Using the CottonGen Breeding Information Management System for Cotton Improvement Jing Yu, Taein Lee, Sook Jung, Don Jones, Todd Campbell, Ksenija Gasic, Jodi Humann, Dorrie Main 2019 Beltwide Cotton Conference January 10, 2019 New Orleans, LA

Outline Introduction to BIMS- the Breeding Information Management Systems in CottonGen How to access BIMS Major components of BIMS Example use of BIMS Read through

BIMS Vision BIMS is a secure, comprehensive, online accessible breeding data management and analysis system developed by our lab It allows breeders to (red completed): Store, manage, archive, analyze their private data Manage data from the Field Book App, an Android app for collecting phenotype data in the field Integrate private data with publicly available data – coming soon Read through

Access BIMS – Public or Private If you have stored private breeding data in BIMS and you want to see your data, you will need to login to cottongen first <click>, otherwise you can directly access BIMS either under the Tool menu in the navigation bar or via the Manage breeding link on the Tools Quick Start on the home page.

BIMS Web Interface & Components This is t the BIMS interface <click1>On top is the BIMS header, <click2>the left panel lists all the BIMS components, clicking on one, the contents within the component will appear such as ‘About BIMS<click3> and ‘Help’ <click4>. Other components are:<click5> <READ through> please note the Data edit, Data analysis packages, Breeding Decision Tools are not yet available On the right side is the main area. The name on the tab <click6>indicates the component and the content you selected to open. below the tab<click7> are its relevant information. Such as<click8> instructions and <click9> data contained within this component

Create Program or Manage Members Looking at the BIMS web interface in more detail. If you access BIMS without login, <click1>an ‘Anonymous’ will appear on the header-right. You will be able to see all publicly available datasets from ‘Program selection’ <click2> Selecting one of them, the selected program name will appear on the head-left<click3> and its details/description appear too<click4>

BIMS: Browsing/Managing Location In the following slides, I will present examples of using BIMS. This slide shows an example when using BIMS ‘Manage Breeding’ <click1>on location<click2> within the selected RBTN dataset <click3>, An instruction <clivk4>tells you how to browse or manage (must be the owner or have permission) Below the Instruction is <click4> A list of multi-environment trials within this dataset, where you can select one or more or all of them and view them on Google Map <click5> This is a view of all locations within RBTN dataset<click6>, different colors indicate the number of trails conducted in the area

BIMS: Browsing/Managing Trait This slide shows BIMS ‘Manage Breeding’ on Trait<click1> within the selected RBTN dataset <click2>, A list of all trait measurements will appear<click3> select a specific measurement E1 (%) from the list<click4> allows user to view details about E1 (elongation)<click5> since this measurement is taken by numerical scores, a histogram <click6> of the distribution of these numerical data will appear too. If selected trait scores are categorical data, <click7>A table of Frequency appears

BIMS: Search

Search: Display and Save Results Or Login and save this result under your BIMS ‘Search Results’

BIMS: Statistical Analysis You can choose two datasets using categories and choose trait descriptor to compare the distribution and the statistical values of the two datasets. Categories include data year, cross, trial and the stock list that you saved in 'Search' section. Choose datasets and compare: Lubbock TX and Westside CA, in years of 2016 and 2017

Ways to import your data to BIMS Using Field Book App Management Import data directly from your FieldBook App. Easy and convenient, requires use of this App Using Data Import Do not have to have FieldBook App but need to fill data into BIMS template before upload Both can be found from BIMS component panel. Latesly, I want to briefly talk about how to import data to BIMS for your breeding program. <read through> <click1> This is Field Book App Management in BIMS <click2> This is Data Import component in BIMS We do recommend using the Field Book App and can provide individual training in using it with BIMS or using the templates

What I presented is just a small amount of the functionality of BIMS, please come to the poster to see more of what it can do. More examples on how to use BIMS are provided in CottonGen User Manual from CottonGen’s ‘Help’ <click1>. From where we ca see that BIMS Manual is showing on the left panel<click2>, you can <click> and read through… Links are also provided in the BIMS pages under the help section on the left.

Acknowledged with thanks Contact us: www.cottongen.org/contact Join our mailing lists: www.cottongen.org/mailing_list Cite us: www.cottongen.org/cite_us