Introduction

The Set Generation Module (SETGEN) is an application under the ICIS Germplasm Management System (GMS). The software produce lists of germplasm descriptors for breeding, evaluation, or any other purpose.

The functions of SETGEN are:

  • to produce lists of germplasm descriptors defining new crosses or selections, or for evaluation, distribution, or management,
  • to retrieve GMS details of existing germplasm needed for field book construction, and
  • to record all GMS details of new germplasm generated by the list process.

SETGEN - Set Generation Module

SETGEN is an application designed for plant breeding and germplasm evaluation. Breeders usually start with a list of potential parents (i.e., a list of rice varieties, each known for specific traits). From this list, the breeder selects male and female parents and makes a crossing list. After crossing and selfing, selections are made from one list and moved to the next list for the next generation. This process continues until successful fixed lines are derived.


Configuration Settings

The ICIS.INI file found in your ICIS installation contains configuration settings which you can specify accordingly. See the table below for the description of settings and its values.

Key | Valid Values | Remarks
CROP | CROP NAME (RICE) | Id CROP=BW (bread wheat), group names are constructed using abbreviated cross names instead of conventional purdy cross expansions.
STANDARDIZE | YES, NO (YES) | If STANDARDIZE=YES, a name is first converted to the ICIS naming convention before it is added to the local GMS.
DEFCTYID | Long Integer (171) | The Location ID of a country whose locations are initially displayed in the Select a Location window. Valid country ID values currently range from 1,2,..,267.
DEFLOCID | Long Integer (9000) | The Location ID whose name appears as a specified default location in windows wherein location may be specified.
GENERATIVEMETHOD | Integer (101) | The generative Method ID of a default method to appear in the Generate Crosses window.
DERIVATIVEMETHOD | Integer (205) | The derivative Method ID of a default method to appear in the Advance a Line One Generation window.
CHECKDERIVATIVE | Integer (10) | If CHECKDERIVATIVE<10, a derivative name is verified for its existence in the GMS. If a name exists, a query appears with several options for the user. Otherwise, if CHECKDERIVATIVE>=10, no checking is done; a derivative is automatically added to the local GMS, whether or not the name already exists.
PNAME_IF_UNKNOWN_GRP | YES, NO (NO) | If PNAME_IF_UNKNOWN_GRP=YES, a germplasm whose group is unknown is displayed as ‘?/? [preferred name]’; otherwise group germplasm is ‘?/?’.
NO_LISTNAME | YES, NO (NO) | If NO_LISTNAME=YES, the default seed source value is displayed as ‘entry code’; otherwise seed source is displayed as ‘list name-entry code’. The default value appears only when an entry is selected from the Browse window.
AUTOCOMMIT | YES, NO (NO) | If AUTOCOMMIT=YES, each change SetGen makes to the local database is automatically saved immediately after the change is done; otherwise, changes have to be made by clicking on the <List><Save> menu.
MULT_ENTRYCD | YES, NO (NO) | Used in the Advance a Line One Generation window. If MULT_ENTRYCD=YES, each derivative has an entry code value as ‘entry code-plant no.’; otherwise, each derivative has the same entry code value.
UPD_GRP | YES, NO (NO) | If UPD_GRP=YES, group germplasm values of entries added by selecting from the Browse window is automatically updated to its cross expansion; otherwise, the group value from the Browse window is copied to the Edit window.
METHODGRP | METHODS.MGRP values (S G) | The group of methods retrieved from the GMS METHODS table and displayed to the user to select from. The default group of methods retrieved are selfing (S) and general (G) methods. Each group of method must be separated by a space. Other groups as cloning (C) and open pollination (O).
MULT_SAMENTYPE | YES, NO (NO) | If MULT_SAMENTYPE=YES, a germplasm can have several names of the same nametype.
MULT_SAMEATYPE | YES, NO (NO) | If MULT_SAMEATYPE=YES, a germplasm can have several attributes of the same Attribute type.
MAX_LISTNAMECHAR | Integer (48) | Number of LISTNAME characters. The maximum value is 48.
AUTO_GENLSTNAMESCALEID | Integer (0) | ScaleID of the SQL to be used to generate the ListName.
AUTO_GENFUNCCODE | CODE | Generate Code String used to identify the algorithm to use to generate ListName.
ENABLE_INV | YES,NO (NO) | Flag whether to enable InTrack(ICIS Inventory Tracker).
MULT_SOURCE | YES,NO (NO) | Used in the Advance a Line One Generation window. If MULT_SOURCE=YES, each derivative has an source value as ‘source-plant no.’; otherwise, each derivative has the same source value.
AUTOFILLVCOL | YES,NO (NO) | Flag to automatically retrieve contents of virtual columns.
HELPFILE | help File Path | The file path of the Helpfile to use.
CHECK_NTYPE | Integer (0) | Flag to provide check for the existence of a Name TYPE id specified for each germplasm whenever a list is being closed.
TEXT_SUFFIX | String | The String to use as suffix for textlines whenever a fill with sequence is done.


