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Objective 2.2 Functionalities and Milestones

Functional Features for the Integrated Breeding Workflow System (IBWS) - December 2012 and June 2013
Phenotypic database
See database action plan document
Workbench
Workbench V1.1.1 - December 2012
Administration and Configuration

  • The Installer will obtain details of the Workbench administrator for new installations. - done
  • The Workbench Administrator can set up new workbench users. Workbench user details are maintained in the Workbench database. Each workbench user may have a set of associated breeding projects with project user details stored in the crop databases. When Workbench users log on to the workbench they will see only their associated projects. - done
  • Workbench users can set up breeding projects as Project Administrators. Local data spaces for GMS, DMS and GDMS are created for each project. The administrator can define users and their roles (by selecting from the existing user list or adding new users), select a workflow template (CB, MAS, MABC or MARS), specify breeding methods to be offered at each stage of the selected programme (if there is any choice), specify the breeding and testing locations (by selection from the existing list of locations or by adding new locations). - done

Workflow Management

  • Implement links between Germplasm Browser and Study Browser: Given a single germplasm entry, query for the set of lists, characterization and evaluation studies where it, or germplasm in its maintenance neighborhood, is represented. Be able to browse to any of those studies and view or download the data. Save selected germplasm into an existing or new germplasm list for characterization or evaluation. - done
  • Use Study Browser to select and export datasets and analysis parameters in the format required by Breeding View. Launch Breeding View into a specific analysis workflow with pre-selected data already exported to input files (no user intervention at the file level). - done
  • Implementation of user roles. - done

Workbench V1.1.2 - June 2013
Project data administration

  • The Installer will verify the identity of the Workbench administrator for updated installations.
  • The Workbench will have an administration section where project users can request a backup of the local project IBDB, and a restore if they have the right privileges. This will use the standard MySQL backup facilities and result in a zipped backup file which could be stored safely. A common use of this feature will be for new users to re-set their database if they make data management mistakes, and for training we use it to set the local environment to a standard state for each lesson.
  • An upload and update procedure will allow a project administrator to select upload from the administration section. This will create a backup of the local IBDB and block write access to the local IBDB until after the update. A copy of the backup will be sent to the central crop administrator who will upload the local data to the central (including project users for first time uploads), clean out the local database and create a new central installer and a local database installer for the project. The Workbench administrator will download and install the new central, and the project administrator will download and install the new local.

Workflow Management

  • Store Breeding View output in IBDB (summary phenotypic data into DMS and QTL info into GDMS).
  • Workbench will launch RAP into a specific analysis workflow with required datasets.
  • Connect to Crop Ontology API for linking ontology data with query tools.
  • Allow Workbench users to customize the steps in their workflows or design new workflows.
  • Closer integration between Workbench and OptiMAS: Getting input data from GDMS (QTL info + genotypes).
  • Closer integration between Workbench and MBDT: Getting input data from GDMS (MTA info + genotypes).
  • Workbench will track and display project activities. (GCP team to confirm). Workbench will provide ways for tools to report on activities done for a project. Workbench will display list of activities done for the project.
  • Workbench will launch Pedigree Input tool and Pedigree Editor.
  • Workbench will launch any tools that a user may want to add.

Query Tools
Germplasm Browser V1.1.1 - December 2012

  • Browse germplasm records in the central and local databases by searching on names and viewing all attributes of selected germplasm. Automatically search on names as typed and with common variants (standardized names) and allow wild cards. - done
  • Display the user lists where the germplasm is included. - done
  • Display inventory information for germplasm. - done
  • Show a list of datasets where germplasm has been evaluated. - done
  • Display a graph of the pedigree of a Germplasm.
  • Save Germplasm entries to a new or existing user List. - done
  • Display Germplasm Lists and details of the entries in them.
  • Allow Germplasm Browser users to download lists of Germplasm.
  • Display the derivative and maintenance neighborhoods, and group relatives. - done
  • Show lists and studies where germplasm from a derivative or maintenance neighborhood occur.

