Download - 1 introduction to cassavabase
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-> Cassavabase and other RTB databases
-> What is new?
-> Account request and login
CASSAVABASE
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• Introduction-> Cassavabase and sister RTB databases-> What s new?-> Account request and login
• “Search” menu-> Search accessions and trials plots (+people & marker data)
-Use single or multiple fields search (wizard search)-> Login Create and use list to manage accessions, trials and traits
• "Manage” menu-> Manage breeding programs & locations
-create new breeding programs & locations-> Manage accessions
-search, accession detail page, pedigree editing, find related trial and population-> Manage crosses-create and edit populations, define parents and siblings-> Manage trials
- 1a- export from Cassavabase an existing trial file- 1b- Import to Cassavabase an existing trial file- 2- Create in Cassavabase a new trial using accession list- 3- Access and edit existing trials & informations:
- field map- field design- available accessions and plots- available phenotypic traits
- 4- Upload/Download features for Phenotypic traits assayed in the trial using Field Book-> Manage genotyping trials
-create genotyping experiment to perform and create submission spreadsheet to Cornell sequencing facility-> Manage Fieldbook app
-create field layout files for field book, uplad data from fieldbook to cassavabase-> Manage phenotypes
-upload phenotypic data in trial experiments-> Manage barcodes
-create barcodes for field phenotyping-> Manage download
-download phenotypic and genotypic bulk data (multiple trials, traits &accessions)
• ”Analyze” menu-> SolGS genomic selection tools,
-> Vizualise GBS sequence data with Jbrowse, perform BLAST, use the Cassava VIGS tool
• Contact-> Contact us! Cassavabase tutorials and websites
Tutorial overview
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https://github.com/solgenomics
https://cassavabase.org
https://yambase.org
https://sweetpotatobase.orghttps://musabase.org
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The Central data store for NEXTGEN CASSAVA :Genomic selection in African cassava breeding programs
http://nextgencassava.org/
• Cassavabase is open to ALL cassava breeders!
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Why Databases?• Data Archiving
• Data Accessibility
• Data Integration
• Data sharing
• Better data analysis
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What do you need to use Cassavabase?
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https://cassavabase.org/
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https://yambase.org/
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https://sweetpotatobase.org/
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https://musabase.org/
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New responsive design
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Caroussel
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New search bar
Navigation bar always visible on top Expandable search box
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Data content
+360 registered users
• ~80,000 accessions
• ~300,000 trial plots
• ~8,000,000 phenotypic observations• ~2 billion genotypic
datapoints
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CASSAVABASE users
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Accounts
Account Type Privileges
none Browse, use tools
“user" User database, forum
“submitter" create trials, add phenotype information etc.
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Create Account
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Sign up link
Create Account
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Email Notification!