Getting Started

Starting SETGEN module

You can run the SETGEN module from the ICIS Launcher menu.

If the user credentials stored in your ICIS.INI are invalid, you will be prompted to type an ICIS username and password as shown below. Enter the correct values and click the "OK" button.

SETGEN Authorization screenshot

Note: The SETGEN application will run only after successful authorization. An error will occur if the any of following is true:

  • An invalid username or password is entered. You will be prompted to re-enter the username or password.
  • An ODBC error occurs. The user does not have write privileges on the computer where either the central or local database resides. If the warning refers to the central database, ignore the warning and continue the session. If the warning refers to the local database, the user must exit the program and request for write privileges to the computer. A warning appears only if a computer can control user-access level, such as Windows NT.
  • Username is not an authorized local GMS user. A popup message will appear that says
    "Setting local GMS to READ-ONLY. The logged on GMS user cannot make any changes to the local database. Name searching will only be allowed." Click the "OK" button to continue.
The user can abort SETGEN before a successful log on. Simply click [Cancel]. The session will immediately terminate.


Overview

Graphical User Interface Overview

SETGEN’s graphical user interface is called List Manager. This is where germplasm lists are viewed, generated, and manipulated. It consists of five sections.

SETGEN sections

Menu
The menu is one of the method of executing SETGEN functions.

Toolbar
The toolbar contains commonly used SETGEN functions.

List Selector
The List Selector displays germplasm lists. Selected list are opened in either the Browse Window or Edit Window.

Browse Window
The Browse Window shows the entries of the selected list in "browse mode" which means no edits is allowed.

Edit Window
The Edit Window shows the entries of the selected list in "edit mode" which means entries can be manipulated.


SETGEN Menu

The main menu is located at the upper leftmost part of the List Manager.

Main Menu

The table below shows the short description and contents of each menu items.
Note: The corresponding shortcut to each item is in brackets (i.e., [..]), given after the description. Press the [Alt] key and the keys that follow. The [Alt] key must be kept pressed always while the other keys are pressed successively.

