1. Copyright OpenHelix. No use or reproduction without express written consent1

2. WormBase Genetics, genomics, and biology resource of C. elegans and related nematodes Materials prepared by: Cynthia Perreault-Micale, Ph.D. Jennifer Williams, Ph.D. www.openhelix.com Updated: Q3-2010 Version 2

3. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent3 http://www.wormbase.org

4. WormBase Introduction Copyright OpenHelix. No use or reproduction without express written consent4 WormBase content is updated regularly http://www.wormbase.org

5. WormBase Credits Team: http://www.wormbase.org/wiki/index.php/WormBase_Consortium http://www.wormbase.org/wiki/index.php/WormBase_Consortium National Human Genome Research Institute: http://www.genome.govhttp://www.genome.gov British Medical Research Council: http://www.mrc.ac.ukhttp://www.mrc.ac.uk Copyright OpenHelix. No use or reproduction without express written consent5 “Founded in 2000, the WormBase Consortium is led by Paul Sternberg of CalTech, Richard Durbin of the Wellcome Trust Sanger Institute, Lincoln Stein of Cold Spring Harbor and John Spieth of the Washington University Genome Sequencing Center.” WormBase is supported by a grant from the National Human Genome Research Institute at the US National Institutes of Health # P41 HG02223 and the British Medical Research Council.

6. WormBase Data Content – Community Participation Copyright OpenHelix. No use or reproduction without express written consent6 www.wormbase.org/wiki

7. WormBase Publications WormBook: http://www.wormbook.org NAR: http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D612 Copyright OpenHelix. No use or reproduction without express written consent7

8. WormBase User Guide Copyright OpenHelix. No use or reproduction without express written consent8

9. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent9 http://www.wormbase.org

10. Basic Searches Choose search category from drop-down menu Enter keyword in query box Select applicable boxes Click “Search” Copyright OpenHelix. No use or reproduction without express written consent10 Keyword Category Search http://www.wormbase.org

11. sqt-3 Sample Search for sqt-3 Sample search: Anything; sqt-3; unclick Wormbase Suggest Click on any result to see more detailed information Copyright OpenHelix. No use or reproduction without express written consent11 Select # of hits Search

12. Gene Summary Display Overview sqt-3 overview Various categories Closer look at sections next Copyright OpenHelix. No use or reproduction without express written consent related data genomic location expression function identification gene ontology genetics homology reagents literature 12

13. Gene Display: Identification Info Copyright OpenHelix. No use or reproduction without express written consent13 Approved gene name Sequenc e name Aliases WormBase Gene ID orthology Click ‘+’ to display additional sequences

14. Gene Display: Genetic Location 14 Genetic Map Position Copyright OpenHelix. No use or reproduction without express written consent Genomic Position

15. Gene Display: Expression Copyright OpenHelix. No use or reproduction without express written consent15

16. Gene Display: Function Copyright OpenHelix. No use or reproduction without express written consent16 Click ‘+’ to expand tables Top Lower

17. Gene Display: Gene Ontology & Genetics Copyright OpenHelix. No use or reproduction without express written consent17 Link to evidence code definitions

18. Gene Display: Homology Copyright OpenHelix. No use or reproduction without express written consent18 Click here for pairwise orthologies Click here for phylogenetic trees

19. Gene Display: Reagents & Bibliography Copyright OpenHelix. No use or reproduction without express written consent19

20. Basic Literature Search From Homepage http://www.wormbase.org Copyright OpenHelix. No use or reproduction without express written consent20 osm-9 Basic & Advanced options Our example: Keyword - osm-9 gene Annotated with disease (all) terms Other options as default

21. Basic Literature Search Results Copyright OpenHelix. No use or reproduction without express written consent21 Toggle open sections Options Full tutorial www.openhelix.com

22. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent22 http://www.wormbase.org

23. Specialized Searches Browse C. elegans and other genomes using the Genome search option Search for sequences in protein, genomic DNA and EST databases with Blast/Blat WormMart provides easy access to diverse categorized data Markers aids mapping experiments by finding SNPs & visible genetic markers Genetic Maps allows examination of entire chromosomes at various levels of detail Copyright OpenHelix. No use or reproduction without express written consent23 Select http://www.wormbase.org

