RosBreed Participant Meeting 2018, East Lansing, MI GDR BIMS Breeding Information Management System Training Workshop March 5, 2018 Taein Lee, Sook Jung, Ksenija Gasic, Jodi Humann, Michael Coe, Dorrie Main RosBreed Participant Meeting 2018, East Lansing, MI

Agenda Introduction to BIMS (Dorrie): 9.00 AM Hands on Training using sweet cherry RB data (Taein): 9.30 AM Browsing trait/cross/trial data with statistical values Demo by a breeder (Ksenija) Beverage Break: 10.15 AM Hands on Training using sweet cherry RB data (Taein): 10.30 AM Search/Download Breeder demo Lunch: 12.00 -12.45 PM Overview of Templates (Sook): 12.45 PM Hands on Training using your data (Taein): 1.30 – 3.30 PM Create a program Load data in template Load data in Field Book output Browse/search your own data! Create an input file for the Field Book App Trouble shooting Beverage Break: 3.30 PM External Presentation: 4.00 PM Open discussion on future functionality and survey: 4.15 PM Agenda

Introduction to Workshop Welcome and Introductions Tripal and BIMS Goals of the Workshop Introduction to Workshop

BIMS and Field Book Archive Manage Breeding Data Import Data Edit Search and Download Field Book App Management Data Analysis Tools Breeding Decision Tools

Goals and Expected Outcomes Demonstrate current and future utility of BIMS Rosaceae breeding program personnel have a understanding of what BIMS can provide as a resource for Rosaceae breeding Provide hands-on training of BIMS v1.0 Rosaceae breeding program personnel know how to use BIMS v1.0 Solicit feedback on future direction of BIMS BIMS continues to develop functionality that is useful for Rosaceae breeding

Introduction to BIMS Vision Components Focus of BIMS V1.0 Future Development

BIMS Vision 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 Utilize their integrated pedigree, phenotype and genotype data in performing genomic analysis and making breeding decisions. Keep incorporating open-source new genomics tool and breeding decision tools with seamless access to HPC – powerful!

Components of BIMS Archive Manage Breeding Data Import Data Edit Search and Download Field Book App Management Data Analysis Tools Breeding Decision Tools

Current Functionality of BIMS In BIMS v1.0 Breeders can Create programs, add members and control permission levels Add their own data (accessions, cross, phenotype data from trials) in template Add phenotype data exported from the Field Book App Create input files for the Field Book App Sync data among multiple devices with the Field Book App through BIMS Perform/view statistical analysis on any list of accessions they created Perform search with various categories and trait cutoff values and save the list and phenotype data Archive the entire data

Available by RGC9! Basic breeding decision tool! Data Editing Generating accession report New types of data: loading, searching, downloading, display Photo Raw SNP Genotype, haplotype, trait-associated allele or haplotype - Breeding value Basic breeding decision tool!

Future Development Plans Analysis tools Genomic analysis: GWAS, Genomic Selection, other open-source breeding software, access to R programs, etc Collaboration ongoing to incorporate iPAT software for GS and GWAS More breeding decision tools Anonymously sharing raw data to use in breeding decision tools upon breeder agreement Field design tools Display tools (eg. Pedigree viewer) Downloading data in a format to be used in desktop software PediMap Visualization tools from Hutton Institute: Flapjack (genotype), Helium (pedigree) Web services to share data from other resources/tools Collaboration with BrAPI ongoing

Hands on Training using sweet cherry RB data Browse trait/location/cross/trial data with statistical values Search/Download

Accessing BIMS Go to www.rosaceae.org/bims Click Crop and choose sweet cherry Click ‘Program’ under Manage Breeding Choose ‘Sweet_Cherry_Demo’

Manage Breeding: Trait Choose one trait See the details and stats of that trait in the entire program on the right side If it’s your program, you can add a new trait by expanding admin menu edit the existing trait

Manage Breeding: Location Choose one location See the details on the right side If it’s your program, you can add a new location by expanding admin menu edit the existing location

Manage Breeding: Cross Choose one cross See the details on the right side Click ‘view’ to see stats for only for the cross Choose one traits to view the stats and the raw data If it’s your program, you can add a new cross by expanding admin menu edit the existing cross

Manage Breeding: Accession Choose one accession See the details on the right side Click ‘view’ to see stats for only for the accession Choose one traits to view the stats and the raw data If it’s your program, you can add a new accession by expanding admin menu edit the existing accession

Manage Breeding: Trial Choose one trial See the details on the right side Click ‘view’ to see stats for only for the trial Choose one traits to view the stats and the raw data If it’s your program, you can add a new trial by expanding admin menu edit the existing trial

Search/Download You can search for accessions with any properties and trait values in combination. When you add another filter, the middle section will only show the filtered results. In search section, you can see how progeny from a parent performs Bulked_Fruit_SSC: All accessions: 19.7 Bing as mom: Mean 18.43 Black republican as mom: Mean 20

Search/Download An example search Parent (black republican as mom) Bulked_Fruit_SSC over 15 Firmness_1 over 250 (6 accessions) View In the search result section, you will see initially the accession names along with any traits that you chose in the search. Click Column options to add any properties and/or trait values and click 'Update'. You can download or save it in your account. You can access them later in 'Search Results'.

