO Trends for 2024
 
9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding Team9 Steps For Building Winning Founding Team
9 Steps For Building Winning Founding Team
 
UiPath Platform: The Backend Engine Powering Your Automation - Session 1
UiPath Platform: The Backend Engine Powering Your Automation - Session 1UiPath Platform: The Backend Engine Powering Your Automation - Session 1
UiPath Platform: The Backend Engine Powering Your Automation - Session 1
 
Computer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and HazardsComputer 10: Lesson 10 - Online Crimes and Hazards
Computer 10: Lesson 10 - Online Crimes and Hazards
 
UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7UiPath Studio Web workshop series - Day 7
UiPath Studio Web workshop series - Day 7
 
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
The Data Metaverse: Unpacking the Roles, Use Cases, and Tech Trends in Data a...
 
Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...
Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...
Connector Corner: Extending LLM automation use cases with UiPath GenAI connec...
 
Bird eye's view on Camunda open source ecosystem
Bird eye's view on Camunda open source ecosystemBird eye's view on Camunda open source ecosystem
Bird eye's view on Camunda open source ecosystem
 
activity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdf
activity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdf
activity_diagram_combine_v4_20190827.pdfactivity_diagram_combine_v4_20190827.pdf
 
KubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCost
KubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCostKubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCost
KubeConEU24-Monitoring Kubernetes and Cloud Spend with OpenCost
 
Machine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdfMachine Learning Model Validation (Aijun Zhang 2024).pdf
Machine Learning Model Validation (Aijun Zhang 2024).pdf
 
Secure your environment with UiPath and CyberArk technologies - Session 1
Secure your environment with UiPath and CyberArk technologies - Session 1Secure your environment with UiPath and CyberArk technologies - Session 1
Secure your environment with UiPath and CyberArk technologies - Session 1
 
Building Your Own AI Instance (TBLC AI )
Building Your Own AI Instance (TBLC AI )Building Your Own AI Instance (TBLC AI )
Building Your Own AI Instance (TBLC AI )
 
Linked Data in Production: Moving Beyond Ontologies
Linked Data in Production: Moving Beyond OntologiesLinked Data in Production: Moving Beyond Ontologies
Linked Data in Production: Moving Beyond Ontologies
 
IaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdf
IaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdfIaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdf
IaC & GitOps in a Nutshell - a FridayInANuthshell Episode.pdf
 

