Cassavabase workshop ibadan March17
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Tutorial and tool exercises using cassavabase
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Cassavabase workshop ibadan March17
- 1. Cassavabase workshop Ibadan March 2017 Afolabi Agbonna A.Afolabi@cgiar.org Guillaume Bauchet gjb99@cornell.edu Bryan Ellerbrock bje24@cornell.edu Alex Ogbonna aco46@cornell.edu Isaak Tecle iyt2@cornell.edu
- 3. Attendees To check: 1- Existing account from previous trainings on test site 2- Tablet/smartphone with Fieldbook application installed
- 4. Overview Cassavabase: -> Roundtrip trial management components (i.e. search tools, list manager, upload and download data with Field book) -> Provide updates on new components. Objectives 1 Explore the different analysis available: -> Selection index -> Genomic selection (SolGS): Create training data, build prediction models, predict breeding values of selection candidates. -> Assess phenotype and genotype data quality used in modeling using univariate and bivariate tools and evaluate accuracy of models. Decision support tools. Objectives 11
- 8. Account Privileges Account Type Privileges none Browse, use tools “user" User database, forum “submitter" create trials, add phenotype information etc. “Curator” All previous + data deletions
- 9. Database training websites • GROUP 3: https://iita-mirror.cassavabase.org/ -copy of the live site, weekly updated. -Personal data (list, trials you create there) is only temporary available. • GROUP 1: https://cassava-test.sgn.cornell.edu/ -Maintained at BTI by the Mueller lab. -Training site for breeding teams and workshops. Access to upload and download data is available for all Account type. • GROUP 2: https://cassava-devel.sgn.cornell.edu/ -Maintained at BTI by the Mueller lab. -Training site for breeding teams and workshops. Access to upload and download data is available for all Account type. Usernames: Workshopuser1 to Workshopuser10 Password: Cassava99
- 12. Create New Trial Fieldbook Creation Traits List Creation Record Phenotypes Import and Setup Trial in Fieldbook App. & Upload Phenotypes Historic Phenotype Uploads Phenotype Analysis Crossings & Nursery Search/Download accessions List Manager Barcode Tools & Fieldbook App Crossing Manager Selection Index tool Summary statistics Genomic selection Wizard Search tool Select / add accessions Databasepipeline and tools + Trait ontologies + SNP marker data
- 14. Wizard search
- 15. Search accession
- 17. View Accession
- 18. Add a specific accession
- 19. Add Accessions
- 20. Add Accessions
- 21. Wizard search
- 22. Wizard download
- 23. Wizard download
- 24. Wizard download
- 28. Exercises Search accession: 1- Search TMEB14, how many trials are associated? 2- How many traits associated? 3- Who is the stock editor? 4-What are the parents of IITA-TMS-IBA30572 ? Wizard search: 1- Select “breeding program “ on the first select box and select “IITA” 2- Select trials “14geneticgainIB” and “14geneticgainUB”. How many accessions are in common? 3- Make list of common accessions in both trials. List name should be “yourname_commonAccession” 4- Make list of accessions that are found in both trials. List name should be “yourname_Accession” Wizard Search tool
- 30. Lists Manager To list manager: Allows you to manipulate a set of Accessions, Traits, Trials, Phenotypes,
- 31. Add New List View list content Delete list Download list Make list public
- 32. Add New List
- 33. Add New List
- 35. Add New List
- 36. Add New List
- 37. Add New List
- 39. View Public List
- 41. Make a list of traits
- 42. See ontology for trait definition
- 43. View lists of accessions and traits
- 44. ADD new accessions to the database Fuzzy search
- 45. ADD new accessions to the database Fuzzy search
- 52. ADD accessions
- 53. ADD accessions
- 54. Create a trial
- 55. Create a trial
- 56. Create a trial
- 59. View trial
- 60. View trial
- 61. ExercisesList Manager List Manager an trial creation : 1- Create an accession list with name “yourname_list” 2- Open to verify that the list type is set correctly 3- Edit the list 4- Set list to public 5- Make a trial with the list of accessions 6- Make a multilocation -trial with the list of accessions 7- Generate plant level entrie on a trial 7- Create a list of traits with the wizard, List name should be “yourname_Trait” 8- Search “root shape” term from the ontology browser and add it to “yourname_Trait” list
- 75. Phenotyping:Create a trait file
- 78. Using the AndroidFieldbook: transferfiles Copy layout file to field_import Copy trait file to trait folder
- 79. Using the AndroidFieldbook: Import layout
- 80. Using the AndroidFieldbook: Import traits
- 81. Using the AndroidFieldbook: Import traits
- 82. Using the AndroidFieldbook: Exportphenotype file New fieldbook version 3.3.0 (Beta version)
- 90. Exercises -1 Create a fieldbook layout file from the trial -2 Download fieldbook layout file -3 Create a fieldbook trait file from the list of traits -4 Download the trait file. -5 Transfer layout and trait files to the tablet -6 Import layout and trait files into Fieldbook App -7 Record some data -8 Export the data from the fieldbook and transfer back to the computer -9 Upload the fieldbook phenotypes to Cassavabase -10 Upload the trial coordinates for the created trial Fieldbook App
- 97. File FormatUsed
- 98. Agenda day 2 9:00 Exploring Summary Statistics 9:30 Analysis: single trial and selection index 9:45 Nursery and crossings 10.30 Break 10:45 Analysis: Genomic selection with SolGS 12:00 Lunch 1:00 This will be hands-on session with time for exercise, bug discovery, and brainstorming 2:00 ctn’d 2:30 ctn’d 3:00 Break 3:15 ctn’d 3:30 ctn’d 4:00 ctn’d 5:00 Session Ends
- 101. Selection Index tool
- 102. Selection Index tool
- 103. Selection Index tool
- 104. Selection Index tool
- 105. ExercisesSelection Index Selection Index: 1- Select 13Ayt23PdIK 2- Set the following traits and weights as part of the Selection Index: root weight in air: 2.5 dry matter content percentage: 2.5 total carotenoid by iCheck method: 5 cassava mosaic disease severity 3-month evaluation: -5 cassava bacterial blight incidence 3-month evaluation: -5 3- What is the obtained Selection Index (SIN) formula? 4- Save your SIN formula under “SIN_formula_your name” 5- Calculate rankings. 6- What is the best performing accession? 7- What is its SIN value? 8- Save the list of the 10 % best performing accessions to a new list called “13Ayt23PdIK SIN_10bestpc_yourname” 9- How many accessions are there ? What are the names? 10- Download the SIN output
- 131. Pedigreedownload
- 135. Contact us!