Current development activities:


General
  • Change Search->Phenotypes menu option name to “Accessions”
  • Identify users with programs, and add program info when creating accessions, crosses, trials, etc.*
  • On any page or pop-up box where a file upload option is available, have a link to a template file format.*

Arcane

  • Add type to lists

Fieldbook*

  • Fieldbook page from Tools menu below Breeder Home, above Barcode Tools.
    • Link to priority traits file compatible with fieldbook
  • Trial selection tool then download fieldbook-compatible file
  • Add upload for fieldbook-formatted file
  • Automatically load phenoype images to fieldbook

Crosses

  • Create progeny names using the naming convention agreement.*
  • Remove the trial drop down box and automatically create a new trial of type “cross.”
  • Filter obsolete crosses from the list.
  • Activate "add parent" feature on accessions.

Trials

  • Add a field to specify a unique name for the trial and report an error if not unique.*
  • Specify metadata when creating a trial
    • plot size (m^2) and density (stakes / m^2) or number of stakes
    • harvested area or harvested number of stakes
    • greenhouse?
    • irrigation?
  • Trigger verification of stock list on an action so that it happens immediately, and show throbber if there is a delay.
  • Implement a trial delete function.
  • Trial selection function:
    • Select a list of locations and a list of years. All trials having that combination of locations and years will be selected. This will be the default if the wizard functions as indicated below.

Phenotypes

  • Incoming measurements will have counts (e.g., of diseased plants) whereas the ontology trait is a proportion. Upload should include dividing the diseased count by the plot count to obtain the ontology trait proportion.* RESOLUTION: we decided to add count traits to the ontology. Unclear who exactly controls the ontology; we may need to have a group discussion about this.
  • Implement an upload removal (delete) feature that obsoletes the phenotypes and moves the uploaded file to a "deleted uploads" section.
  • Implement a download previous uploaded files feature.
  • Plot-level data:
    • We want analysis tools to work on the means of clones within trials, not on the plot level data itself
    • Upon upload, means of clones are computed as a function of the experimental design

Search Wizard

  • Add “cross” to the filter options.
  • Add check box that by default only shows accessions belonging to the user's program.
  • Wizard with lists: on the list dialogue box, add a "wizard" link to populate the first wizard selector with the contents of that list. List would have to be a trial, location, year, or trait list.
  • Under each drop down, put how many items are in the drop down. [Currently that is only given for the accessions or the plots]
  • Under each drop down, add an option that would allow you to add the selected items in that drop down to a typed list

Genomic Selection

  • Use lists!!
    • Provide a list of trials, a list of accessions, and a list of traits: those become the training population. I guess it should be possible to give this training population a name so that its results can be saved. You will probably need a default that indicates a minimum number of accessions evaluated for a trait in a given trial before that trial is used in the training population. By default, all markers available will be used, at least for now. Might want to have MAF filters and %missing data filters.
    • Provide a list of accessions for prediction

* High priority activities



Recent completed activities:


Crosses

  • Auto refresh the page after adding a cross. (Jeremy 7-30-13)

Phenotypes

  • Store the uploaded file location in metadata.* (Jeremy 9-11-13)
  • Store the uploaded phenotype files in an archive directory.* (7-31-13)
  • Display a list of uploaded phenotype files (Lukas 7-30-13)

Locations

  • Fix error when adding new location without coordinates. (Jeremy 7-31-13)
  • Fix: Can't use NaCRRI, Central Uganda as location in the crossing tool. (Jeremy 7-31-13)


Genomic Selection


  • Add genomic selection tool to the production database (Jeremy/Isaak 8-30-13)