1. Progress on TripalBIMS Breeding Information Management System in Tripal Sook Jung, Taein Lee, Chun-Huai Chen, Jing Yu, Ksenija Gasic, Todd Campbell, Kate Evans, Cameron Peace, Dorrie Main Tripal Database Network & Initiatives Workshop January 10, 2016 PAG Conference 2016

2. To provide individual breeders with a secure and comprehensive online breeding management system which will allow them to: Store, manage, archive and analyze their private breeding program data Fully integrate their data with publicly available genomic, genetic and breeding data in the community database Manage data from the Field Book App, an android app for collecting phenotype data in the field Available for any Tripal-based crop/animal databases to implement Vision

3. Chado: Natural diversity module is developed for storing large scale phenotypic and genotypic data and integrating the data with germplasm, location, marker and sequence data BIMS in the existing crop/animal databases – Enhanced Data Utility New and better marker development From markers that breeders use -> marker page in CottonGen-> genome browser -> sequence and polymorphism data From traits (linked to trait ontology) -> QTL page in CottonGen -> genome browser -> sequence and polymorphism data Compare trait data between private germplasm and publically available germplasm Aids in breeding decision making and it’s free! Why BIMS in Tripal Databases

4. Private and public data Data in template is sent to GDR, loaded by GDR team Templates for stock, phenotype, genotype, dataset, trait descriptors, location, cross, propagation, etc Tools Data management tools: To search, browse and download by dataset, genotype, phenotype and parental information Data conversion tools: To convert data into format to use in other software (Pedimap) Breeding decision tools: To aid breeders in breeding decisions (choosing parents & selecting seedlings) Current Breeder’s Toolbox in GDR

5. Archive Manage Breeding Data Import Search/Download Field Book App Management Data Analysis Tools Breeding Decision Tools Components of TripalBIMS

6. Drupal7 and Postgresql DOJO Tool Kit (https://dojotoolkit.org/) interface for BIMS JSTree (https://www.jstree.com/) Visualization of the relationships between projects and sub-proejct in chado in a tree PHPExcel (https://phpexcel.codeplex.com/) to read / write MS excel file Tools used to built TripalBIMS

7. Manage Breeding You will manage who has access to your program data, controlled by permission levels

8. Manage Breeding: View Descriptors

9. Manage Breeding: Creating a New Program

10. Manage Breeding: Manage List* You can create lists of germplasm and traits to make phenotypic data collection sheets, download phenotypic or genotypic data in ‘Download page’ or any other future BIMS tools. The lists is accessed in your account page.

11. View existing locations or create new locations for trials Manage Breeding: Manage Locations

12. Manage Breeding: Create a New Location

13. View and download trial data When viewing trials, you can create folders to manage your trial data. We will also add a functionality to “create a new trial” that will create a field design and a file for collecting phenotype based on users input. Manage Breeding: Manage Trials*

14. View data on crosses, such as name, location, parents, progeny, etc, and/or create a new cross. Manage Breeding: Manage Crosses*

15. Data Import: Individual Data Upload - Germplasm Also will add a data edit function so you can fix any errors you find in the data, with notes recorded on who changed what data points and what the previous values were

16. Data Import: Individual Data Upload - Traits

17. Data Import: Templates*

18. Search: By Germplasm Name

19. Search: By Parentage

20. View trials in your program and download the data. Download: By Trial Download data by trial (multiple selectable)

21. View lists in your account and choose to download the phenotypic and genotypic data for the list of germplasm Download: By List*

22. Field Book App Management* Upload trait evaluation data collected with Field Book App to BIMS Download trait data collection files in Field Book Format

23. Choose trials and traits to calculate and visualize means and standard deviation for the dataset. Data Analysis: Statistical Analysis*

24. You specify how many seedlings you'd like to create that are above your specified trait thresholds. Cross Assist will generate a list of the most efficient parental combinations to achieve your targets. Breeding Decisions: Cross Assist*

25. A tool to enable accurate and flexible cost estimation for marker-assisted seedling selection (MASS) Breeding Decisions: Seedling Assist*

26. Archive*

27. Adding real breeding program data and test functionality Add more statistical analysis and decision tools QTL discovery tools? Further development Import data in the format of software you are using (eg. AgroBase) Future Development

28. Acknowledgements Funding Sources The Cotton Community, The Rosaceae community The Tripal Developers Community The Bioinformatics Community

29. Main Lab Team