Overview of templates Where to find templates Details of templates Matching column names in templates and the Field Book App How to add more columns in templates

Where to find template

Dataset, Contact, Site Dataset: Trial of your program Contact: personal information *dataset_name comments description ark_2016 trial in 2016 *contact_name alias *type first_name Last_name Sook Jung person Sook Jung Site: Location of your crops *site_name site_long_name latitude longitude altitude geodetic_datum type country state region address comments Clemson_1 Clemson_orchard_KG 34.68344 82.83736 222 orchard USA SC Florence_1 Columns with * are required Use real number format for latitude, longitude and altitude

Descriptor: Trait descriptors used in your program *descriptor_name alias trait_name *format categories data_unit minimum maximum defaultvalue definition Rank numeric 1 10 1-10 Scale for overall evaluation rating. (10 being the highest score) Blush% percent % average % of blush overlay on surface of 5 fruits FleshC categorical White/Yellow/Red FruitSet 9 1-9 scale (9 being the heaviest set) Attractiveness 1-10 scale (10 being most attractive) Adhesion Freestone/Clingstone/Semifree/Semicling Format follows those in FieldBook App numeric, categorical, date, percent, Boolean, text, photo, audio, counter, disease rating, multicat, location For descriptors with ‘categorical’ format, all the possible categories need to be entered in ‘categories’ column, separated by ‘/’ one category should not have ‘/’ So Yellowish_Red is okay as a category but Yellowish/Red is not. Trait descriptor can be loaded using ‘.trt’ file from Field Book App

How to organize your photo using trait descriptors Create a descriptor(s) of ‘photo’ format Make several descriptors with ‘photo’ format such as ‘leaf_photo’, ‘fruit_photo’, etc Then you can view/search your photos in more organized way Field Book will automatically name the photo file with unique_id, trait descriptor and time You can load this info using the exported file from Field Book App If you don’t use Field Book App, you can still load the file name as phenotype We will soon have an interface where you can upload your photos to BIMS.

Accession vs. Progeny sheet Accessions Cross information? Progeny sheet Accession sheet Yes No

Cross, Progeny Cross Progeny site_name *cross_number *mother mother_location *father father_location cross_date Clemson_1 SC13-26 A825 A860 7/1/2013 SC13-29 A819 A836CN Progeny *progeny_name alias *genus *species *cross_number description advanced_to_2nd advanced_to_3rd advanced_to_4th SC13-26-1 Prunus persica SC13-26 SC13-26-10 SC13-26-11 SC13-26-12 SC13-26-13 SC13-26-15 SC13-26-16 SC13-29-1 SC13-29 SC13-29-16 SC13-29-17 SC13-29-2 SC13-29-20 mother or father in cross sheet should exist In the database already or In accession sheet

Accession *accession *type *genus *species secondary_ID maternal_parent paternal_parent pedigree description comments good_peach cultivar Prunus persica better_peach A825 breeding_research_material A819 A860 good_peachg A836CN 99P4388 A806CN A809 A816CN A827 Paternal parent maybe A809 or A819 A864CN maternal_parent or paternal_parent in cross sheet should exist In the database already or In accession sheet If you are not sure about maternal or paternal parent, add short info in ‘pedigree’ and/or longer info in ‘description’

Phenotype Four required columns in addition to dataset_name column *accession *genus *species *Field ID *primary *secondary clone_ID evaluator site_name plant_date data_year evaluation_date pick_date barcode comments #Rank #Blush% #FLESHC ark_2016 SC13-26-1 Prunus persica P28H_SC13-26-1 1 Ksenija Gasic Clemson_1 2016.7.12 50 White SC13-26-10 P28H_SC13-26-10 10 2016.7.26 3 SC13-26-11 P28H_SC13-26-11 11 2 SC13-26-12 P28H_SC13-26-12 12 5 94 Yellow SC13-26-13 P28H_SC13-26-13 13 90 Four required columns in addition to dataset_name column Field ID is a unique ID for the row (the phenotyped sample) within the dataset Trait descriptors are added as column headings with ‘#’ prefix

Column names in Field Book App and templates *dataset_name *accession *genus *species *Field ID *primary *secondary ark_2016 SC13-26-1 Prunus persica P28H_SC13-26-1 1 SC13-26-10 P28H_SC13-26-10 10 SC13-26-11 P28H_SC13-26-11 11 SC13-26-12 P28H_SC13-26-12 12 SC13-26-13 P28H_SC13-26-13 13 SC13-26-15 P28H_SC13-26-15 15 SC13-26-16 P28H_SC13-26-16 16 SC13-29-1 P28H_SC13-29-1 4 38 SC13-29-16 P28H_SC13-29-16 53 SC13-29-17 P28H_SC13-29-17 54 SC13-29-2 P28H_SC13-29-2 39 SC13-29-20 P28H_SC13-29-20 57 Field Book App allows you to rename the three required column, and accession BIMS allows you to set them up when you create a program and change it if necessary in configuration panel

