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Cassavabase workshop Ibadan March 2017
Afolabi Agbonna [email protected]@cornell.eduBryanEllerbrock [email protected] [email protected]
IsaakTecle [email protected]
Outline
#Generalobjectives:
->TrainattendeesintheuseCassavabase anditsbreedingmanagementfunctionalities(dataloading,datavisualizationandanalysis)throughrealistic,hands-onexamples.
->Interactonanindividual/groupbasiswithbreedersandscientist.
#Audience:
Group1:trialmanagersanddatacollectionteamsGroup2: datacuratorsandanalystGroup3: PhDstudentandscientists
Attendees
To check:1- Existingaccount fromprevioustrainingsontestsite2- Tablet/smartphone withFieldbook applicationinstalled
OverviewCassavabase:->Roundtriptrialmanagementcomponents(i.e.searchtools,listmanager,uploadanddownloaddatawithFieldbook)->Provideupdatesonnewcomponents.
Objectives 1
Explore the different analysis available:-> Selection index-> Genomic selection (SolGS): Create training data, build prediction models, predictbreeding values of selection candidates.-> Assess phenotype and genotype data quality used in modeling using univariate andbivariate tools and evaluate accuracy of models. Decision support tools.
Objectives 11
QUIZ
Haveyouusedcassavabase?
Howoften?
1/week?
1/month?
1/year?
Whatfor?
-Checkdata?
-Uploaddata?
-Downloaddata?
Anyspecificrequestbeforegettingstarted?
https://github.com/solgenomics
https://yambase.orghttps://sweetpotatobase.org
https://musabase.org
https://cassavabase.org
Account Privileges
AccountType Privileges
none Browse,usetools
“user" Userdatabase,forum
“submitter" createtrials,addphenotypeinformationetc.
“Curator” All previous+datadeletions
Database training websites• GROUP3:https://iita-mirror.cassavabase.org/-copyofthelivesite,weeklyupdated.-Personal data(list,trials youcreatethere)isonlytemporary available.
• GROUP1:https://cassava-test.sgn.cornell.edu/-MaintainedatBTIbytheMueller lab.-Trainingsiteforbreeding teamsandworkshops.AccesstouploadanddownloaddataisavailableforallAccounttype.
• GROUP2:https://cassava-devel.sgn.cornell.edu/-MaintainedatBTIbytheMueller lab.-Trainingsiteforbreeding teamsandworkshops.AccesstouploadanddownloaddataisavailableforallAccounttype.
Usernames:Workshopuser1to Workshopuser10
Password:Cassava99
Forauthentication:User:sgn
Password:eggplant
A general passord will be requested
cassavabase-test.sgn.cornell.edu
Topracticecreatingtrials
andphenotyping,youwillneedtosignup forasubmitteraccount
CreateNewTrial
FieldbookCreation
TraitsListCreation
RecordPhenotypes
ImportandSetup TrialinFieldbook App.
&
UploadPhenotypes
Historic PhenotypeUploads
PhenotypeAnalysis
Crossings&Nursery
Search/Downloadaccessions
ListManager
BarcodeTools&
FieldbookApp
CrossingManager
Selection IndextoolSummarystatisticsGenomicselection
WizardSearchtool
Select /add accessions
Database pipeline and tools
+Traitontologies+SNPmarkerdata
Search/DownloadaccessionsWizard
Searchtool
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
Searchaccession:1- SearchTMEB14,howmanytrialsareassociated?2- Howmanytraitsassociated?3- Whoisthestockeditor?4-WhataretheparentsofIITA-TMS-IBA30572?
Wizardsearch:1- Select “breedingprogram“onthefirstselect boxandselect “IITA”2- Select trials“14geneticgainIB” and“14geneticgainUB”. Howmanyaccessions areincommon?3- Make listofcommonaccessions inbothtrials.Listnameshouldbe“yourname_commonAccession”4- Make listofaccessions thatarefoundinbothtrials.Listnameshouldbe“yourname_Accession”
WizardSearchtool
CreateNewTrial
FieldbookCreation
TraitsListCreation
&
Search/Downloadaccessions
ListManager
WizardSearchtool
Select /add accessions
Lists Manager
Tolistmanager:
Allows youtomanipulate a
setofAccessions,Traits,Trials,
Phenotypes,
Add New List
Viewlistcontent
Delete list Downloadlist
Make listpublic
Add New List
Add New List
Add New List
Viewlistcontent
Add New List
Add New List
Add New List
Make List Public
Makepublic
View Public List
Make List Private
Makeprivate
Make a list of traits
See ontology for trait definition
View lists of accessions and traits
ADD new accessions to the database
Fuzzysearch
ADD new accessions to the database
Fuzzysearch
ADD accessions
Fuzzysearch
ADD accessions
Fuzzysearch
ADD accessions
Fuzzysearch
ADD accessions
Fuzzysearch
ADD accessions
Fuzzysearch
ADD accessions
Fuzzysearch
ADD accessions
ADD accessions
Create a trial
Create a trial
Create a trial
Create a trial
Fieldmap
View trial
View trial
ExercisesListManager
ListManagerantrialcreation:1- Createanaccession list withname“yourname_list”2- Opentoverifythatthelisttype issetcorrectly3- Editthelist4- Setlisttopublic5- Makeatrialwiththe listofaccessions6- Makeamultilocation -trialwiththe listofaccessions7- Generateplant levelentrie onatrial7- Createalistoftraitswiththewizard,Listnameshouldbe“yourname_Trait”8- Search“rootshape”termfromtheontologybrowser andadditto“yourname_Trait”list
CreateNewTrial
FieldbookCreation
TraitsListCreation
RecordPhenotypes
ImportandSetup TrialinFieldbook App.
