Aug. 20, JPL, SoCalBSI '091 The power of bioinformatics tools in cancer research Early Detection Research Network, JPL Mentors: Dr. Chris Mattmann, Andrew Hart Andrew Clark Southern California Bioinformatics Summer Institute, 2009

Aug. 20, JPL, SoCalBSI '092 Agenda  Introduction  Biomarkers and cancer research  Early Detection Research Network (EDRN)  The NCI & JPL  EDRN Infrastructure  Project objective  eCAS Curator additions  The eCAS  Catalog and Archive Service  Data curation  Architectural & design considerations  Software engineering  Meta-data processing  Results & conclusions  Acknowledgements

Aug. 20, JPL, SoCalBSI '093 Introduction  Biomarkers and cancer research  Constant research is underway to discover and identify reliable biomarkers of cancer in the human body.  What is a biomarker?  “ A biological molecule found in blood, other body fluids, or tissues that is a sign of a normal or abnormal process, or of a condition or disease. ”  source:

Aug. 20, JPL, SoCalBSI '094 Biomarker research  The more information that is collected and shared between research sites and medical laboratories:  The more effective diagnosis will become.  The more specialized treatments can be devised to minimize the devastating effects of cancer on its host.

Aug. 20, JPL, SoCalBSI '095 The Early Detection Research Network  The NCI is concerned with managing biomarker research data and disseminating information to the public.  Formed the EDRN in 1999  “to provide up-to-date information on biomarker research” to the scientific and medical communities and to the general public. source:

Aug. 20, JPL, SoCalBSI '096 The Jet Propulsion Laboratory  FFRDC, operated by Cal-Tech, for NASA  JPL’s technology for cataloging and managing extremely large sets of data provided the underlying infrastructure needed by the EDRN to accomplish its own mission.

Aug. 20, JPL, SoCalBSI '097 The EDRN Infrastructure  My mentors, Dr. Chris Mattmann and Andrew Hart, and their team continue ongoing development of the underlying software grid.  JPL software engineers work with bioinformatics experts to develop the public interface to the EDRN, a web-based portal available to the general public:

Aug. 20, JPL, SoCalBSI '098 Project objective  Overall:  To participate as a bioinformatics software engineer at JPL.  To contribute to the EDRN software infrastructure.  Specifically:  Improve the functionality of the eCAS Curator.

Aug. 20, JPL, SoCalBSI '099 EDRN Catalog and Archive Service  JPL software customized for cataloging and archiving biomarker data, including specimen details, specimen images and related information. A B C EDRN Staging Server EDRN Public Portal WWW Research data 2. Curation -Meta-data edits -Pub. survey & cross reference -Expert review 1. Data Ingestion 3. Product Release Pre-release data Released data xml Dataset meta-data Curator

Aug. 20, JPL, SoCalBSI '0910 eCAS data curation  Data ingested from research sites undergoes a curation phase before its publication to the public portal. A B C EDRN Staging Server EDRN Public Portal WWW Research data 2. Curation -Meta-data edits -Pub. survey & cross reference -Expert review 1. Data Ingestion 3. Product Release Pre-release data Released data xml Dataset meta-data Curator

Aug. 20, JPL, SoCalBSI '0911 eCAS Curator  The curation activities would benefit from additional software tools as part of the overall eCAS workflow. A B C EDRN Staging Server EDRN Public Portal WWW Research data 2. Curation -Meta-data edits -Pub. survey & cross reference -Expert review 1. Data Ingestion 3. Product Release Pre-release data Released data xml Dataset meta-data Curator

Aug. 20, JPL, SoCalBSI '0912 Architectural & design considerations  Software engineering:  EDRN tools are primarily web applications  Design and integrate modular components  Meta-data management:  Meta-data: information that describes the content of other information.  Meta-data management is crucial to the data curation and the operation of the EDRN system.

Aug. 20, JPL, SoCalBSI '0913 Data curation with eCAS A B C EDRN Staging Server EDRN Public Portal WWW Research data 2. Curation -Meta-data edits -Pub. survey & cross reference -Expert review 1. Data Ingestion 3. Product Release Pre-release data Released data xml Dataset meta-data Curator Internal EDRN policy files contain meta-data definitions and configuration details that describe the dataset expected from each research site. 1

Aug. 20, JPL, SoCalBSI '0914 Data curation with eCAS A B C EDRN Staging Server EDRN Public Portal WWW Research data 2. Curation -Meta-data edits -Pub. survey & cross reference -Expert review 1. Data Ingestion 3. Product Release Pre-release data Released data xml Dataset meta-data Curator Curators edit and revise dataset meta-data to make the final product records complete and accurate. 2

Aug. 20, JPL, SoCalBSI '0915 Data curation with eCAS A B C EDRN Staging Server EDRN Public Portal WWW Research data 2. Curation -Meta-data edits -Pub. survey & cross reference -Expert review 1. Data Ingestion 3. Product Release Pre-release data Released data xml Dataset meta-data Curator Accepted data made available through web portal. Meta-data definitions provide searchable fields and descriptions of dataset contents to portal users. 3

Aug. 20, JPL, SoCalBSI ' A dataset policy file

Aug. 20, JPL, SoCalBSI '0917 Dataset meta-data configuration

Aug. 20, JPL, SoCalBSI '0918 Curator tool Browser based meta-data editor.

Aug. 20, JPL, SoCalBSI '0919 Curator tool Selecting datasets for metadata editing Metadata items retrieved from backend.

Aug. 20, JPL, SoCalBSI '0920 Results and conclusions  Final result  Meta-data management tool integrated with the eCAS and curation functionality incorporated into the workflow.

Aug. 20, JPL, SoCalBSI '0921 Conclusion  The goal of software engineering in bioinformatics should be to:  support scientists’ activities  facilitate better research and collaboration  simplify/bring clarity to complex tasks

Aug. 20, JPL, SoCalBSI '0922 Conclusion The combined effectiveness of software tools and expert curation make the EDRN a more powerful scientific resource that helps drive progress in biomarker research.

Aug. 20, JPL, SoCalBSI '0923 Acknowledgements  Thanks to my mentors and supporters at JPL:  Chris Mattmann, Andrew Hart  Thanks to the SoCalBSI faculty and staff:  Dr. Momand, Drs. Johnston, Dr. Sharp, Dr. Warter-Perez, Ronnie Cheng  Thanks to the SoCalBSI funding sources:  The National Science Foundation  The National Institutes of Health  Economic and Workforce Development