Study Browser V1.1.1 - December 2012

  • Study Browser will be able to export datasets in the Excel format used by the Workbook/Fieldbook.
  • GIDs in the dataset tables in the Study Browser have links to display the germplasm details. - done

Breeding manager
Breeding Manager V1.0.3 September 2012

  • Users is able to launch the appropriate Breeding Manager tool from the workbench according to their position on the workflow they have chosen. done
  • Import a set of germplasm specified in a excel file into the local GMS in a very simple way. done
  • Prepare lists of germplasm for characterization, evaluation and genotyping. done
  • Prepare a crossing block for planting and characterizing breeding material and import the results of the crossing nursery to form the F1 nursery list with pedigree. done
  • Advance Nurseries and prepare pedigree nursery lists based on previous nursery harvest lists, merged with check entries and exported as planting lists. Import the results of selection nurseries and save them (with pedigrees) as lists for further population development or evaluation. done
  • Wheat customization: BCIDs and complete list of crossing methods available. done
  • Wheat customization: Advanced nursery method able to use the wheat naming convention done

Breeding Manager V1.1.3 - December, 2012

  • Import a set of germplasm, including inventory data where available.
  • Seed Inventory update method added to advance nursery process. done
  • Maize customization: Maize naming conventions and breeding methods available
  • Breeding Manager using IBP Middleware for some data access functions. done
  • View seed inventory in germplasm lists. done
  • Display of pedigree strings in germplasm lists, nurseries and fieldbooks. done
  • Add delete options for lists, entries, studies and nurseries. done

Breeding manager V1.1.4 - June 2013

  • Breeding Manager available as a separate application from IBFieldbook.
  • Germplasm Import Wizard implemented.
  • Crossing Nursery Wizard implemented.
  • Prepare lists of germplasm for characterization, evaluation and genotyping, using access to inventory information.
  • List manager tool for Breeding manager (concatenate and merge lists)
  • Delete options for germplasm records without descendants added (for editing purpose).
  • Additional Seed Inventory Functions - reservations and shipments
  • Storeman's interface for seed inventory (storage, splitting, mixing and shipping).

IB Fieldbook
IBFieldbook V1.0.3 - September 2012

  • Prepare fieldbooks for single or multi-environment evaluation trials from germplasm lists, trait templates and layout plans. Export seed packing and planting lists, as well as data recording files for printed fieldbooks and hand-held data entry devices. done
  • Import evaluation data for quality assurance and data storage in the IB database. Export data sets for analysis. done
  • Maize customization: Access to the CIMMYT R-scripts for analysis. done

IBFieldbook V1.1.3 - December 2012

  • Be able to read row column designs with 'use my own design feature'.
  • Using IBP Middleware V1 for some database access. done
  • Delete option (entries; lists; trials; nurseries and studies). done
  • Using the trial fieldbook as a template for next season. Done?
  • Export files for Fieldlab. done

Fieldbook V1.1.4 - June 2013

  • Germplasm Import Wizard accessible from Fieldbook wizard Germplasm page.
  • Multi factorial field treatment structures.
  • Simple rectangular Field layout/map.
  • Additional options for field layout - non rectangular layouts, additional labels on plot markers.
  • IBFieldbook available as a separate application from Breeding Manager.
  • Advancing germplasm and updating seed inventory from trial harvest lists.
  • Improved label printing - custom design of seed, plot and harvest labels.
  • Implement support for sampling schemes - quadrants or plants within plots.
  • Add new traits to an existing fieldbook

Genealogy Manager V1.1.1 June 2013

  • Pedigree Import tool
  • Pedigree Editor tool
  • Pedigree analysis tool - find germplasm by parents and crosses, trace descendants, compute mendelgrams and COPs, cluster and ordinate germplasm based on COP matrices.

Handheld application
FieldLab - December 2012

  • Tutorial or Help
    • Included in the application
    • Available but has yet to be completed and modified
  • Reads a Fieldbook Excel template
  • Measurement of Traits
    • Facility to display all or hide some traits
    • With good description of the traits when "i" or info icon is clicked
    • Users can specify min and max values in the scoring excel file (Not automatic at this moment but can be by getting the min, max from the database)
    • Imposes data types. If the trait is numeric, it displays a numeric keypad. If the trait to score is of type character, it automatically displays a character keypad.
  • View options
    • Users can specify the number of entries to display per page
  • Data validation
    • Min and max values for specific traits can be assigned in the settings section
    • Users are warned if it's not a valid value (checks against min and max values) but it can keep those values upon confirmation from the user. A message is displayed.
    • Pre-defined values can be set too. Ex. for Phenotypic Acceptability trait where it allows only these values - 1: Excellent, 3: Good, 5: Fair, 7: Poor and 9: Unacceptable. Users will choose among these scores.
  • Input Range
    • Allows specifying the plots or records that will have similar values. Ex. plots 1-10 will have the same score for Flowering
  • Exports the recorded values in Fieldbook template format in excel.
    • This format is read directly by IB Fieldbook.
  • Barcode
    • Available in the settings section

