1. The multi-laboratory project management
The Global Project Tracking System
Lukasz Szajkowski 1, 3, Anuradha Padki 2, 3, Paola Pace 2, 3, Kristen M Taylor 1, 3, Leila A Hornick 2, 3, Greg M Werner 1, 3, Darren M Platt 1, 3
1. Lawrence Livermore National Laboratory
2. Lawrence Berkeley National Laboratory
3. DOE Joint Genome Institute (JGI)

2. Agenda
Sequencing process at the JGI
Global Project Tracking System
GPTS – technology
GPTS Data and interface
System Architecture
Data exchange

3. JGI – Joint Genome Institute
~25 12
The DOE Joint Genome Institute (JGI) is a "virtual institute" that integrates the genomic capabilities of six partner institutions: Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, Los Alamos National Laboratory, Oak Ridge National Laboratory, Stanford University, and Pacific Northwest National Laboratory. In January 1999, high-throughput sequencing began at the Production Genomics Facility (PGF) in Walnut Creek, California, which also is home to the informatics and research and development groups. 6 2 2 1
1997
2001
2002
2003
2004
2005
2006
2007
Human Genome

4. Sequencing process JGI
Users
CSP
Stanford
DNA/Library
LANL
Sequencing
ORNL
Assembly
JGI
LLNL
Annotation
Users
Distribution

5. Sequencing process JGI
Users
CSP
Stanford
Create library
Venonat
DNA/Library
LANL
Sequencing
ORNL
Assembly
JGI
LLNL
Annotation
Twiki
meetings s
Web pages ?
Users
Distribution

6. Sequencing process – black hole
Users
CSP
Stanford
Create library
Venonat
DNA/Library
LANL
Sequencing
ORNL
Assembly
JGI
LLNL
Anntotation
Twiki
meetings s
Web pages ?
Users
Distribution

7. Global Project Tracking System
CSP
Stanford
Create library
Venonat
DNA/Library
GPTS
LANL
Sequencing
ORNL
Assembly
JGI
LLNL
Annotation
Users
Distribution

8. GPTS – technology
Three tier application
Java Swing client + Java Web Start
JavaServer Faces client
SOAP + SSL between client and server
Hibernate - Relational Persistence

9. GPTS Data and interface
Attributes
Name, type
ProjectData
Value
Projects
Name, type

10. System Architecture :System :System :Component GPTS Database GPTS Kiwi
Global Project
Tracking System
Attributes
Name, type
:Component
:Interface
GPTS
Server
Hibernate
SOAP
SOAP
ProjectData
Value
SOAP Attributes
SOAP Projects
SOAP ProjectData
:Component
Projects
Name, type
SOAP
GPTS
Web
:System
Grum - Authorization

11. System Architecture :System :System GPTS Database Global Project
Tracking System
Attributes
Name, type
:Component
GPTS
Server
Hibernate
ProjectData
Value
SOAP Attributes
SOAP Projects
SOAP ProjectData
Projects
Name, type
SOAP
:System
Grum - Authorization

12. System Architecture :System :System GPTS Database Global Project
Tracking System
Attributes
Name, type
:Component
GPTS
Server
Hibernate
ProjectData
Value
SOAP Attributes
SOAP Projects
SOAP ProjectData
Projects
Name, type
SOAP
:System
Grum - Authorization

13. System Architecture

14. System Architecture :System :System GPTS Database Global Project
Tracking System
Attributes
Name, type
:Component
GPTS
Server
Hibernate
ProjectData
Value
SOAP Attributes
Java Web Start
SOAP Projects
SOAP ProjectData
Projects
Name, type
SOAP
:System
Grum - Authorization

15. GPTS UI

16. Data exchange :System :System GPTS Database Global Project
JGI
:System
:System
Venonat
GPTS
Database
Global Project
Tracking System
ORNL
Create library
pipeline
Attributes
Name, type
:Component
GPTS
Server
SOAP
Stanford
Hibernate
pipeline
ProjectData
Value
SOAP Attributes
SOAP
SOAP Projects
SOAP ProjectData
Projects
Name, type
SOAP
:System
LANL
Grum - Authorization
LLNL

17. Future releases
Filter sharing
notification
Data history
Web reports
Project status page
Flexible API calls

18. Acknowledgement Very active users GPTS Team Lynne Goodwin Anu Padki
David Bruce
Harris Shapiro
Fang Cheng
Kerrie Barry
Erika Lindquist
GPTS Team
Anu Padki
Paola Pace
Kristen Taylor
Amber Shao
Greg Werner
Darren Platt
Contact Lukasz Szajkowski