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Objective 2.2 IB Workbench

Integrated Breeding Workbench

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A Gliffy Diagram named: IBWorkBench-V1

Workbench Installations (Administration)

An Installation of the WorkBench specifies the crop which identifies the central (public) data resources that will be accessible to the project. This includes a central GMS database, a central DMS database, a public GEMS database and a central Genotyping database. Each installation provides access to local (private) data resources. These data resources include a local GMS, DMS, IMS and Fingerprinting data. Each Installation has at least one user with Administrative privileges. Users are identified by authentication codes (username and password) for access to specific private data resources. (Private simply means 'requiring authentication for access' and several users may have access to the same private (local) data).

There are two types of users, 'official users' known to the curator of the public crop information whose identification, authority and credentials are stored with the public data and who have or intend to contribute data to the central public databases. Such data is linked to their identification for attribution and authentication. Then there are 'unofficial users' who have installed the workbench and created local databases but who have not, and may not ever, publish data or who have been assigned credentials remotely (without reference to the central curator). The credentials for unofficial users are stored in the private databases. Unofficial users can be made official by the central curator if and when they choose to publish data.

The Administration tools depend on the authority of the user. For example if the user is the administrator of the local data resources the he should have a tool to create new users (and hence new projects) with access to that data. If the user has higher authority he should have access to a tool to create new local data resources but initially this will be an installation function of the IBWB.

WorkBench Projects (Configuration)

Each user for an installation defines a project (one person may have several user credentials and hence several projects). Project configuration details need to be available in some form of data store such as a locally maintained ini file or xml configuration file. If they are maintained locally and privately they may even contain the user authentication codes explicitly so that the user needs only to select the project to open it, if they are accessible to non authorized users they should not contain these details and the user should be required to enter the authentication codes after selecting the project.
The first functionality of the IBWB will be to ask the user to open a project by selecting from a list of available project configuration 'files'. Once the configuration is selected, the availability of the public data resources should be checked, the user authentication codes verified and the local data resources checked. Next, the list of modules should be reviewed and checked for availability, and depending on the state of the workflow, icons or menus should be made available for modules and tools.

The Configuration Tools allow users to:

  • select or specify naming conventions for germplasm, germplasm lists, studies etc.
  • to use and update ontologies such as germplasm methods and the trait dictionary
  • to update breeding, testing or collection locations
  • to create and modify study templates.

The Query Tools will depend on the data resources specified in the project configuration but examples are:

  • germplasm and pedigree viewer - GMSSearch or CrossInfo
  • study browser - Eg query functions of WorkBook
  • data miner - eg the Data Mining Tool
  • cross study query builder - eg CropFinder
  • gene catalogue viewer - eg GEMSCAT
  • genotype and trait viewer - eg Flapjack

Breeding Workflows are constructed by users to match their project activities. The user will only see the WorkBench Tools and settings for those tools required to execute the steps in the Workflow, and at the appropriate step in the Workflow. Some Workflows and the tools they require are:

Development sequence for the IB WorkBench

  • Version 1 of the workbench (Feb 2011) will contain the the IB Field Book (5.3 in the figure). Tasks performed by the Administration Tools (Open a Project), Configuration Tools (Trait Dictionary and Templates), the Germplasm Manager (Trial Lists) and the Analytical Pipeline will only be available by manual loading or by using existing ICIS or FieldBook tools.
  • Version 2 of the Workbench (June 2011) will have components of the Germplasm Manager (2) and the analytical pipeline (3) included as well as the IB Nursery Planner (5)
  • Version 3 of the Workbench (Dec 2011) will include some configuration tools (1), further germplasm manager tools (2), and the IB Lab Book tool (6).

Functionality and Design for Components of the IB Workbench

Links to Tools Grouped by Breeding Application

Administration and Configuration

  • 1.1 Installation
  • 1.2 Users
  • 1.3 Projects
  • 2.1 Locations
  • 2.2 Persons
  • 2.3 Institutions
  • 2.4 Breeding Methods
  • 2.5 Naming Conventions
  • 2.6 Storage Conventions
  • 2.7 Trait Dictionary
  • 2.8 Trait Templates
  • 2.9 Gene Catalogue
  • 2.10 Database Implementation
  • 2.11 Data Access Layer

Query Tools

  • 3.1 Pedigree Viewer
  • 3.2 Study Browser
  • 3.3 Genotype Viewer

Genealogy Manager

  • 4.1 Pedigree Import
  • 4.2 Pedigree Editor

Breeding Manager

  • 4.3 Seed Inventory
  • 4.5 Crossing Block
  • 4.6 Nursery List
  • 5.2 Nursery Book

Data Management

  • 5.1 Phenotype Data Import
  • 4.7 Trial Entries
  • 5.3 Trial Field Book
  • 5.4 Site Characterization
  • 5.5 Soil Data
  • 5.6 Climate Data
  • 5.7 Socioeconomic Data
  • 6.1 Genotype Data Import
  • 4.4 Sample List
  • 6.2 Lab Book
  • 6.3 Genotyping Data
  • 6.4 Fingerprinting Data

Analytical Pipeline

  • 7.1 Experimental Design
  • 7.2 Quality Assurance
  • 7.3 Data Manipulation
  • 7.4 Single Site Analysis
  • 7.5 Multi-Environment Trials
  • 7.6 Genetic Component Analysis
  • 7.7 GxE Analysis
  • 7.8 Genetic Map Construction
  • 7.9 Haplotyping Tool
  • 7.10 QTL Analysis
  • 7.11 QTL x E Analysis
  • 7.12 Genetic Diversity Tool
  • 7.13 Selection Indices
  • 7.14 QTL Chooser

Decision Support

  • 8.2 Design Tool (MBDT)
  • 8.3 MAS Application (MOSEL)
  • 8.4 MA Back-crossing (MABC)
  • 8.5 MA Recurrent Selection (MARS)
  • 8.6 Genome-wide Selection (GWS)
  • 8.7 Cross Prediction
  • 8.8 Simulation Tools
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