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breeding informatics solutions at SGN

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Solgenomics conference talk 2018, Mueller lab

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breeding informatics solutions at SGN

  1. 1. Breeding Informatics Solutions at SGN (solgenomics.net) Isaak Yosief Tecle Mueller Lab Boyce Thompson Institute, Ithaca, NY
  2. 2. Overview n Database n Large scale, high dimension n Field work tools n Trial design and data collection n Analysis tools n Exploratory and inferential
  3. 3. Towards a one-stop digital ecosystem
  4. 4. Why it is necessary? n High-throughput data n Access, sharing, security n Multiple partners n Efficiency, data integrity, result reproducibility n Integrated data collection and analysis tools n Data validation n Automation of repetitive tasks n Knowledge discovery n Internal and external cross-references
  5. 5. SGN: Accessible from any device…
  6. 6. Ontology
  7. 7. § Links QTLs to annotated genomes and genetic maps
  8. 8. YourCropBase.org ‘Half-sib’ databases…
  9. 9. Register genetic material Accessions Populations Crosses and progenies Seedlot
  10. 10. Register crosses and progenies
  11. 11. Design genotyping plates
  12. 12. Register seedlot
  13. 13. View pedigree
  14. 14. Field work tools
  15. 15. Design trials
  16. 16. Barcode observation units
  17. 17. Collect data: FieldBook app • Trial layout • Traits • Phenotype data
  18. 18. Exploratory tools
  19. 19. Filter interactively
  20. 20. Compare traits across trials
  21. 21. Analysis tools
  22. 22. Check traits correlation
  23. 23. Run ANOVA
  24. 24. Calculate selection index
  25. 25. Check population structure (PCA)…
  26. 26. Create groups (clusters)
  27. 27. Genomic Selection Tool (solGS) Tecle et. al. (2014) BMC Bioinformatics 15:398
  28. 28. Create a training dataset
  29. 29. Accessing and downloading data
  30. 30. Summary Genetic material Ontologies Trial data Data repository Data exploring and analysis Phenotype & genotype collection tools User-Friendly interface
  31. 31. Sponsors and collaborators
  32. 32. n solgenomics.net/contact/form/ n Here: n Lukas n Suzy n Isaak n Demo: Cassavabase.org Thank You!

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