Bioconductor on the RosettaHUB community platform...Bioconductor on the RosettaHUB community...
Transcript of Bioconductor on the RosettaHUB community platform...Bioconductor on the RosettaHUB community...
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Bioconductor on the RosettaHUBcommunity platform
www.rosettahub.com
Karim ChineRosettaHUB, Inc
BioC 2016
24th June 2016
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A universal open platformfor scientific computing and collaboration
Computational ComponentsR packages, Bioconductor, Wrapped C,C++,Fortran code, Python modules, Matlab
Toolkits…
Open source or commercial
Computational ResourcesClusters, grids, private or public clouds
Free or pay-per-use
Computational GUIsHTML5 and Desktop Workbench
Built-in views /Plugins /Collaborative views
Shiny apps
Open source or commercial
Computational ScriptsR / Python / Matlab / Groovy
Computational APIsJava / SOAP / REST, Stateless and stateful
Computational StorageLocal, NFS, FTP, Amazon S3, EBS, HDFS
Generated Computational Web ServicesStateful or stateless, mapping of R objects/functions
RosettaHUB
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Infrastructures federation: RosettaHUB cloud
Public Clouds
Private Cloud
rosettahub.com
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AWS: programmable infrastructure
Command Line
Web Console
SDK
API
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RosettaHUB Command Line
RosettaHUB Web Console
RosettaHUB SDKs
RosettaHUB API
RosettaHUB: programming with data andinfrastructure
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Google Docs-like real time collaboration
rosettahub.com
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Traceable and reproducible data science
RosettaHUB
Machine Image A
R 3.1
Bioconductor 3.0
RosettaHUB Amazon Machine Images
RosettaHUB
Machine Instance 1
Bsaed on Image A
Amazon Elastic Block Stores
rosettahub.com
RosettaHUB
EBS 2
Data Set D2
RosettaHUB
Machine Image B
R 3.2
Bioconductor 3.1 RosettaHUB
Machine Image C
R 3.2
Bioconductor 3.2
RosettaHUB
EBS 2
Data Set D2
RosettaHUB
Machine Instance 2
Bsaed on Image A
Researcher
Reviewer
RosettaHUB
EBS 2
Data Set D2
RosettaHUB
EBS 1
Data Set D1
RosettaHUB
EBS 4
Data Set D4
RosettaHUB
EBS 3
Data Set D3
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A multi-language framework
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A universal data science engine
• Reactive data science micro services platform
• Based on Java/R/Python processes
• Events-driven remote objects/engines
• Fully Dockerized
• Collaborative spreadsheets
• Collaborative scientific graphics canvas
• Collaborative dashboards
• Collaborative widgets
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The platform architecture
Docker Swarm
Linux cluster
RosettaHUB Cloud Broker
Data Science Portal
Platform Message Broker
Liferay MySQL
Database
RosettaHUB MySQL Database
Ro
settaHU
B P
latform
System Administrator
Clouds Management
Console
Azure API
Job Sched
uler A
PI
OpenN
ebula API
Do
cker/Swarm
AP
I
Data Science Workbench
Views
Science Gateways
Factory
eLearning Apps
Social Apps MarketplaceReal-time
Collaboration Apps
LiferayAPI
RosettaHUB Public API
VM
VM
VM
GCE API OpenStack APIAWS API
Researcher Teacher Student
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Inside the containers and engines
Rosetta Engine
PythonWolframLanguage
Julia SQLEmbeddedderbyDB
GraphDB
EmbeddedorientDB
JDBC SQLMySql
PostgreSQLRedshift
...
Scala/
Spark
Java Platform
LanguagesGroovyJython
...JNI JNIJNI
Jupyter Server
R Studio
shiny
R
JNI
VNC Server
JSON / NoSQL cloud databaseEquiv. Firebase
Server
ParaviewWeb ServerSsh
Unified Data Bus
Java Virtual Machine
SpreadsheetEngine
Cross-language Interactive/Collaborative
Widgets
Cross-language MacrosHTTPFile
Server
Rosetta Engine SOAP API
Rosetta Engine JSON HTTP API
Rosetta Engine Real-time Events Bus
Rosetta Gateway
FTP File ServerSecurity Policy
Manager
Docker Container
Virtual Machine