1. Aug. 20, 2009EDRN @ 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

2. Aug. 20, 2009EDRN @ 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

3. Aug. 20, 2009EDRN @ 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: http://www.cancer.gov/dictionary/?searchTxt=biomarkerhttp://www.cancer.gov/dictionary/?searchTxt=biomarker

4. Aug. 20, 2009EDRN @ 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.

5. Aug. 20, 2009EDRN @ 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: http://edrn.nci.nih.gov/about-edrnhttp://edrn.nci.nih.gov/about-edrn

6. Aug. 20, 2009EDRN @ 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.

7. Aug. 20, 2009EDRN @ 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: http://edrn.nci.nih.gov

8. Aug. 20, 2009EDRN @ 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.

9. Aug. 20, 2009EDRN @ 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

10. Aug. 20, 2009EDRN @ 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

11. Aug. 20, 2009EDRN @ 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

12. Aug. 20, 2009EDRN @ 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.

13. Aug. 20, 2009EDRN @ 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

14. Aug. 20, 2009EDRN @ 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

15. Aug. 20, 2009EDRN @ 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

16. Aug. 20, 2009EDRN @ JPL, SoCalBSI '0916... A dataset policy file

17. Aug. 20, 2009EDRN @ JPL, SoCalBSI '0917 Dataset meta-data configuration

18. Aug. 20, 2009EDRN @ JPL, SoCalBSI '0918 Curator tool Browser based meta-data editor.

19. Aug. 20, 2009EDRN @ JPL, SoCalBSI '0919 Curator tool Selecting datasets for metadata editing Metadata items retrieved from backend.

20. Aug. 20, 2009EDRN @ JPL, SoCalBSI '0920 Results and conclusions  Final result  Meta-data management tool integrated with the eCAS and curation functionality incorporated into the workflow.

21. Aug. 20, 2009EDRN @ 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

22. Aug. 20, 2009EDRN @ 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.

23. Aug. 20, 2009EDRN @ 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