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)

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

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

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

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

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

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

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

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

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

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

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

System Architecture

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

GPTS UI

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

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

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 szajkowski2@llnl.gov