HPC and Precision Medicine: A New Framework for Alzheimer's and Parkinson's

  • 1. HPC and Precision Medicine - A New Framework for Alzheimer's and Parkinson's Joseph Lombardo Executive Director, UNLV’s National Supercomputing Institute April 2018 Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number 5P20GM109025. The University of Nevada, Las Vegas and the Cleveland Clinic Lou Ruvo Center for Brain Health have been awarded an $11 million federal grant from the National Institutes of Health and National Institute of General Medical Sciences to advance the understanding of Alzheimer's and Parkinson's diseases. In this session, we will present how UNLV's National Supercomputing Institute plays a critical role in this research by fusing brain imaging, neuropsychological and behavioral studies along with the diagnostic exome sequencing models to increase our knowledge of dementia-related and age-associated degenerative disorders.
  • 2. Agenda • About the NSI @ Switch • UNLV Supercomputing Boosted Through New Collaboration with Altair • Computing Challenges • Spotlight on Alzheimer’s and Parkinson's Research • Other Research Areas that Benefit from HPC • Data Flow and Analytics in support of Neurodegenerative Diseases • Fusing brain imaging, neuropsychological and behavioral studies along with the diagnostic exome sequencing models • Questions
  • 3. About the NSI Full-service supercomputing facility Mission for excellence in education and research in supercomputing and its applications Provides supercomputing training and services to academic and research institutions, government and private industry Supports energy, the environment, medical informatics and health care Serves researchers at the University of Nevada Las Vegas and other statewide, nationwide and global research
  • 4. NSI @ Switch • 2014 - UNLV moved its NSCEE facilities to Switch facility in Las Vegas • Hosted on Cherry Creek system – large Intel system for scientific and economic R&D • > 26,000 compute cores • Intel Xeon E5-2697v2 12C 2.700GHz, Intel Truscale, Intel Xeon Phi 7120P • Dedicated Research Network (DMZ) with 200Gb/s potential
  • 6. NSI Computing Challenges Numerous and complex workloads • Hundreds of projects worldwide • Highly compute-intensive research Massive data needs • Users must access massive data remotely to do their work Time-sensitive projects • Many NSI projects have critical governmental and environmental significance, so timely and reliable performance is a key requirement Powerful and reliable infrastructure is mandatory!
  • 7. Spotlight: Alzheimer’s Research The need for innovation • Alzheimer's Disease continue to cause tremendous family, social, and economic burdens to modern society • Despite substantial progress, existing treatment approaches are limited – so new therapeutic approaches are desperately needed The NSI project • NSI works with researchers to compare genomes of Alzheimer's patient with normal patients • Challenge: Researchers wanted to enhance the statistical power of previous analyses by including more than 10,000 additional patients (and thus genomic data sets) in the study – meaning a massive leap in computational requirements
  • 8. Specific Projects: • The Relationship between Neuropsychological Testing and MRI, PET and Blood Biomarkers in Neurodegenerative Disease - Sarah J. Banks, Ph.D • Establish the relationship between neuropsychological tests results to findings on resting state fMRI in the AD continuum (mild cognitive impairment [MCI], mild to moderate AD) in comparison with cognitively normal controls (CNC) • Freezing of Gait (FOG) in Parkinson's Disease (PD) - Brent Bluett, DO • Evaluate brain network functional and structural connectivity using multimodal neuroimaging in PD-FOG, in comparison to PD and healthy participants • The Role of GABA in Microglial Activation and Neurodegeneration in Alzheimer's Disease - Jefferson W. Kinney, Ph.D. • Examination of GABA and immune alterations in a mouse model of AD.
  • 9. New Data Excel & Exome (NeuroPsych data saved as comma-separated values -CSV SAM & BAM) FreeSurfer (MRI data, which is converted by an NSI application to CSV format) Double Entry Lou Ruvo (Screening & Demographic Interviews – Double Entry is supported by OpenClinica ) NSI (National Supercomputing Institute )CSV Data (comma-separated values) 1. Reformat data + study meta-data (NSI’s multiple data parsing applications automates the conversion of data from other applications (Excel) to a format that OpenClinica’s data import application understands ) 2. OpenClinica (OC) data import application (produces XML) 3. XML - Extensible Markup Language) (this data gets imported into OC) OpenClinica OpenClinica Output (non-exhaustive) XML SPSS CSV Note: these formats can be exported to programs that store data in tables, such as Microsoft Excel CNTN researcher 1. CNTN Defined Archive (XML, SPSS, CSV & Data Dictionary files) 2. Subscriber Defined Download (same as CNTN Defined Archive with the exception that the remote user selects specific fields in the record that they