NextGen Cassava workshop IITA Ibadan- October 2016

Guillaume Bauchet & Isaak Tecle, Mueller labgjb99@cornell.eduiyt2@cornell.edu

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

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

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

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 ?

 

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

https://github.com/solgenomics

https://yambase.orghttps://sweetpotatobase.org

https://musabase.org

https://cassavabase.org

Account PrivilegesAccount Type Privileges

none Browse, use tools

“user" User database, forum

“submitter" create trials, add phenotype information etc.

“Curator” All previous + data deletions

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: contactform@solgenomics.net

The mirror sites are maintained at IITA by the Cassava team.Contact person: p.prasad@cgiar.org

For authentication:User: sgn

Password: eggplant

A general passord will be requested

cassavabase-test.sgn.cornell.edu

To practice creating trials

and phenotyping, you will need to sign up for a submitter

account

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

Search/Download accessionsWizard

Search tool

Select / add accessions

Wizard search

Search accession

Search accessions

View Accession

Add a specific accession

Add Accessions

Add Accessions

Wizard search

Wizard download

Wizard download

Wizard download

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

Create New Trial

Fieldbook Creation

Traits List Creation

&

Search/Download accessions

ListManager

Wizard Search tool

Select / add accessions

Lists Manager

To list manager:

Allows you to manipulate a

set of Accessions,

Traits,Trials,

Phenotypes,

Add New List

View list content

Delete list Download list

Make list public

Add New List

Add New List

Add New List

View list content

Add New List

Add New List

Add New List

Make List Public

Make public

View Public List

Make List Private

Make private

Make a list of traits

See ontology for trait definition

View lists of accessions and traits

Create a trial

Create a trial

Create a trial

View trial

View trial

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

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

Phenotyping: Manage Fieldbook app tools

Phenotyping: Manage Fieldbook app tools

Phenotyping: Create a trait file

Phenotyping: Download Files

The Android Fieldbook

Using the Android Fieldbook: transfer files

Copy layout file to field_import

Copy trait file to trait folder

Using the Android Fieldbook: Import layout

Using the Android Fieldbook: Import traits

Using the Android Fieldbook: Import traits

Using the Android Fieldbook: Export phenotype file

Phenotyping: Download Files

Upload exported phenotype

Upload exported phenotype

Upload exported phenotype

Upload exported phenotype

Upload exported phenotype

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

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

Historic Trial upload

Historic Trial upload

Historic Trial upload

Historic Trial upload

Historic Trial upload

File Format Used

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

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

View uploaded phenotype

Ranking tool

Ranking tool

Ranking tool

Ranking tool

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

Nursery and crossing tools

Nursery and crossing tools

Pedigree upload

Pedigree download

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/

Homework

Exercises list enclosed in this email

Open hours in Musa room Thursday and Friday 9-10 am and 1-2 pm

Contact us!

USER MANUAL

CONTACT SGN TEAM

Contact us!

Lukas Mueller

AlexOgbonna

BryanEllerbrock

NaamaMenda

IsaakTecle

NickMorales

AKNOWLEDGEMENTS

BMGF

ChiedozieEgesi

PeterKulakow

Robert Kawuki

IsmailRabbi

Prasad Peteti

Afola Agbona