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Cassavabase workshop ibadan March17
This document outlines an agenda for a Cassavabase workshop to be held in Ibadan, Nigeria in March 2017. It provides details on the workshop objectives, audience, attendees, an overview of Cassavabase, and exercises for days 1 and 2. The objectives are to train attendees on using Cassavabase for data loading, visualization, analysis and breeding management through hands-on examples. The audience includes trial managers, data curators/analysts, and scientists/PhD students. Details are provided on checking accounts, tablets, and websites for training. The agenda covers searching, downloading accessions, list management, barcoding, fieldbook use, phenotype analysis including selection indices and genomic selection, and solving issues.
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Cassavabase workshop ibadan March17
- 1. Cassavabase workshop Ibadan March2017 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
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- 3. Attendees To check: 1- Existing accountfrom 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 thedifferent 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
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- 8. Account Privileges Account Type Privileges noneBrowse, 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
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- 18. Add a specificaccession
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- 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
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- 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 listDownload list Make list public
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- 41. Make a listof traits
- 42. See ontology fortrait definition
- 43. View lists ofaccessions and traits
- 44. ADD new accessionsto the database Fuzzy search
- 45. ADD new accessionsto the database Fuzzy search
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- 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
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- 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)
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- 90. Exercises -1 Create a fieldbook layout file from the trial -2 Download fieldbook layout file -3 Create a fieldbooktrait 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
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- 98. Agenda day 2 9:00Exploring 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
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- 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 iCheckmethod: 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
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