BMS Development

Jan Erik Backlund & Mariano Crimi

IBP Board Meeting
Kampala, Uganda
21-23 October 2018
Outline
 Strong team
 Strong process
 Good progress
 Complex landscape
 SWOT
 Roadmap
 Strategy summary

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Buenos Aires

Manila
Main achievements over last 6 months
 New features
 Calculated traits
 Sample list management
 Nurseries and Trials merged into Studies
 Improvements
 Coding and fixing
 Germplasm naming
 Sharing lists and locations
 Admin: functionality by role
 Re-engineering

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Long-term achievements from Darla
 From multiple databases per program to Single DB per
crop

 Server Version
 Transaction and File Management
 Performance Improvements
 BMS running on Linux

 Code Quality
 Continuous inspection of code quality through
SonarQube
 SonarQube metrics improvement

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Long-term achievements from Darla
 Installers
 From multiple installers to single installer
 Reliable Installer Build Process
 Better process for DB changes propagation from IBP
DM team

 Continuous Integration (CI) framework (Jenkins)

 Build automation
 Self-testing build
 Easy deployment to test/UAT servers

 Use of Liquibase for database changes

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

SonarQube Dashboard

• Gives overview of health of software code

• Measures code coverage (tests) and tracks news issues
introduced according to set of code review rules
• Inspections build automatically runs once a day and
SonarQube dashboard is refreshed
SonarQube Metrics (2014 vs 2018)

2014 2018

Average Code 8% 41.6% *

Coverage
Code Issues ~30,000 17,169

* Excluding GDMS and Migrator code

SonarQube Metrics (2017 vs 2018)

2017 2018 Progress

Average Code 34% 41.6%

Coverage 7.6%

Code Issues 21,526 17,169 ~4K

issues

* Excluding GDMS and Migrator code

Landscape
 Last year for direct funding of IBP through BMGF
 EiB module 5 umbrella
 Bioinformatics, biometrics, data management
 BrAPI
 Two major public-sphere projects in breeding data mgmt
 Enterprise Breeding System
 B4R from IRRI
 Enterprise Architecture
 ARS Breeding Insight Platform

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Enterprise Breeding System Modules
14 1 13
Breeding
On Farm Breeding Trial
Program
Outcomes Decision Making
Planning

8 2 11 12
GOBii Germinate
B4R Breeding
Genotyping & Breeding Trial Germplasm
Experiment
Other Analytical Analytics Knowledge
Creation
Procedures Management

7 3 5 9 15
Sample Tracker EiB Module
KDX/S Nursery KDX/S Trial
Sample High Throughput 5 Meta &
Location Location
Workflow Phenotyping Big Data
Implementation Implementation
Management Analytics

10
16 4 6
Grin-Global B4R Seed KDX/S Trial Envirotyping
Genebank Inventory Location
Management Management Phenotyping

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

ARS Breeding Insight Platform

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

 ARS Breeding Insight Platform

Proposed integration process of existing open source software tools into the BIP stack.

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

BMS and the Architecture Diagram
BMS Support
Full

Partial

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

BMS strengths
 Deployment
 Currently available to all interested parties
 Both LAN and cloud deployment
 Ease of installation
 IBP: support the adopting institution in the process
 Strong support for importing existing data
 User-friendly interface
 Wide range of crops with methods and dictionaries
 Excellent support for experimental design and analysis
 Excellent support for breeding processes
 Open-sourced core
 Documentation!
IBP Board Meeting – Kampala, Uganda, 21-23 October 2018
SWOT
Strengths Weaknesses
• System • Customer engagement
• Deployable today • Technical debt
• User-friendly • Limited extensibility
• Strong core functionality • Missing functionality
• Documentation • Seed inventory
• Strong teams • Field layout
• Dev and deployment
• Strong customer base

Opportunities Threats
• Services model • Getting over-extended
• BioSci • Culture of ‘Free’
• VSNi DataLive • Post phase II destiny
• BrAPI • Enterprise bandwagon
• Almost customers • ICRISAT
• KALRO • Lack of umbrella for
• EIAR coordination across orgs

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

2018-2019 Roadmap (Draft)

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Estimated resource allocation for 2019

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Overall strategy
 Focus on germplasm and studies
 Services orientation

Provide services

Consume services
 Lean on BrAPI
v9 Resource distribution

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

v10 Resource distribution

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

Bug fixing: Cumulative Resolved vs. New

IBP Board Meeting – Kampala, Uganda, 21-23 October 2018

SonarQube Metrics (2017 vs 2018)

2017 2018 Increment

BMSApi 67.1 69.2
2.1
Breeding Manager 40.3 50.8
10.5
Commons 41.6 44.9
3.3
Fieldbook 34.7 39.1
4.4
Middleware 31.1 35.1
4.0
Workbench 20.1 27.8
7.7
Workbench Launcher 21.9 24.7
2.8
BMS + BrAPI: Graphical Filtering Tool
Excellence in Breeding (EiB) initiative

“… modernize breeding programs … access to cutting-edge tools,

services and best practices, application-oriented training and practical
advice.”