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Adding trials to Cassavabase



Accessing the Breeder Home Page


Go to:
Cassavabase Breeders Home

The link to access the Breeder's Home page is located under the "analyze" tab in the CassavaBase toolbar. You will be asked to sign in if you haven't done so already. To create an account see: Creating an account
However, only CassavaBase users with the account status of "submitter" may create trials. To learn how to change your account status from "user" to "submitter" visit the Managing Your Account page.


Breeders Home link.png


• Breeder Home Page:

Breeder Home Page.png



Adding Trials


Prerequisites:
To add a trial, all of your accessions should already exist in the database before you begin to design a trial. If you have accessions that are not in the database, see the instructions for adding accessions here:
Add stocks

A location for your trial should also exist in the database. If you need to add a location, see instructions for adding a location here:
Enter location data

Step 1. Create a list of accessions to use in the trial


To create a new trial a list of the accessions that are to be used needs to be created first. Lists can be viewed, created, and modified with the "lists" tool at the upper right of the screen. For more information on lists or to learn how to create and manage lists, click here.

Lists, creating trials.png

Step 2. Open the "Add trial" dialog


The dialog to add trials is opened with the button on the right side of the trials section on the breeders home page, "Add trial".
Add A Trial .png



Step 3. Specify year, location and description for the trial


A year, location, breeding program, and description of the trial are mandatory fields. In the standard workflow, check the box to create a trial using the trial design tool (this is selected by default).

Add a new trial window.png



Step 4. Select the type of experimental design.


Choose a design type from the pull-down menu.

Available design types include:

• Completely randomized screenshot
• Complete block screenshot
• Alpha Lattice Designs screenshot
• Augmented screenshot

Screen Shot 2014-01-24 at 11.53.06 AM.png


Options to customize plot naming are available. You may specify a prefix, starting number, and increment number. In this example, every plot would begin with "exampleprefix", the first plot would be #1000, and the second plot would be #1010.

custom_options.png


Step 5. Select the list of stocks.


Select the list of stocks to use in the trial. This list was created in step 1, here. If the list contains stocks that are not in the database, an error message will be displayed listing the incorrect stock names. For the augmented design, you must also select a list of stocks to use as controls.

Creating Trials - Lists to include.png



Step 6. Specify parameters of the experimental design.


Specify the parameters that are required for the selected experimental design.

Specify Parameters - Creating Trials.png



Step 7. Verify that the trial design is correct before adding it to the database.


Confirm that the trial design is correct. Press the view trial layout button to see the field layout.

verify_trial.png

The view trial layout button shows the plot names/numbers, stock names, block numbers, and rep numbers.

verify_trial_layout.png

Step 8. Confirm and save the trial.


Close the trial design layout window and press confirm if everything is correct.
The following message is displayed after the trial is saved.

trial_design_success.png




Alternative workflows


Adding an empty trial

...
Screenshot

Adding a trial from an uploaded file


A trial may be created from an uploaded file listing plot names, block number, rep number, and stock names (genotypes). These files may be created in a spreadsheet program (e.g., Excel, Calc, etc.) by saving in the appropriate delimited format. An option for direct uploading of Excel files may be available in the near future.
Screenshot


File requirements:

  • All stock names in the file must exist in the database. See adding stocks for more information.
  • The uploaded file should be tab delimited or comma delimited (CSV).
  • The first row (header) must contain the column names

Example:

plot_name
block_number
rep_number
stock_name
plot1
1
1
example_stockA
plot2
1
2
example_stockB
plot3
2
1
example_stockC


File validation:
In case of errors in the uploaded file such as missing or invalid data, a window will appear listing the specific errors in the file that must be corrected before a successful upload. Screenshot



Demonstration slides:



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