need … CNTN will use the selected choices to determine which data is most valuable to the remote research community ) and/or • FreeSurfer Software Suite: An open source software suite for processing and analyzing (human) brain MRI images. • Statistical Package for the Social Sciences (SPSS): SPSS is a software package used for logical batched and non-batched statistical analysis. • Operational Data Model (ODM)-XML: a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information. • ODM clinical data extraction application: NSI’s software that produces an extract of clinical data from an ODM file produced by OpenClinica and then writes MRI thickness data for left and right hemispheres to a new file. • NSI application: Software created by the National Supercomputing Institute (NSI) in support of CNTN. • Secure Sockets Layer (SSL): is a protocol for encrypting data transferred between two computers. Data & Software Archives (freestanding files for download – no access to the OpenClincal environment is allowed) Data Management and Statistics Core Data Flow Summary (NSI’s ODM clinical data extraction application is applied here to create the archive files ) 3. Software Archive Shared Archive Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption Firewall SSL Encryption Remote Researcher Firewall SSL Encryption Excel XML-DD SPSS-DD CSV-DD XML-DD SPSS-DD CSV-DD XML-DD SPSS-DD CSV-DD . . . . . . . . . XML-DD SPSS-DD CSV-DD
  • 10. • FreeSurfer Software Suite: An open source software suite for processing and analyzing (human) brain MRI images. • Statistical Package for the Social Sciences (SPSS): SPSS is a software package used for logical batched and non-batched statistical analysis. • Operational Data Model (ODM)-XML: a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information. • ODM clinical data extraction application: NSI’s software that produces an extract of clinical data from an ODM file produced by OpenClinica and then writes MRI thickness data for left and right hemispheres to a new file. • NSI application: Software created by the National Supercomputing Institute (NSI) in support of CNTN. • Secure Sockets Layer (SSL): is a protocol for encrypting data transferred between two computers. Data Management and Statistics Core Data Flow Summary New Data Excel & Exome (NeuroPsych data saved as comma-separated values –CSV SAM BAM) FreeSurfer (MRI data, which is converted by an NSI application to CSV format) Double Entry Lou Ruvo (Screening & Demographic Interviews – Double Entry is supported by OpenClinica ) NSI (National Supercomputing Institute ) Firewall SSL Encryption Firewall SSL Encryption Firewall SSL Encryption
  • 11. Data Management and Statistics Core Data Flow Summary New Data Excel & Exome (NeuroPsych data saved as comma- separated values –CSV SAM BAM FreeSurfer (MRI data, which is converted by an NSI application to CSV format) Double Entry Lou Ruvo (Screening & Demographic Interviews – Double Entry is supported by OpenClinica ) NSI (National Supercomputing Institute )CSV Data (comma-separated values) 1. Reformat data + study meta-data (NSI’s multiple data parsing applications automates the conversion of data from other applications (Excel) to a format that OpenClinica’s data import application understands ) 2. OpenClinica (OC) data import application (produces XML) 3. XML - Extensible Markup Language) (this data gets imported into OC) OpenClinica Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption
  • 12. Data Management and Statistics Core Data Flow Summary New Data Excel & Exome (NeuroPsych data saved as comma- separated values –CSV SAM BAM FreeSurfer (MRI data, which is converted by an NSI application to CSV format) Double Entry Lou Ruvo (Screening & Demographic Interviews – Double Entry is supported by OpenClinica ) NSI (National Supercomputing Institute )CSV Data (comma-separated values) 1. Reformat data + study meta-data (NSI’s multiple data parsing applications automates the conversion of data from other applications (Excel) to a format that OpenClinica’s data import application understands ) 2. OpenClinica (OC) data import application (produces XML) 3. XML - Extensible Markup Language) (this data gets imported into OC) OpenClinica OpenClinica Output (non-exhaustive) XML SPSS CSV Note: these formats can be exported to programs that store data in tables, such as Microsoft Excel CNTN researcher Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption Firewall SSL Encryption Excel
  • 13. Data Management and Statistics Core Data Flow Summary Shared ArchiveOpenClinica 1. CNTN Defined Archive (XML, SPSS, CSV & Data Dictionary files) 2. Subscriber Defined Download (same as CNTN Defined Archive with the exception that the remote user selects specific fields in the record that they need … CNTN will use the selected choices to determine which data is most valuable to the remote research community ) and/or Data & Software Archives (freestanding files for download – no access to the OpenClincal environment is allowed) (NSI’s ODM clinical data extraction application is applied here to create the archive files ) 3. Software Archive XML-DD SPSS-DD CSV-DD XML-DD SPSS-DD CSV-DD XML-DD SPSS-DD CSV-DD . . . . . . . . . XML-DD SPSS-DD CSV-DD
