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The role of cloud compu.ng in big biologyDeepak Singh
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Via Reavel under a CC-BY-NC-ND license
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life science industry
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Credit: Bosco Ho
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By ~Prescott under a CC-BY-NC license
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context
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analysis methods
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technology
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technology
?
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?
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back of the room
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technology
technology
technologytechnology
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technology
technology
technologytechnology
techn
ology
technology
technology
tech
nolo
gy
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Image: Keith Allison under a CC-BY-SA license
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inherent characteristics
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data driven
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multi-dimensional
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collaborative
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distributed
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<amazon web services>
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the cloud
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has_many :definitions
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infrastructure as a service
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precursors
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virtualization
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service oriented architecure
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distributed computing
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ComputeAmazon Elastic Compute
Cloud (EC2)- Elastic Load Balancing- Auto Scaling
StorageAmazon Simple
Storage Service (S3)- AWS Import/Export
DatabaseAmazon RDS and
SimpleDB
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ComputeAmazon Elastic Compute
Cloud (EC2)- Elastic Load Balancing- Auto Scaling
StorageAmazon Simple
Storage Service (S3)- AWS Import/Export
Content DeliveryAmazon CloudFront
MessagingAmazon Simple
Queue Service (SQS)
PaymentsAmazon Flexible Payments Service
(FPS)
On-Demand Workforce
Amazon Mechanical Turk
Parallel ProcessingAmazon Elastic
MapReduce
DatabaseAmazon RDS and
SimpleDB
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ComputeAmazon Elastic Compute
Cloud (EC2)- Elastic Load Balancing- Auto Scaling
StorageAmazon Simple
Storage Service (S3)- AWS Import/Export
Content DeliveryAmazon CloudFront
MessagingAmazon Simple
Queue Service (SQS)
PaymentsAmazon Flexible Payments Service
(FPS)
On-Demand Workforce
Amazon Mechanical Turk
Parallel ProcessingAmazon Elastic
MapReduce
MonitoringAmazon CloudWatch
ManagementAWS Management Console
ToolsAWS Toolkit for Eclipse
Isolated NetworksAmazon Virtual Private
Cloud
DatabaseAmazon RDS and
SimpleDB
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ComputeAmazon Elastic Compute
Cloud (EC2)- Elastic Load Balancing- Auto Scaling
StorageAmazon Simple
Storage Service (S3)- AWS Import/Export
Your Custom Applications and Services
Content DeliveryAmazon CloudFront
MessagingAmazon Simple
Queue Service (SQS)
PaymentsAmazon Flexible Payments Service
(FPS)
On-Demand Workforce
Amazon Mechanical Turk
Parallel ProcessingAmazon Elastic
MapReduce
MonitoringAmazon CloudWatch
ManagementAWS Management Console
ToolsAWS Toolkit for Eclipse
Isolated NetworksAmazon Virtual Private
Cloud
DatabaseAmazon RDS and
SimpleDB
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scalable
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cost effectivescalable
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cost effectivescalable
Pay as y
ou go
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cost effectivescalable
reliable
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cost effectivescalable
reliablesecure
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Amazon EC2
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servers on demand
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highly scalable
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3000 CPU’s for one firm’s risk management application
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design for failure
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“Everything fails, all the time”-- Werner Vogels
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assume failure
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design backwards
assume failure
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nothing fails
design backwards
assume failure
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highly available systems
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elastic block store
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elastic IP
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SQS
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US East Region
Availability Zone A
Availability Zone B
Availability Zone C
Availability Zone D
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data storage
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one size does not fit all
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Amazon S3
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distributed object store
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durable
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available
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!"#$%&'()*+
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TT
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scalable
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fast
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simple
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structured data anyone?
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Amazon SimpleDB
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zero administration
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highly available
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schema less
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key-value store
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Amazon Relational Data Service
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single API call
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MySQL database
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automatic backup
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scale up with API call
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futu
res
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master-slave replicationfu
ture
s
data center failover
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what do people do?
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solve problems
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> 1PB of data in S3
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provide platforms & services
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http://heroku.com
Platform as a Service
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http://cyclecomputing.com
Computation as a Service
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http://cyclecomputing.comhttp://wiki.github.com/documentcloud/cloud-crowd
Computational Platforms
sudo gem install cloud-crowd
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http://cyclecomputing.comhttp://wiki.github.com/documentcloud/cloud-crowd
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Image: Matt Wood
they do science
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3.7 million classifications in just over three days~15 million in less than a month>2.6 million clicks in 100 hours
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Image via image editor under a CC-‐BY License
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Protein Docking @ Pfizer
http://bioteam.net
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http://aws.amazon.com/publicdatasets/
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</amazon web services>
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anecdote
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collaborative project
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800 GB
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Image: Wikipedia Commons
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weeks to get started
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Image: Matt Wood
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Image: Chris Dagdigian
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gigabytes
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terabytes
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petabytes
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really fast
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constant flux
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Image: Chris Dagdigian
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data management is not data storage
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masterclassBig data & Biology: The implications of
petascale scienceTuesday November 17
1:30PM - 3:00PM Room: PB253-254-257-258
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“science data platform”
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deliver data to applications
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deliver data to people
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typical informatics workflow
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Via Christolakis under a CC-BY-NC-ND license
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Via Argonne National Labs under a CC-BY-SA license
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Via Argonne National Labs under a CC-BY-SA license
killer a
pp
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Data
Apps
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Data Platform
App Platform
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Data Platform
App Platform
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Data Platform
App Platform
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data services
Data Platform
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application services
App Platform
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Scalable Data Platform
Services
APIs
Getters Filters Savers
WORK
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must accommodate change
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must scale
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highly available
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loosely coupled
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dynamic
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task-based resources
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one projectone set of resources
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no waiting
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Protein Docking @ Pfizer
http://bioteam.net
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distributed mindset
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one approach
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disk read/writesslow & expensive
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data processingfast & cheap
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distribute dataparallelize reads
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map/reduce
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distributed data processingat scale
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abstracting away hadoop
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apache hive
http://hadoop.apache.org/hive/
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apache pig
http://hadoop.apache.org/pig/
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hosted hadoop service
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hadoop easy & simple
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Input S3 bucket
Output S3 bucket
Amazon S3
Hadoop
Amazon EC2 Instances
Input dataset
outputresults
Deploy Application
Web Console, Command line tools
End
Notify
Get ResultsInput Data
Amazon Elastic MapReduce
Hadoop Hadoop
Hadoop
Hadoop
Hadoop
Elastic MapReduce
Elastic MapReduce
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developersdevelop & distribute
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scientists/analystsconsume
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CloudBurst
Catalog k-mers Collect seeds End-to-end alignment
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Mike Schatz, University of Maryland
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Scalable Data Platform
Services
APIs
Getters Filters Savers
WORK
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IN CONCLUSION
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large scale biology
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complex multidimensional data
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whole lot of data
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distributed collaborations
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new computing and data architectures
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a solution: cloud services
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distributed
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scalable
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economical
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here today
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[email protected] Twi<er:@mndoci Presenta?on ideas from @mza, James Hamilton, and @lessig
Thank you!