Cassavabase workshop IITA oct2016
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The document summarizes a NextGen Cassava workshop held at IITA Ibadan in October 2016. The workshop aimed to train attendees in using Cassavabase for cassava breeding data management and analysis. Over two days, participants learned how to search and manage data, design trials, record phenotypes using Fieldbook, analyze data, and utilize genomic selection and crossing tools. Hands-on exercises helped attendees practice the various Cassavabase functions. Support was provided for using the tool and participants received homework assignments.
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Cassavabase workshop IITA oct2016
- 1. NextGen Cassava workshop IITA Ibadan- October 2016 Guillaume Bauchet & Isaak Tecle, Mueller lab gjb99@cornell.edu iyt2@cornell.edu
- 2. Outline #General objectives: -> Train attendees in the use Cassavabase and its breeding management functionalities (data loading, data visualization and analysis) through realistic, hands-on examples. -> Interact on an individual/group basis with breeders and scientist. #Audience: Group 1: trial managers and data collection teams Group 2: data curators and analyst Group 3: PhD student and scientists Group4: Breeders and NextGen staff
- 3. Cassava IITA 1. Ismail Rabbi 2. Peter Kulakow 3. Elizabeth Parkes 4. Prasad Peteti 5. Moshood Bakare 6. Afolabi Agbona 1. Esther Olaniyi 2. Owoade Durodola 3. Oke Esezobor 4. Kayode Olasupo 5. Iluebbey Peter 6. Gideon 7. Thankgod 8. Ikpan Andrew 9. Cynthia 10. Kayode 11. Olumide Alabi Attendees Banana 1. Trogun Finsbury Yams 1. Ranjana Bhattacharjee 2. Staff 1 (??) Cassava NRCRI: 1. Ahamefula Nwogu 2. Uba Ezenwanyi 3. Simon Peter 4. Favour Ewa 5. Chinedozi Amaefula 6. Amarachukwu Uzoechi 7. Ikechukwu Nnaji 8. Ugochukwu Ikeogu 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 Day 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 Day 2
- 5. QUIZ Have you used cassavabase? How often? 1/week? 1/month? 1/year? What for? -Check accession data? -Upload data? -Download data? -For fun ???? Any specific request before getting started ?
- 6. 9:00 Welcome and Introduction 9:30 Cassavabase recap: Overview and Manual 10:00 What’s new 10:30 Break 10:45 Trial and Accession Search 11:00 The Search Wizard and Saving to Lists 11:30 Working with Lists 12:00 Lunch 1:30 Adding Accessions, pedigree and images (NEW) 2:00 Creating Crosses (NEW) 2:30 Designing and Organizing Trials (NEW) 3:00 Break 3:15 Uploading Trials (NEW) 3:45 Phenotyping: Generating Phenotyping Files & Fieldbook 4:30 Uploading Phenotypic Data 5:00 Session Ends Agenda day 1
- 9. 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
- 10. Different websites adresses and uses • MIRROR LIVE site at IITA: https://iita-mirror.cassavabase.org/ -copy of the live site, weekly updated. -Personal data (list, trials you create there) is only temporary available. • MIRROR TEST site at IITA: 172.30.2.199 -copy of the test site, for training at IITA -Personal data (list, trials you create there) is temporary available. • LIVE SITE: https://cassavabase.org/ -Official data repository. -All the breeding teams data is available here. -Access is restricted according to Account type. • TEST SITE: 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. Maintained at BTI by the Mueller lab Contact person: contactform@solgenomics.net The mirror sites are maintained at IITA by the Cassava team. Contact person: p.prasad@cgiar.org
- 11. For authentication: User: sgn Password: eggplant A general passord will be requested
- 12. cassavabase-test.sgn.cornell.edu To practice creating trials and phenotyping, you will need to sign up for a submitter account
- 13. 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 Fieldbook App & tools Crossing Manager Selection Index tool Wizard Search tool Select / add accessions
- 14. Search/Download accessions Wizard Search tool Select / add accessions
- 15. Wizard search
- 16. Search accession
- 18. View Accession
- 19. Add a specific accession
- 20. Add Accessions
- 21. Add Accessions
- 22. Wizard search
- 23. Wizard download
- 24. Wizard download
- 25. Wizard download
- 29. Exercise s 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. Create New Trial Fieldbook Creation Traits List Creation & Search/Download accessions List Manager Wizard Search tool Select / add accessions
- 31. Lists Manager To list manager: Allows you to manipulate a set of Accessions, Traits, Trials, Phenotypes,
- 32. Add New List View list content Delete list Download list Make list public
- 33. Add New List
- 34. Add New List
- 35. Add New List View list content
- 36. Add New List
- 37. Add New List
- 38. Add New List
- 39. Make List Public Make public
- 40. View Public List
- 41. Make List Private Make private
- 42. Make a list of traits
- 43. See ontology for trait definition
- 44. View lists of accessions and traits
- 45. Create a trial
- 46. Create a trial
- 47. Create a trial
- 49. View trial
- 50. View trial
- 51. 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
- 52. Create New Trial Fieldbook Creation Traits List Creation Record Phenotypes Import and Setup Trial in Fieldbook App. & Upload Phenotypes Search/Download accessions List Manager Fieldbook App & tools Wizard Search tool Select / add accessions
- 53. Phenotyping: Manage Fieldbook app tools
- 54. Phenotyping: Manage Fieldbook app tools
- 55. Phenotyping: Create a trait file
- 58. Using the Android Fieldbook: transfer files Copy layout file to field_import Copy trait file to trait folder
- 59. Using the Android Fieldbook: Import layout
- 60. Using the Android Fieldbook: Import traits
- 61. Using the Android Fieldbook: Import traits
- 62. Using the Android Fieldbook: Export phenotype file
- 69. 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
- 70. Create New Trial Fieldbook Creation Traits List Creation Record Phenotypes Import and Setup Trial in Fieldbook App. & Upload Phenotypes Historic Phenotype Uploads Search/Download accessions List Manager Fieldbook App & tools Wizard Search tool Select / add accessions
- 76. File Format Used
- 77. 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
- 78. Create New Trial Fieldbook Creation Traits List Creation Record Phenotypes Import and Setup Trial in Fieldbook App. & Upload Phenotypes Historic Phenotype Uploads Phenotype Analysis Search/Download accessions List Manager Fieldbook App & tools Selection Index tool Wizard Search tool Select / add accessions
- 80. Ranking tool
- 81. Ranking tool
- 82. Ranking tool
- 83. Ranking tool
- 84. 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 Fieldbook App & tools Crossing Manager Selection Index tool Wizard Search tool Select / add accessions
- 85. Nursery and crossing tools
- 86. Nursery and crossing tools
- 87. Pedigree upload
- 89. Reminder Mirror site at IITA: https://iita-mirror.cassavabase.org/ Mirror test site at IITA: 172.30.2.199 Production: https://cassavabase.org/ Test: https://cassava-test.sgn.cornell.edu/
- 90. Homework Exercises list enclosed in this email Open hours in Musa room Thursday and Friday 9-10 am and 1-2 pm
- 91. Contact us! USER MANUAL CONTACT SGN TEAM
- 92. Contact us!