Item | Description
List Submenu | Contains operations to manipulate lists.
New | Generate a new list ot Folder. • List - Create a new List in the Edit Window [Alt-L-N-L] • List - Create a new Folder [Alt-L-N-F]
Open | Open an existing list in the Edit window [Alt-L-O]
Browse | Open an existing list in the Browse window [Alt-L-B]
Save | Save a list currently open in the Edit window [Alt-L-S]
Export As | Export a list highlighted in the List Selector in a specified file format. File formats to export to are: • XLS Excel File Format [Alt-L-E-X] • INI File Format [Alt-L-E-I] • TAB Delimited Text File [Alt-L-E-T] • Fixed Format ASCII File [Alt-L-E-F] • XLS Fieldbook [Alt-L-E-B]
Close List | Close a list, which can be: • Edit [Alt-L-C-E] • Browse [Alt-L-C-B] • Both [Alt-L-C-O]
Add Virtual Column | Add a virtual column, which can be: • Edit [Alt-L-V-E] • Browse [Alt-L-V-B] • Both [Alt-L-V-O]
Import List | Import germplasms into a list [Alt-L-I]
Add Checks to List | Add or Insert check germplasms into a list [Alt-L-C]
Delete List | Delete a list highlighted in the List Selector from the local GMS [Alt-L-D]
Hide/Unhide List | Show/hide lists in/from the List Selector [Alt-L-H]
Auto Commit | If checked, each change made to the local GMS is immediately saved. [Alt-L-A]
Print | Print: • List contents [Alt-L-P-L] • Characteristics of each list entry [Alt-L-P-C] • Both, list contents and corresponding characteristics [Alt-L-P-B]
Exit | Terminate SETGEN session [Alt-L-X]
List Entry Submenu | Contains interactive operations to add a list entry. [Note: A list must be currently open in the Edit window for List Entry operations.]
Add an Entry | Open the <Add a List Entry> window to specify an entry to add [Alt-N-A]
Generate a Cross | Open the <Generate Crosses> window to add a generative cross to the local GMS and the currently open list [Alt-N-C]
Advance a Line | Check to automatically save all transactions made [Alt-N-V]
Find | Search for a value in any of the columns of a list open in the Edit window. [Alt-N-F]
Edit Submenu | Contains operations that modify the contents of a list open in the Edit window. The items in the Edit submenu can also be displayed by right clicking on the mouse while the mouse is pointed over the Edit window.
Edit Entry Fields | Edit the fields of a highlighted entry [Alt-E-E] or <F2>
Remove Entry | Remove the highlighted entry from the list [Alt-E-R]
Add Blank Entry | Add a blank entry to the end of the list [Alt-E-A]
Replace Entry | Replace highlighted entry with another entry [Alt-E-Y]
Cut | Cut to clipboard one or more tagged entries. [Alt-E-T] or <Ctrl X>
Copy | Copy to clipboard one or more tagged entries. [Alt-E-C] or <Ctrl C>
Paste | Paste entries in clipboard before tagged entries in the list, or at the end of the list. [Alt-E-P] or <Ctrl V>
Random Sort Entries | Sort the entries of a list randomly. [Alt-E-S]
GMS Submenu | Contains operations to view or modify a GMS record. The items in the GMS submenu can also be displayed by right clicking on the mouse while the mouse is pointed over the Edit window.
View Characteristics | View characteristics of a highlighted entry [Alt-G-V]
Edit Germplasm in GMS | Modify characteristics of a GMS record [Alt-G-E]
Delete Germplasm from GMS | Delete a GMS record [Alt-G-D]
Replace Germplasm from GMS | Replace a GMS germplasm record with another one [Alt-G-R]
Batch Submenu | Contains batch mode operations.
Add Entries | Generate a list of entries [Alt-B-A]
Generate Crosses | Generate a list of new crosses [Alt-B-C]
Generate Derivatives | Generate a list of new derivatives [Alt-B-D]
Generate GIDs | Generate GIDs for a list of entries {Alt-B-G]
Matrix Crossing | Generate new crosses by a matrix [Alt-B-M]
Relative Search | Search for germplasm relatives [Alt-T-R]
Help Submenu | Contains version information.
Help | Open the on-line help. [Alt-H-H]
About | Display the current version. [Alt-H-A]


SETGEN Toolbar

The main menu is located at the upper leftmost part of the List Manager just below the main menu. It consist of buttons that corresponds to commonly used actions in SETGEN.

Toolbar


List Selector

The vertical window on the left area of the List Manager is the List Selector. It displays germplasm lists sorted in alphabetical order.

List Selector

Functions and Operations:

Open a list in Browse Window
Highlight a list in the List Selector then choose the menu item [List]->[Browse]. Alternatively, you can highlight a list in the List Selector and right-click to open the context-sensitive menu and choose [Browse].
If a selected list is currently open in either Browse or Edit window, a warning message appears.

Open a list in Edit Window
Double-click a list from the List Selector and its contents will be displayed in the Edit window.

View a list characteristics
Highlight a list in the List Selector then right-click to open the context-sensitive menu and choose and [List Characteristics].

Delete a list
Highlight a list in the List Selector then choose the menu item [List]->[Delete List]. Alternatively, you can highlight a list in the List Selector and right-click to open the context-sensitive menu and choose [Delete List]. The list must not be open in either Browse or Edit window to be able to delete the list.

Sort a list
A list can also be sorted by type. Check the "Sort By Type" checkbox at the bottom of the List Selector to sort the lists by type. Uncheck the box to sort by name.

