1. Advancing Science with DNA Sequence GENEBOREE A Tool for Collaborative Gene Annotation DOE Joint Genome Institute Integrated Microbial Genomes Annette Greiner Anya Kartavenko Rowena Luk

2. Advancing Science with DNA Sequence A Genetics Primer

3. Advancing Science with DNA Sequence Geneboree Collaborative gene annotation Geographically distributed Open to all bioscientists

4. Advancing Science with DNA Sequence Goals Credibility Security Standards Ease of use Seamless integration

5. Advancing Science with DNA Sequence Developing Personas Interviews at JGI: –Professional annotators (3) –Scientists (1) Interviews with field scientists: –UC Berkeley (2) –LBL (3)

6. Advancing Science with DNA Sequence Personas Bill Newman, PhD, 48 –Staff Scientist at Los Alamos National Lab –Microbial bioterrorism –Naïve computer user and recognized authority in his field Martha Jane Gilbert, PhD, 30 –Postdoctoral fellow at University of Oxford, UK –Metagenomics –Intermediate computer user and fairly experienced professional Phil Dupont, 24 (Primary User) –Third year PhD student at Rutgers University –Fungi studies in evolutionary biology –Expert computer user and least experienced professional

7. Advancing Science with DNA Sequence Fourth Persona Bill Newman, PhD, 48 –Staff Scientist at Los Alamos National Lab –Microbial bioterrorism –Naïve computer user and recognized authority in his field Martha Jane Gilbert, PhD, 30 –Postdoctoral fellow at University of Oxford, UK –Metagenomics –Experienced computer user and fairly experienced professional Phil Dupont, 24 (Primary User ) –Third year PhD student at Rutgers University –Fungi studies in evolutionary biology –Expert computer user and least experienced professional Ann Taylor, 35 –Professional annotator at Sanger Institute, UK –Updates automatic annotations –Intermediate computer user and expert annotator

8. Advancing Science with DNA Sequence Scenario: Bill Compares gene sequences from Chernobyl and finds an oddball Verifies annotator’s credibility Updates annotation

9. Advancing Science with DNA Sequence Scenario: Martha Jane Searches IMG for genes involved in carbon fixation Notices that most results were automatically annotated and not reliable Makes a comment on all of the genes in her set

10. Advancing Science with DNA Sequence Scenario: Phil Decides to transfer annotation from one homolog to his gene of interest Just to be sure, he checks his assumptions against a phylogenetic tree and finds that the annotation he wanted to transfer was inaccurate Corrects annotation of the homolog and annotates his gene of interest

11. Advancing Science with DNA Sequence First Interactive Prototype Built with Dreamweaver/PHP/MySQL Dreamweaver templates control navigation, headers PHP and MySQL make pages dynamic

12. Advancing Science with DNA Sequence First Interactive Prototype Prototype uses the existing IMG site for existing IMG functions IMG (http://img.jgi.doe.gov) Gene searches Comparative tools Geneboree (http://groups.sims.berkeley.edu/annotation) Collaborative annotation Discussion about gene function Authentication

13. Advancing Science with DNA Sequence First Interactive Prototype Differences from paper prototype No drafts Replies to batch discussion Automatic previews (can be turned off in prefs) Voting buttons on gene cart page Hyperlinks in discussions Flags to indicate genes recently annotated New method of comparing and transferring annotations from other genes Additional evidence fields (Pfam and UniProt)

14. Advancing Science with DNA Sequence First Interactive Prototype

15. Advancing Science with DNA Sequence First Interactive Prototype http://groups.sims.berkeley.edu/annotation/

16. Advancing Science with DNA Sequence Lessons Learned Users are different! Manual checking vs automatic annotation Homology vs. phylogeny vs. experimental data More evidence Open question: does voting work?

17. Advancing Science with DNA Sequence Questions?