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Drivers

Approvers

Contributors

Stakeholders

Yaw Nti-Addae

Victor Ulat

Pedro MEDEIROS BARBOSA

Liz Jones

Kelly Robbins

Tom Hagen

Stephan Einarson

Moira Sheehan

Lukas Muller

EiB

EBS

Breeding Insight

Innovation Lab

Objective

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

Due date

Key outcomes

Status

NOT STARTED

Problem Statement

Scope of v1

 Must 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)

      • Simple model

    • Experiment design

  • Integration with breeding management system

 Nice to have

 Not 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 v1

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

50

12

  • modeling

  • requirement specification

  • UAT

QA

20

6

  • Write and build test scenarios

  • Testing

  • UAT

Timeline for v1

Apr2020MayJunJulAugSepOctNovDecJan2021FebMarAprReview 1Review 2Review 3Review 4UATReview 5Release
Authentication
Database
Process
Stat Model
BrAPI
UI
DevOps

IAM

Federation

Roles

User config

Jobs DM

Report DM

Analysis DM

Model DM

Pipeline

RabbitMQ

Job submission

ASReml prep

R prep

Calc Engine

Report Engine

UAT

ASReml models

Test models

Test models

R - Exp Design

R Simple model

Analysis statistics

Report summaries

API Framework

User config

Analysis

Models

Request analysis

Job status

Report

Angular setup

Authentication

User config

Phenotypic analysis view

Pheno data

Request form

Job status

Report view

UAT

IAM & DM

API & UI

Dev deploy

Automated test framework

Test deploy

Prod deploy

Milestones and deadlines for v1

Milestone

Deliverables

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

NOT STARTED

Review 2

  • Role management

  • Analysis and Model data models

  • Message queuing

  • Experiment design statistics

  • Anova model statistics

  • Simple model statistics

NOT STARTED

Review 3

  • UI - Analysis request form

  • Report data model

NOT STARTED

Review 4

  • Report view

  • Job status

NOT STARTED

UAT

  • User acceptance testing

NOT STARTED

Review 5

  • Project review and lessons learned

NOT STARTED

v1 Release

  • Production release and integration with EBS

NOT 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 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


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