&
UploadPhenotypes
Search/Downloadaccessions
ListManager
BarcodeTools&
FieldbookApp
WizardSearchtool
Select /add accessions
Phenotyping: Barcode tool
Barcodetool
Phenotyping: Barcode tool
Phenotyping: Barcode tool
Phenotyping: Barcode tool
Phenotyping: Barcode tool
Barcodetool
Phenotyping: Barcode tool
Barcodetool
Phenotyping: Barcode tool
Barcodetool
Barcodetool
Phenotyping: Barcode tool
Phenotyping: Barcode tool
Phenotyping: Barcode tool
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 layoutfile tofield_import
Copy traitfiletotraitfolder
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
Newfieldbook version3.3.0(Betaversion)
Phenotyping: Download Files
Upload exported phenotype
Upload exported phenotype
Upload exported phenotype
Upload exported phenotype
Upload exported phenotype
Exercises
-1Makealistofplotsoraccessions-2Uploadittothebarcodeapp-3Design2Dbarcodeincludingfieldinformation/pedigreeinduplicates-4Addyournameastextlabel-5Generatethebarcodes-6Downloadthepdf-7Adjustbarcodedimensionsaccordingly-8DownloadQRcodescannerapponyourhandhelddevice-9Scanthebarcodewithyourhandhelddevice
BarcodeTools
Exercises
-1Createafieldbook layoutfilefromthetrial-2Downloadfieldbook layoutfile-3Createafieldbook traitfilefromthelistoftraits-4Downloadthetraitfile.-5Transferlayoutandtraitfilestothetablet-6ImportlayoutandtraitfilesintoFieldbook App-7Recordsomedata-8Exportthedatafromthefieldbook andtransferbacktothecomputer-9Uploadthefieldbook phenotypestoCassavabase-10Uploadthetrialcoordinatesforthecreatedtrial
FieldbookApp
CreateNewTrial
FieldbookCreation
TraitsListCreation
RecordPhenotypes
ImportandSetup TrialinFieldbook App.
&
UploadPhenotypes
Historic PhenotypeUploads
Search/Downloadaccessions
ListManager
BarcodeTools&
FieldbookApp
WizardSearchtool
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 ExploringSummaryStatistics9:30 Analysis:single trialandselection index9:45 Nurseryandcrossings10.30 Break10:45Analysis:Genomicselection withSolGS12:00 Lunch1:00 Thiswillbehands-onsessionwithtimeforexercise, bugdiscovery,andbrainstorming2:00 ctn’d2:30 ctn’d3:00 Break3:15 ctn’d3:30 ctn’d4:00 ctn’d5:00 SessionEnds
CreateNewTrial
FieldbookCreation
TraitsListCreation
RecordPhenotypes
ImportandSetup TrialinFieldbook App.
&
UploadPhenotypes
Historic PhenotypeUploads
PhenotypeAnalysis
Search/Downloadaccessions
ListManager
BarcodeTools&
FieldbookApp
SelectionIndextool
WizardSearchtool
Select /add accessions
View uploaded phenotype
Selection Index tool
Selection Index tool
Selection Index tool
Selection Index tool
ExercisesSelectionIndex
SelectionIndex:1- Select 13Ayt23PdIK2- SetthefollowingtraitsandweightsaspartoftheSelection Index:
rootweightinair:2.5drymattercontentpercentage: 2.5totalcarotenoidbyiCheck method: 5cassavamosaicdisease severity3-monthevaluation:-5cassavabacterial blight incidence 3-monthevaluation: -5
3- Whatistheobtained Selection Index(SIN)formula?4- SaveyourSINformulaunder“SIN_formula_your name”5- Calculate rankings.6- Whatisthebestperformingaccession?7- Whatis itsSINvalue?8- Savethe listofthe10%bestperformingaccessions toanewlistcalled“13Ayt23PdIKSIN_10bestpc_yourname”9- Howmanyaccessions arethere?Whatarethenames?10- DownloadtheSINoutput
CreateNewTrial
FieldbookCreation
TraitsListCreation
RecordPhenotypes
ImportandSetup TrialinFieldbook App.
&
UploadPhenotypes
Historic PhenotypeUploads
PhenotypeAnalysis
Crossings&Nursery
Search/Downloadaccessions
ListManager
BarcodeTools&
FieldbookApp
CrossingManager Selection
Indextool
WizardSearchtool
Select /add accessions
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Nursery and crossing tools
Exercises
-1Createabiparental cross-2Savethecrossunder“Your_name_wk17”-3Createamulticross usingalistof5malesand5femalesofyourchoice-4Generate20progenies-5Add2017asprefix-6Savecrossesunderafolder“Your_name_multiwk17”-7gotothe“Your_name_multiwk17” folderpageyoucreated-8selectthefirstcrossinthelist-9Add10extraprogeniestothiscross-10Downloadthelistofprogeniesinalist“Your_name_plantingwk17”
CrossingsAnd
Nursery
Pedigree download
Reminder
MirrorsiteatIITA:https://iita-mirror.cassavabase.org/
MirrortestsiteatIITA:172.30.2.199
Production:https://cassavabase.org/
Test:https://cassava-test.sgn.cornell.edu/
Homework
Exercises listenclosed inthisemail
OpenhoursinMusaroomThursdayandFriday9-10amand1-2pm
Contact us!
USERMANUAL
CONTACT SGNTEAM
Contact us!
LukasMueller
AlexOgbonna
BryanEllerbrock
NaamaMenda
IsaakTecle
NickMorales
AKNOWLEDGEMENTS
BMGF
ChiedozieEgesi
PeterKulakow
RobertKawuki
IsmailRabbi
PrasadPeteti
AfolaAgbona
TitimaTantikanjana