24. Genome Browser Copyright OpenHelix. No use or reproduction without express written consent 24 Click here Suite of tools for further analysis, see http://galaxy.psu.edu/ improvements

25. Overview of Search Results Copyright OpenHelix. No use or reproduction without express written consent25 Genomic Region shown in top three sections Overview, Region and Details panels Data Tracks – annotations you can customize Display Settings & Add your own tracks Closer look at sections next Display Settings & Add your own tracks Data Tracks Detail Panel Region Panel Overview Panel

26. Basic Features of the Three Panels Copyright OpenHelix. No use or reproduction without express written consent26 Genetic markers Sequence 10X vs. Details Show, hide, share or change tracks Mouse-over or click

27. Navigation Methods Copyright OpenHelix. No use or reproduction without express written consent27 Navigate from here using Scroll/Zoom & dropdown Rubber band navigation from any rulers Click on rulers & drag to select region

28. Data Tracks Copyright OpenHelix. No use or reproduction without express written consent28 Click here Check boxes to turn tracks all on or all off Or add individual track New Track Drag this to top New track & new order Drag to re-order tracks vertically

29. Configuring your Tracks Copyright OpenHelix. No use or reproduction without express written consent29 Select Configure tracks to open Track Options

30. More Browser Options Copyright OpenHelix. No use or reproduction without express written consent30 Display Settings & Add your own tracks are at the end of the results page Display Settings & Add your own tracks

31. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent31 http://www.wormbase.org

32. Sequence Searches Copyright OpenHelix. No use or reproduction without express written consent32 Click here to Search Choose to search a protein or nucleotide database Click Here Choose database to search

33. Sequence Search Results Copyright OpenHelix. No use or reproduction without express written consent33 Click Here

34. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent34 http://www.wormbase.org

35. WormMart http://www.wormbase.org/wiki/index.php/Data_mining:WormMart Copyright OpenHelix. No use or reproduction without express written consent35 Click here for WormMart Search

36. WormMart Background Copyright OpenHelix. No use or reproduction without express written consent36 http://www.biomart.org/

37. A Basic WormMart Search Copyright OpenHelix. No use or reproduction without express written consent37 Click WormMart’s 3 Simple Steps: 1.Select data 2.Select filters & attributes 3.Select results display

38. Selecting Filters Copyright OpenHelix. No use or reproduction without express written consent38 Click on any + to expand filter category Click here

39. Selecting Search Criteria Copyright OpenHelix. No use or reproduction without express written consent39 Select Men u Scroll to Scroll bar

40. Accessing Results Copyright OpenHelix. No use or reproduction without express written consent40 Click

41. Results Page Copyright OpenHelix. No use or reproduction without express written consent41

42. Customizing Your Results - Attributes Copyright OpenHelix. No use or reproduction without express written consent42

43. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent43 http://www.wormbase.org

44. SNPs, Markers and Strains Search Copyright OpenHelix. No use or reproduction without express written consent44 SNPs, Markers and Strains

45. SNPs, Markers and Strains Search Form Copyright OpenHelix. No use or reproduction without express written consent45 Click Here

46. Graphic Search Results Copyright OpenHelix. No use or reproduction without express written consent46 fog-2

47. Tabular Search Results & Links Copyright OpenHelix. No use or reproduction without express written consent47 Listed in order of position

48. WormBase Agenda Introduction and Credits Basic Search and Gene Display Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent48 http://www.wormbase.org

49. Summary of WormBase Extensive Gene Summary Page Copyright OpenHelix. No use or reproduction without express written consent49 Many Search Options Powerful Genome Browser

50. Comprehensive Copyright OpenHelix. No use or reproduction without express written consent50 WormMart Search for a sequence Display markers, SNPs & strains carrying SNPS

51. WormBase Agenda Introduction and Credits Basic Search and Gene Display Gene Summary Page Genome Browser Sequence Searches WormMart Tool Searching SNPs, Markers, and Strains Summary Exercises Copyright OpenHelix. No use or reproduction without express written consent51 http://www.wormbase.org

52. Copyright OpenHelix. No use or reproduction without express written consent52