Future:

  • Complete the Help section included in the tool
  • Facility to add new traits observed in the field
  • Searching facility
    • Example also is to search for materials with null values
  • Capture and save photo

Genotypic Data Management (GDMS)
GDMS: available now

  • Ability to run as a standalone tool (without the need to conform to any of the IBP naming conventions and QC routines) and integrated in the IBP workbench. done
  • Able to load QTL, genetic map and genotyping data (SNP, SSR and DArT markers). done
  • Able to retrieve QTL, genetic map and genotyping data (SNP, SSR and Dart markers) as csv files and flapjack format (including flapjack project file) and as A B H or genotyping calls. done
  • Query for marker names, Accessions, GIDs. Query polymorphic markers between 2 or more lines. Query for QTL information. All query options use wildcard to retrieve all data. done

GDMS V1.1.1 - December 2012

  • Be able to edit part of a dataset instead of having to reload the complete dataset. Mark to confirm
  • Connection to Genealogy Management System (GMS) (browse and open a list; validate GIDs before loading data). done
  • Validation of uploads and QC eg: SNP convertor, Pedigree checking to ensure data conforms to IBP data standards. Done
  • SNP and MTA selection for genotyping project. done

GDMS V1.1.2 - June 2013

  • Conformity testing for genotype score

Genotyping ordering tool - June 2013

  • Prepare germplasm and marker lists for genotyping, include check as appropriate.
  • Send order to genotyping provider.
  • Accept genotyping results from the genotyping lab, allow quality check on the lab, and save genotyping data into the GDMS.

Genotyping Query Tools V1.1.1 - December 2012

  • Given a list of germplasm, query for the set of all markers at which any of the germplasm (or their maintenance neighbors) have been characterized. Visualize genotyping data of selected germplasm and markers (Flapjack) and download the matrix of germplasm X genotype data in various formats for further analysis. done
  • View the matrix of germplasm X untested markers and select and export sets of germplasm and markers for genotyping. done

Genotyping Query Tools V1.1.2 - June 2013

  • Analysis and decision support tools accessing data directly from GDMS via the IBP Middleware.
  • SNP Selector. Given a set of parental lines query genotypic data in GDMS to display all polymorphic makers and diagnostic markers. Give the user the option to manually select markers or automatically select a marker on a user-chosen window size. From this selection automatically produce the genotyping order form for KBioscience.
  • Mark to list additional tools to develop (similarity matrix, etc.)
  • Progeny Selector. A query interface able to query GDMS for a marker(s) correlated to a trait(s) of interest in making a cross and subsequently send the population for genotyping this marker(s) to KBioscience. On receipt of the genotyping results translate these into predicted phenotypes that are presented to the breeder in the field or greenhouse to select those individual plants that possess the favourable allele.

BREEDING VIEW GENSTAT
Breeding View - December 2012
Phenotypic analysis

  • Load phenotypic data for a particular study from the crop database. done
  • Quality control of phenotypes - descriptive statistics (including histograms; boxplot; normal plot). done
  • Single site phenotypic analysis (randomized block; incomplete block; resolvable incomplete block design). Done
  • Single site mixed model analysis with lattice and spatial adjustment. done
  • Multi-site phenotypic analysis of adjusted means from single site analysis.
  • Extend the Breeding View project file format to allow the integrated loading of data from Fieldbook into the Breeding View in the correct breeding pipeline. done
  • Extend the single-site field-trial analysis pipelines to handle multiple traits (with the "analyse-all" facilities that users requested earlier in the month) - check details with analyse all (H for each trait; genetic correlations). done

QTL analysis

  • Load genotypic data and reference map and phenotypic means. done
  • Quality control genotypes (genetic map, missing values; summary statistics; genotype data plot). done
  • Conduct QTL analysis (Simple interval mapping & Composite interval mapping). done
  • Export to Flapjack done
  • Extend the QTL pipelines to handle multiple traits (with the "analyse-all" facilities that users requested earlier in the month) - check details with analyse all (H for each trait; genetic correlations). done
  • Extend the field-trial pipeline for row-column analyses (including spatial covariance models). done
  • Improve the reports (and act on other feedback from Beijing) (tabular viewer output). done

Breeding View - June 2013
Phenotypic analysis

  • Store the means of the traits and other summary information in the crop database.
  • Line x Tester Analysis

