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Bioconductor on the RosettaHUBcommunity platform
www.rosettahub.com
Karim ChineRosettaHUB, Inc
BioC 2016
24th June 2016
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
Infrastructures federation: RosettaHUB cloud
Public Clouds
Private Cloud
rosettahub.com
AWS: programmable infrastructure
Command Line
Web Console
SDK
API
RosettaHUB Command Line
RosettaHUB Web Console
RosettaHUB SDKs
RosettaHUB API
RosettaHUB: programming with data andinfrastructure
Google Docs-like real time collaboration
rosettahub.com
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
A multi-language framework
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
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
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
