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Old Version 1

changes.mady.by.user Yaw Nti-Addae

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changes.mady.by.user Monica Franciscus

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Objective

Driver

Approver

Contributors

Stakeholder

Drivers

Approvers

Associated Projects

Stakeholders

Yaw Nti-Addae

Victor Ulat

Pedro MEDEIROS BARBOSA

Kelly Robbins

Tom Hagen

Stephan Einarson

Moira Sheehan

Lukas Muller

EiB

  • Liz Jones

  • Michael Quinn

EBS - Technical Oversight Committee

Breeding Insight

Innovation Lab

Objective

Develop an analytics framework that will allow breeders to analyze and summarize their phenotypic and genotypic data

Due date

Jan 2019 

Key outcomes

  • Agreement on project timelines, resources and scope.

  • Open-source application with emphasis on EBS integration?

Status

Status
titleNOT STARTED

Problem Statement

Scope

Must have:

Nice to have:

Not in scope:

...

Scope of Phase 1

Expand
titleMust have

  • User interface through which an analysis request can be submitted

  • Analysis pipeline for processing data

  • Job tracking

  • Analysis and Models:

    • Phenotypic analysis

      • ANOVA

      • Simple mixed model (without genotypic information)

      • D-Stat model

    • Experiment design simulator

  • Integration with breeding management system

Expand
titleNice to have

Expand
titleNot in scope

  • User input file processing (Data will be acquired through web services)

  • file output of summary reports (Export features will be provided in UI)

  • Genotypic analysis (will be provided in the future)

  • Covariance matrices (GRM) (will be provided in the future)

  • Integration with genotype management system (will be provided in the future)

Resources for Phase 1

Skill set

% FTE

Duration (months)

Components

Data modeler

10

6

  • Database

  • Liquibase

General developer

100

12

  • Authentication

  • Data process layer

Full stack developer

100

12

  • Web services

  • User interface

DevOps

5

12

  • Automated deployment scripts

  • Automated testing scripts

  • Integration to EBS

Statistician

100

12

  • modeling

  • requirement specification

  • UAT

QA

20

6

  • Write and build test scenarios

  • Testing

  • UAT

Timeline for Phase 1

Roadmap Planner
maplinks
timelinetrue
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titleRoadmap%20Planner
hash99db96ab148b6cd09636af75811d7f1ab68f946f863c47dc84ca58821c5a170b

Milestones and deadlines for Phase 1

Milestone

OwnerDeliverables

Deadline

Status

Review 1

  • Install and configure IAM, including connections to Cornell University OAuth, Google authenticator, and Active Directory

  • Develop and deploy data models for user configuration and job tracking

Status
titleNOT STARTED

Review 2

  • Role management

  • Analysis and Model data models

  • Message queuing

  • Experiment design statistics

  • Anova model statistics

  • Simple model statistics

Status
titlenot started

Review 3

  • UI - Analysis request form

  • Report data model

Status
titlenot started

Review 4

  • Report view

  • Job status

Status
titlenot started

UAT

  • User acceptance testing

Status
titlenot started

Review 5

  • Project review and lessons learned

Status
titlenot started

v1 Release

  • Production release and integration with EBS

Status
titlenot started

Technologies

Layer

Technologies

Notes

Code repository

  • Github

Makes it easy for all parties to pull code into their repos

Authentication

  • WSO2 IAM and/or Keycloak IAM

WSO2 does not officially support openJDK

Database

  • PostgreSQL

Data processing

  • RabbitMQ

  • Java and/or Python

Statistics

  • ASReml 4

  • R

R has got strict versioning, which means that packages/libraries are not guaranteed to be forward or backward compatible

API

  • BrAPI standards

  • WSO2 API manager

  • Java and/or Python

We will use Swagger for API management for easy integration with SWO2 API manager

User interface

  • Angular or Vue or React

Browser compatibility for

  • MS Edge

  • Chrome

  • Firefox

  • Safari

DevOps

  • Ansible

Testing

  • Selinium

  • Unit test

Test browser compatibility for MS Edge, Chrome, Firefox and Safari, which covers ~85% of browser usage in the industry.

Reference materials