  • 14. New Data Excel & Exome (NeuroPsych data saved as comma-separated values - CSV) FreeSurfer (MRI data, which is converted by an NSI application to CSV format) Double Entry Lou Ruvo (Screening & Demographic Interviews – Double Entry is supported by OpenClinica ) NSI (National Supercomputing Institute )CSV Data (comma-separated values) 1. Reformat data + study meta-data (NSI’s multiple data parsing applications automates the conversion of data from other applications (Excel) to a format that OpenClinica’s data import application understands ) 2. OpenClinica (OC) data import application (produces XML) 3. XML - Extensible Markup Language) (this data gets imported into OC) OpenClinica OpenClinica Output (non-exhaustive) XML SPSS CSV Note: these formats can be exported to programs that store data in tables, such as Microsoft Excel CNTN researcher 1. CNTN Defined Archive (XML, SPSS, CSV & Data Dictionary files) 2. Subscriber Defined Download (same as CNTN Defined Archive with the exception that the remote user selects specific fields in the record that they need … CNTN will use the selected choices to determine which data is most valuable to the remote research community ) and/or • FreeSurfer Software Suite: An open source software suite for processing and analyzing (human) brain MRI images. • Statistical Package for the Social Sciences (SPSS): SPSS is a software package used for logical batched and non-batched statistical analysis. • Operational Data Model (ODM)-XML: a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information. • ODM clinical data extraction application: NSI’s software that produces an extract of clinical data from an ODM file produced by OpenClinica and then writes MRI thickness data for left and right hemispheres to a new file. • NSI application: Software created by the National Supercomputing Institute (NSI) in support of CNTN. • Secure Sockets Layer (SSL): is a protocol for encrypting data transferred between two computers. Data & Software Archives (freestanding files for download – no access to the OpenClincal environment is allowed) Data Management and Statistics Core Data Flow Summary (NSI’s ODM clinical data extraction application is applied here to create the archive files ) 3. Software Archive Shared Archive Firewall SSL Encryption Firewall SSL EncryptionFirewall SSL Encryption Firewall SSL Encryption Remote Researcher Firewall SSL Encryption Excel XML-DD SPSS-DD CSV-DD XML-DD SPSS-DD CSV-DD XML-DD SPSS-DD CSV-DD . . . . . . . . . XML-DD SPSS-DD CSV-DD
  • 15. Alzheimer’s Project Results • Reduced overall runtimes for processing workload • Decreased processing time by more than 50% using PBS Professional in conjunction with Rocks and an improved system with shared memory compute node • 3 hours instead of the 8+ hours to process a genome • Fast, easy implementation • Powerful, flexible customization capabilities -- can be easily extended by adding site- specific processing plugins/hooks • Improved system manageability and extensibility: • Lightweight solution • Very easy to manage • Not dependent on any specific operating system
  • 16. Other NSI Research that Benefits from HPC… Quantum Dynamics of Chemical Reactions • HPC dramatically improves ability to understand how atoms and molecules interact and the chemical reactions that occur in different environments • Researchers use complex theoretical calculations to explore how molecules behave at absolute zero temperatures and other conditions Fracking • Hydraulic fracturing often takes place >1 mile below groundwater supplies • Mechanical engineers use sophisticated numerical models to more accurately predict prime locations for extraction and assess possible contamination associated with the process Magnetically Dominated Jets in Gamma-Ray Burst • Gamma-ray bursts are the most luminous, and violent, explosions in the universe -- they signify the deaths, collisions or swallowing up of stars • Astrophysicists’ computational research advances our understanding of the physical mechanisms behind GRBs and other high-energy astrophysical phenomena
  • 17. Acknowledgements – non-exhaustive list more than 50 projects Personalized and Precision Medicine Research: • Martin R. Schiller, Executive Director, Nevada Institute of Personalized Medicine • Professor School of Life Science • martin.schiller@unlv.edu Quantum Dynamics of Chemical Reactions: • Balakrishnan Naduvalath, Professor of Chemistry • naduvala@unlv.nevada.edu Fracking: • Darrell Pepper, Professor of Mechanical Engineering • darrell.pepper@unlv.edu Magnetically Dominated Jets in Gamma-Ray Burst: • Bing Zhang Professor of Astrophysics • zhang@physics.unlv.edu
  • 18. Thank you for your attention! Joseph Lombardo Executive Director UNLV’s National Supercomputing Institute lombardo@nscee.edu Research reported in this publication was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant number 5P20GM109025. Questions?