Accessing configuration panel If you change the column names here, the column names in templates also changes

Property sheet In property sheet, you can define new columns for Progeny, Accession, Cross, Phenotype sheets Property types are accession: progeny and accession sheet cross: cross sheet sample: phenotype sheet *name *type alias definition treatment sample treatment type done to the sample The terms can be added as a column heading with a prefix of '##'. *dataset_name *accession genus species unique_id plot row ##treatment site_name data_year #Bloom_Date #Perc_Pitting Sweet_cherry_CRS_phenotyping_2010 Ambrunes Prunus Avium rb-sw-0000001 1 A Pear Acres 2010 4 Cashmere rb-sw-0000002 B 16 Chelan rb-sw-0000003 Roza 3/30/2010

‘Type’ columns Site, Accession, Property sheets How to check the available types ‘Header’ sheet of each template Type dropdown of ‘Add location’ or Add accession’ menu Request GDR team if you need to add more types.

Hands on Training using your data (or sample data) Create a program Load data in template Load data in FieldBook output Browse/search your own data! Create an input file for the FieldBook App New trial Existing trial Cross Trouble Shooting Archive

Manage Breeding: Create a program Create a new program To create a new breeding program, expand 'Program Admin Menu' and click 'Create’. You can rename accession and three required columns in Field Book App This will change column names of BIMS template Add members To add or remove members to your program, click 'Members' under 'Program Admin Menu'. You can add anyone with a GDR account to your program and give permission to 'edit' or 'read only'.

Data Import Template List Upload data (data in template): Loading group Name group1 Baylee Miller Wendy Hoashi-Erhardt Margaret Worthington Amy Iezzoni group2 Bill Shane David Byrne Cameron Peace group3 Jason Zurn Upinder Gill Lise Mahoney Nahla Bassil Template List Upload data (data in template): Group1: own data in excel Group2 and 3 : sample data (template_sample_data_final.xlsx) Check if your data has been loaded by checking trait, accession and Trial

Field Book Management: upload exported file Upload exported field file (field_book_sample_final.csv) Browse/Search your data! Save a search result to use it for generating Field Book input file Archive! Loading group Name group2 Bill Shane David Byrne Cameron Peace group3 Jason Zurn Upinder Gill Lise Mahoney Nahla Bassil

Field Book Management: generate trait file When you have trait descriptors already in BIMS, you don’t have to create trait manually in Field Book App Trait file: choose the trait descriptors then click!

Field Book Management: generate Field file New Trial: when you want to do another trial with accessions in BIMS Existing Trial: as a way to sync devices through BIMS New Cross: to generate progeny names to add to Field Book Field input file and BIMS

Field Book Management: generate input file New Trial choose an accession list and add them in the input file You need to add unique_id, primary_order and secondary_order

Field Book Management: generate input file Existing Trial: a way of syncing data from multiple devices You can load the exported file to BIMS and then recreate input file with a indication (a trait) which have been already phenotyped. The exported file in database format, however, only contains the unique_id that have been phenotyped. So make sure you first upload the original field book input file for the trial before you upload the exported database file. You can add trait values, accession properties and/or sample properties in the input file

Configuration Panel Allows you to choose the properties and traits to be displayed in ‘generating Field Book Input File’ section. As well as to change the names for the ‘accession’ and the three required columns for the Field Book Input file

Field Book Management: generate input file for a new cross This allows you to generate input file for a new cross. Please upload a file with cross name, row and the number of progeny for each row that you will phenotype per each row for BIMS to generate a Field Book input file with new progeny names. … Prefix: KG

Follow up Join the GDR-BIMS mailing list at https://www.rosaceae.org/mailing_lists to receive emails about GDR-BIMS meetings, new functionality, bug fixes etc. Contact us about GDR-BIMS at https://www.rosaceae.org/contact Participate in monthly BIMS webinars (starting April 2018) where we demonstrate functionality, answer questions, etc. Request individual program online meetings to get help for your program Access GDR-BIMS at https://www.rosaceae.org/bims Access GDR-BIMS User Guide at https://www.rosaceae.org/BIMS_manual

Future Plans Discussion Analysis tools Genomic analysis: GWAS, Genomic Selection, other open-source breeding software, access to R programs, etc Collaboration ongoing to incorporate iPAT software for GS and GWAS More breeding decision tools Anonymously sharing raw data to use in breeding decision tools upon breeder agreement Field design tools Display tools (eg. Pedigree viewer) Downloading data in a format to be used in desktop software PediMap Visualization tools from Hutton Institute: Flapjack (genotype), Helium (pedigree) Web services to share data from other resources/tools Collaboration with BrAPI ongoing