QTL analysis

  • Add facilities for automatic export of information to OptiMAS via GDMS.
  • QTL x E analysis

Breeding View - RAP
R-scripts standalone -December 2012

  • Load phenotypic and genotypic data. done
  • Quality control phenotypes done
  • Single site analysis (complete randomized designs; randomized complete block designs; incomplete block designs; resolvable alpha designs and row-column designs). done
  • Multi-site phenotypic analysis (diagnostic plots, AMMI biplots; GGE biplots). done
  • GxE analysis. done
  • Quality control genotypes. done
  • QTL analysis (SIM & CIM). done
  • Single site mixed model analysis with lattice and spatial adjustment. done
  • QTL x E analysis. Done
  • Diversity analysis
  • Line x tester analysis done

January 2013

  • Proof of concept of Breeding View-RAP - Single trial phenotypic analysis pipeline (initially randomized block design)

R-Scripts in Fieldbook
December 2012

  • Single site mixed model analysis. done
  • Single site mixed model analysis with lattice and spatial adjustment. done
  • Multi site mixed model analysis. done
  • Multi site mixed model analysis with spatial adjustment. done
  • Line X tester mixed model analysis. done

Breeding Decision Tools
TableViewer V1.1.1 June 2013

  • Application to facilitate the annotation, sorting and viewing of phenotypic and genotype analysis results.

OptiMAS
Version 1.0 - December 2012

  • Prediction of genetic value of individuals based on QTL information. weighting of individual QTL. Graphical output generated of average molecular scores over cycles of selection. done
  • Selection of "best" individuals, based on several methods of selection, including truncation selection, weighted molecular score and a utility criterion. Visualization of pedigree information. In addition QTL complementation method added. done
  • Identification of best crosses to make at each cycle of selection. Half diallel between selected candidates or "better half" strategy which consists of avoiding crosses between the worst selected individuals. Graphical output of the crosses done. Possibility to cross one list of selected individuals with another using a factorial design. done
  • Stand-alone GUI and standalone computational modules - Steps 1-3 in OptiMAS. done
  • Addition of a quantitative score column that may correspond to a genomic selection prediction or a phenotypic value. Marc to follow up

Version 2.0 - June 2013

  • Development of a simulation procedure (step 4) to produce "virtual" next generation. Indication of the number of individuals needed in the next generation in order to reach the ideotype.
  • Computation of diversity score based on the pedigree (effective population size) to be included.

MABC application (MBDT)
December 2012

  • Import a list of germplasm. done
  • Create a target ideotype. done
  • Identify recurrent and donor parent. done
  • Select background and foreground markers. done
  • Determine the minimum number of individuals to be genotyped in each BC generation (Popmin). Done
  • Documentation and tutorial manual

June 2013

  • MBDT obtaining input directly from the database using the IB Middleware.
  • View individual chromosomes rather than all chromosomes together.
  • Improve zoom functionality and the selection of markers that are closely mapped on a chromosome.
  • Be able to weight in the selection heterozygous markers on one side of the QTL region.
  • MBDT linked to the middleware and able to import the relevant data from the crop and genotyping databases.

Selection Indices (standalone R-script application at this time)
December 2012

  • Import a file of QTL; genotypic, weights and phenotypes done
  • Phenotypic selection indices (Smith selection index, Restrictive Kempthorne & Nordskog selection index, Eigen Selection Index and Restrictive Eigen selection index) done
  • MARS Marker selection indices (Lande and Thompson selection index and the Molecular Eigen Selection Index done

June 2013

  • Ability to apply selection based on Genome wide selection.

Installer
Installer Version 1.1.1 (Schema 1, IBP middleware 1, release 1) December 2012

  • Install the system on a local computer (Windows XP to Windows 7) using separate installers for the central crop database and the IB Workbench. done
  • The database installers installs or updates MySQL in the IBP-CWS environment and installs or updates a crop database: GMS, DMS and the GDMS for the crop of interest. Multiple crops may be present in the system. Save the database connection details for use by the Workbench and tools.
  • A clean crop database available for installation for new crops. The installer enters the crop database description and central administrator.
  • The workbench installer installs or updates the Java environment, the R statistical package, the IB Middleware, the IB Workbench, the Breeding Manager, the Field Trial Manager, the R analytical Pipeline, Breeding View, ISMAB and OptiMAS as well as other tools which may be available and required. done

Breeding Planner
June 2013

  • Conventional breeding, MAS and MARS planning tool implemented
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