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1 introduction to cassavabase

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Presentation of cassavabase, its goal and current main features for cassava breeding and genomics

Publié dans : Sciences
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1 introduction to cassavabase

  1. 1. -> Cassavabase and other RTB databases -> What is new? -> Account request and login CASSAVABASE
  2. 2. • 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
  3. 3. https://github.com/solgenomics https://cassavabase.org https://yambase.org https://sweetpotatobase.org https://musabase.org
  4. 4. The Central data store for NEXTGEN CASSAVA : Genomic selection in African cassava breeding programs http://nextgencassava.org/ • Cassavabase is open to ALL cassava breeders!
  5. 5. Why Databases? • Data Archiving • Data Accessibility • Data Integration • Data sharing • Better data analysis
  6. 6. What do you need to use Cassavabase?
  7. 7. https://cassavabase.org/
  8. 8. https://yambase.org/
  9. 9. https://sweetpotatobase.org/
  10. 10. https://musabase.org/
  11. 11. New responsive design
  12. 12. Caroussel
  13. 13. New search bar Navigation bar always visible on top Expandable search box
  14. 14. Data content +360 registered users • ~80,000 accessions • ~300,000 trial plots • ~8,000,000 phenotypic observations • ~2 billion genotypic datapoints
  15. 15. CASSAVABASE users
  16. 16. Accounts Account Type Privileges none Browse, use tools “user" User database, forum “submitter" create trials, add phenotype information etc.
  17. 17. Create Account
  18. 18. Sign up link Create Account
  19. 19. Email Notification!