Mass Spec Database Paper Outline

1) Abstract

2) Introduction

    a.  Overview of what will be presented
    b.  Brief background of mass spec
    c.  Brief description of database web interfaces
        i.  How do they handle large amounts of data?
        ii. How can the data be organized and meaningful to user?
    d.  Overview of database features 

3) Requirements/Use cases

    a. Describe other databases available
    b. Describe how our database is different
    c. Describe specific user interaction scenarios
        i.   User submits, edits, or deletes an accession or mass spectrum record
        ii.  User views public records or her/his own records
        iii. User submits record for curation
        iv.  User submits unknown spectrum/spectra for identification 

4) Design

    a. Describe database schema 
        i.  Discussion of important aspects of schema
    b. Describe web interface design
    c. Include diagram of database schema 
    d. Describe how database is maintained

5) Implementation

    a.  Describe associated software
        i.  Tomcat, MySql, Subversion

6) Performance results

    a. Running time of search
    b. Accuracy of search
    c. Describe how our results are better than others

7) Conclusion

    a.  Summary   
    b.  Unresolved issues; possible improvements

8) Acknowledgements

    a.  Supported by ANL, NSF grant #…..