This document outlines the steps and procedures for demonstrating the Musabase phenotyping workflow, including: 1) Creating trials, accessions, crosses, and lists in Musabase 2) Designing fieldbook layouts and trait lists for phenotyping 3) Using the Android Fieldbook app to record phenotypes in the field 4) Uploading the exported phenotype data into Musabase

1. Musabase
Phenotyping Workflow Demo
MUSABASE
IITA Arusha - IITA Sendusu- NARO Kawanda September 2016
Guillaume Bauchet, Mueller lab
gjb99@cornell.edu

2. MUSABASE
Day 19:00 Welcome and Introductions
9:30 Intro: Musabase Overview and Manual
10:00 Intro: Setting up Accounts and Logins
10:30 Break
10:45 Basics: Trial and Accession Search
11:00 Basics: The Search Wizard and Saving to Lists
11:30 Basics: Working with Lists
12:00 Lunch
1:30 Basics: Adding Accessions
2:00 Basics: Adding Pedigrees
2:30 Basics: Adding Images
3:00 Break
3:15 Design Tools: Creating Crosses
3:45 Design Tools: Designing and Organizing Trials
4:30 Design Tools: Uploading Trials
5:00 Session Ends

3. New Trial
Design
Fieldbook
Creation
Traits List
Creation
Record
Phenotypes
Import and
Setup Trial in
Fieldbook App.
&
Upload
Phenotypes
Historic Phenotype
Uploads
Phenotype
Analysis
Crossing
MUSABASE

4. For authentication:
User: sgn
Password: eggplant
musabase-test.sgn.cornell.edu
MUSABASE

5. musabase-test.sgn.cornell.edu
To practice
creating trials
and
phenotyping,
you will need
to sign up for a
submitter
account
MUSABASE

6. Add Accessions
MUSABASE

7. Add Accessions
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8. Add Accessions
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9. Add Accessions
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10. Add Accessions
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11. Create a Cross
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12. Create a Cross
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13. Create a Cross
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14. Create a Cross
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15. Add the progeny to a list
MUSABASE

16. To list
manager
Allows you to
manipulate a
set of
Accessions,
Traits,
Trials,
Phenotypes,
MUSABASE
List Manager

17. MUSABASE
View lists

18. Create a trial
MUSABASE

19. Create a trial
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20. Create a trial
MUSABASE

21. View trial
MUSABASE

22. View trial
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23. Phenotyping: Create a field book layout file
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24. Phenotyping: Create a list of traits
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25. Phenotyping: Create a list of traits
MUSABASE
Ontology is being
modified
Wizard is not
updated

26. Phenotyping: Manage Fieldbook app tools
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27. Phenotyping: Manage Fieldbook app tools
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28. Phenotyping: Create a trait file
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29. Phenotyping: Download Files
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30. The Android Fieldbook
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31. Using the Android Fieldbook: transfer files
Copy layout file to field_import
Copy trait file to trait folder
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32. Using the Android Fieldbook: Import layout
MUSABASE

33. Using the Android Fieldbook: Import traits
MUSABASE

34. Using the Android Fieldbook: Import traits
MUSABASE

35. Using the Android Fieldbook: Export phenotype file
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36. Phenotyping: Download Files
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37. Upload exported phenotype
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38. Upload exported phenotype
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39. Upload exported phenotype
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40. Upload exported phenotype
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41. View uploaded phenotype
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42. Uploading Historic Trials

43. Historic Trial upload
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44. Historic Trial upload
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45. Historic Trial upload
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46. Historic Trial upload
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47. Historic Trial upload
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48. File Format Used
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49. Lukas
Mueller
Alex
Ogbonna
Bryan
Ellerbrock
Naama
Menda
Isaak
Tecle
Nick
Morales
AKNOWLEDGEMENTS

50. MUSABASE
Contact us!
USER MANUAL
CONTACT SGN TEAM

51. MUSABASE
Contact us!