1. Attie Bioinformatics Server Redesign
Andrew Broman & Brian Yandell
October 2010
October 2010
Attie Bioinformatics Server Redesign

2. Attie Bioinformatics Server Redesign
overview
scanone tool web page for biologists
Attie islet mRNA data
minimal functionality for now
system architecture
scanone and other tools as services
authentication and authorization
access to and use of databases
interface to R and other analysis engines
collaboration with off-site scientists
October 2010
Attie Bioinformatics Server Redesign

3. Attie Bioinformatics Server Redesign
big picture
user
user services page
security
authenticate
scanone
service
authorize
October 2010
Attie Bioinformatics Server Redesign

4. Attie Bioinformatics Server Redesign
security modules
authenticate: who is this?
authorize: what can this person do/see?
off-the-shelf tools
well tested
popular
easy to implement
authenticate & authorize are service units
model-view-control architecture
October 2010
Attie Bioinformatics Server Redesign

5. Attie Bioinformatics Server Redesign
scanone service unit
Dataset: UCLA
Tissue: liver
Task: scanone
plot
summary
MongoDB
R analysis engine
October 2010
Attie Bioinformatics Server Redesign

6. Attie Bioinformatics Server Redesign
service philosophy
each service is self-contained, modular
IT team designed or provided by other locations
each service can contain other services
use URLs to find data, code, etc.
could be anywhere
allows expansion to multiple centers
REpresentational State Transfer (REST)
key design idiom
stateless client-server architecture
web services are resources identified by URLs
RESTful Web Services (2007) by Richardson and Ruby
October 2010
Attie Bioinformatics Server Redesign

7. benefits of service architecture
decoupled/modular
easier to create new tools
easier to test & modify isolated parts of the system
scalable
any isolated service can be moved to a new server
no need to alter to the rest of the system
enables remote mirrors to be transparent to user
understandable
architecture easy to grasp
isolated services easy to understand
easily to maintain/extend individual services
October 2010
Attie Bioinformatics Server Redesign

8. Attie Bioinformatics Server Redesign
MongoDB
document-oriented database system
not relational (MySQL, Oracle, …)
DB is collection of documents
each document can have user-specified parts
accommodates huge data files
quick access to desired components
no schemas required: flexible data formats
GenePattern has only two data formats
October 2010
Attie Bioinformatics Server Redesign

9. Attie Bioinformatics Server Redesign
data and metadata
metadata describes what data are
provenance/history of data creation/acquisition
type of data, size of data, other characteristics
small “flat” file template to design new data
data can be raw or processed
large data object
save time/space by passing metadata to R
access data only as needed
October 2010
Attie Bioinformatics Server Redesign

10. scanone service MVC components
view
controller
modify view
Dataset: UCLA
Tissue: liver
pass details
plot
summary
Task: scanone
return objects
pass details
MongoDB
model
R analysis engine
October 2010
Attie Bioinformatics Server Redesign

11. Attie Bioinformatics Server Redesign
project timeline
task duration completion date
scanone HTML mockup now summer
islet scanone results
database integration 1 wk 15 oct
merge annotation, values (mRNA)
expect speed, organization benefits
multiple tissues 2 wks 1 nov
tissues plus clinical
MVC service architecture 2 wks 15 nov
security integration 1 wk 1 dec
authenticate, authorize services
communication between services
multiple services 4 wks 1 jan
means, hotspots, qtlnet
multiple projects 4 wks 1 feb
UCLA, Florida, yeast
October 2010
Attie Bioinformatics Server Redesign

12. MVC service architecture plans
view (what you see)
extract from HTML mockup
modular redesign
controller (how information is passed)
extract Ruby-on-Rails from HTML mockup
add communication features (RESTful API)
model (how tasks are performed)
little modification needed
October 2010
Attie Bioinformatics Server Redesign

13. analyst pipeline integration
R analysis
engine
raw data
processed
data
get
put
MongoDB
October 2010
Attie Bioinformatics Server Redesign

14. analyst pipeline details
R engine
analysis libraries housed at github.org
CHTC cluster offloads major workload
get/put functions
automate with periodic revision
standardized metadata sheet
owner, project, tissue, etc.
dropdown menu of data service type
scanone, peaks, causal
negotiated by IT team
each data type will have MVC service architecture(s)
October 2010
Attie Bioinformatics Server Redesign

15. Attie Bioinformatics Server Redesign
future enhancements
ideas not fully formed yet
use sockets to connect objects
save on I/O: don’t pass large objects, just open them
avoid CSV, PDF, PNG unless user wants them
plot, summary, result tables from R operations
model passes socket information to tools
connect R and MongoDB database directly
controller passes socket info from model to view
display results by opening RESTful resource
October 2010
Attie Bioinformatics Server Redesign