Cassavabase workshop IITA oct2016
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NextGen Cassava workshop IITA Ibadan- October 2016
Guillaume Bauchet & Isaak Tecle, Mueller [email protected]@cornell.edu
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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 teamsGroup 2: data curators and analystGroup 3: PhD student and scientistsGroup4: Breeders and NextGen staff
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Cassava IITA1. Ismail Rabbi2. Peter Kulakow3. Elizabeth Parkes4. Prasad Peteti5. Moshood Bakare6. Afolabi Agbona 7. Esther Olaniyi8. Owoade Durodola9. Oke Esezobor 10. Kayode Olasupo11. Iluebbey Peter12. Gideon13. Thankgod14.Ikpan Andrew15. Cynthia16. Kayode 17. Olumide Alabi
Attendees Banana
1. Trogun Finsbury Yams2. Ranjana Bhattacharjee3. Staff 1 (??)
Cassava NRCRI:1. Ahamefula Nwogu2. Uba Ezenwanyi3. Simon Peter4. Favour Ewa5. Chinedozi Amaefula6. Amarachukwu Uzoechi7. Ikechukwu Nnaji8. Ugochukwu Ikeogu
To check:1- Existing account from previous trainings on test site2- Tablet/smartphone with Fieldbook application installed
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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
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QUIZHave 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 ?
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9:00 Welcome and Introduction9:30 Cassavabase recap: Overview and Manual10:00 What’s new10:30 Break10:45 Trial and Accession Search11:00 The Search Wizard and Saving to Lists11:30 Working with Lists12:00 Lunch1:30 Adding Accessions, pedigree and images (NEW)2:00 Creating Crosses (NEW)2:30 Designing and Organizing Trials (NEW)3:00 Break3:15 Uploading Trials (NEW)3:45 Phenotyping: Generating Phenotyping Files & Fieldbook4:30 Uploading Phenotypic Data5:00 Session Ends
Agenda day 1
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https://github.com/solgenomics
https://yambase.orghttps://sweetpotatobase.org
https://musabase.org
https://cassavabase.org
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Account PrivilegesAccount Type Privileges
none Browse, use tools
“user" User database, forum
“submitter" create trials, add phenotype information etc.
“Curator” All previous + data deletions
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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 labContact person: [email protected]
The mirror sites are maintained at IITA by the Cassava team.Contact person: [email protected]
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For authentication:User: sgn
Password: eggplant
A general passord will be requested
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cassavabase-test.sgn.cornell.edu
To practice creating trials
and phenotyping, you will need to sign up for a submitter
account
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Create New Trial
Fieldbook Creation
Traits List Creation
RecordPhenotypes
Import and Setup Trial in
Fieldbook App.
&
Upload Phenotypes
Historic Phenotype Uploads
PhenotypeAnalysis
Crossings & Nursery
Search/Download accessions
ListManager
FieldbookApp & tools
CrossingManager Selection
Index tool
Wizard Search tool
Select / add accessions
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Search/Download accessionsWizard
Search tool
Select / add accessions
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Wizard search
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Search accession
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Search accessions
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View Accession
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Add a specific accession
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Add Accessions
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Add Accessions
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Wizard search
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Wizard download
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Wizard download
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Wizard download
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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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Create New Trial
Fieldbook Creation
Traits List Creation
&
Search/Download accessions
ListManager
Wizard Search tool
Select / add accessions
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Lists Manager
To list manager:
Allows you to manipulate a
set of Accessions,
Traits,Trials,
Phenotypes,
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Add New List
View list content
Delete list Download list
Make list public
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Add New List
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Add New List
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Add New List
View list content
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Add New List
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Add New List
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Add New List
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Make List Public
Make public
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View Public List
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Make List Private
Make private
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Make a list of traits
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See ontology for trait definition
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View lists of accessions and traits
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Create a trial
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Create a trial
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Create a trial
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View trial
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View trial
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ExercisesListManager
List Manager an trial creation :1- Create an accession list with name “yourname_list”2- Open to verify that the list type is set correctly3- Edit the list4- Set list to public5- Make a trial with the list of accessions6- Make a multilocation -trial with the list of accessions7- Generate plant level entrie on a trial7- 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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Create New Trial
Fieldbook Creation
Traits List Creation
RecordPhenotypes
Import and Setup Trial in
Fieldbook App.
&
Upload Phenotypes
Search/Download accessions
ListManager
FieldbookApp & tools
Wizard Search tool
Select / add accessions
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Phenotyping: Manage Fieldbook app tools
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Phenotyping: Manage Fieldbook app tools
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Phenotyping: Create a trait file
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Phenotyping: Download Files
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The Android Fieldbook
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Using the Android Fieldbook: transfer files
Copy layout file to field_import
Copy trait file to trait folder
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Using the Android Fieldbook: Import layout
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Using the Android Fieldbook: Import traits
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Using the Android Fieldbook: Import traits
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Using the Android Fieldbook: Export phenotype file
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Phenotyping: Download Files
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Upload exported phenotype
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Upload exported phenotype
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Upload exported phenotype
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Upload exported phenotype
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Upload exported phenotype
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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
FieldbookApp
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Create New Trial
Fieldbook Creation
Traits List Creation
RecordPhenotypes
Import and Setup Trial in
Fieldbook App.
&
Upload Phenotypes
Historic Phenotype Uploads
Search/Download accessions
ListManager
FieldbookApp & tools
Wizard Search tool
Select / add accessions
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Historic Trial upload
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Historic Trial upload
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Historic Trial upload
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Historic Trial upload
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Historic Trial upload
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File Format Used
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Agenda day 2
9:00 Exploring Summary Statistics9:30 Analysis: single trial and selection index9:45 Nursery and crossings10.30 Break10:45 Analysis: Genomic selection with SolGS12:00 Lunch1:00 This will be hands-on session with time for exercise, bug discovery, and brainstorming2:00 ctn’d2:30 ctn’d3:00 Break3:15 ctn’d3:30 ctn’d4:00 ctn’d5:00 Session Ends
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Create New Trial
Fieldbook Creation
Traits List Creation
RecordPhenotypes
Import and Setup Trial in
Fieldbook App.
&
Upload Phenotypes
Historic Phenotype Uploads
PhenotypeAnalysis
Search/Download accessions
ListManager
FieldbookApp & tools
SelectionIndex tool
Wizard Search tool
Select / add accessions
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View uploaded phenotype
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Ranking tool
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Ranking tool
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Ranking tool
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Ranking tool
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Create New Trial
Fieldbook Creation
Traits List Creation
RecordPhenotypes
Import and Setup Trial in
Fieldbook App.
&
Upload Phenotypes
Historic Phenotype Uploads
PhenotypeAnalysis
Crossings & Nursery
Search/Download accessions
ListManager
FieldbookApp & tools
CrossingManager Selection
Index tool
Wizard Search tool
Select / add accessions
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Nursery and crossing tools
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Nursery and crossing tools
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Pedigree upload
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Pedigree download
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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/
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Homework
Exercises list enclosed in this email
Open hours in Musa room Thursday and Friday 9-10 am and 1-2 pm
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Contact us!
USER MANUAL
CONTACT SGN TEAM
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Contact us!
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Lukas Mueller
AlexOgbonna
BryanEllerbrock
NaamaMenda
IsaakTecle
NickMorales
AKNOWLEDGEMENTS
BMGF
ChiedozieEgesi
PeterKulakow
Robert Kawuki
IsmailRabbi
Prasad Peteti
Afola Agbona