Hide lists
The List Selector can be configured which lists will be displayed. Click the menu item [List]->[Hide/Unhide List]. Alternatively, point the mouse over the List Selector and press right click then select [Hide/Unhide List]. The form below appears.

Check the list you want to be displayed and uncheck the list you want to hide. Click the [Close] button. The List Selector will reflect your choices.

Invoking the List Selector context menu
Right-click on a list to access the context menu designed for the List Selector.


Browse Window

The Browse Window is located at the top right of the List Manager. Its primary function is to be a source of germplasm entries for the Edit Window. List entries in the Browse window cannot be edited.

Browse Window

Functions and Operations:

Open list in Browse Window
Highlight a list in the List Selector then choose the menu item [List]->[Browse]. Alternatively, you can highlight a list in the List Selector and right-click to open the context-sensitive menu and choose [Browse].
If a selected list is currently open in either Browse or Edit window, a warning message appears.

Adjust column width
The width of each column can be adjusted by dragging the column border of the column title.

Adjust Browse Window height
The height of the entire Browse window can adjusted dragging the bottom border.

Tag list entries
To tag a list entry in the Browse window, click on a record. An entry is identified as tagged if the last column has 'x' symbol. Similarly, you can remove the tag by clicking on the entry.
The purpose of tagging is to identify which entries will be processed. For example, tagged entries can be added to the Edit window. It can also be used to generate new germplasm, or have its germplasm characteristics viewed.

Sort list entries
To sort list entries by column, right-click on a column heading to open the context-sensitive menu and choose [ascending] or [descending].

Close Browse Window content
To close the list loaded in the Browse window, use the menu item [List]->[Close List]->[Browse]. Alternatively, you can right-click on the Browse window area to open the context-sensitive menu and choose [Close List].

Invoking the Browse Window context menu
Right-click on a list to access the context menu designed for the List Selector.


Edit Window

The Edit window is located at the bottom right of the List Manager under the Browse window. This is the main workspace that is used for creating or manipulating germplasm list entries.

Edit Window

Functions and Operations:

Open a list in Edit Window
Double-click a list from the List Selector and its contents will be displayed in the Edit window. If there is a previously opened list, you will be prompted to save changes.

Adjust column width
The width of each column can be adjusted by dragging the column border of the column title.

Adjust Edit window height
The height of the entire Edit window can adjusted dragging the bottom border.

Create a new list
To create a new list, use the menu item [List] -> [New] or you can right-click on the Edit Window area to open the context-sensitive menu and choose [New]. If there is a previously opened list, you will be prompted to save changes.
Enter the list name, select the list type, specify a list date, and a list description or title in their appropriate places. The list name is required while all other fields are optional.

Specify a naming convention
To assign entry code values automatically, check the "Entry Code Naming Convention" checkbox. This will invoke the form shown below.

Start Constant / End Constant
Consist of any combination of alphanumeric characters and/or blanks, up to a maximum length of eight.
Next Integer
The numeric field width default value is the number of digits in the next integer field. A value larger than the number of digits can be specified. The next integer value automatically increments by one, if a value other than zero is specified.
Include Leading Zeros
The include leading zeros check box is initially disabled. If an integer greater than zero is specified in the "Start Constant" or "End Constant", it becomes enabled. To display entry code values in fixed format, check this checkbox.
Numeric Field Width
The Numeric Field Width is initially disabled. If an integer greater than zero is specified in the "Start Constant" or "End Constant", it becomes enabled.
Note: The maximum length an entry code value can have is 11. Any value whose length is greater than 11 is truncated.

Save a germplasm list
To commit changes to the database, use the menu item [List] -> [Save]. There is no need to do this action if "Auto Commit" is checked in the configuration file.

Save as a new list
To save an opened list as another list, change the list name and modify other list characteristics as desired then use the menu item [List]->[Save As].

Export a list
A list may be exported to various external file formats.

  • MS Excel Spreadsheet (*.xls)
  • INI file format (*.ini)
  • TAB delimited textfile (*.txt)
  • fixed format textfile
  • MS Excel Spreadsheet (Fieldbook Template) (*.xls)

To export the list that is loaded in the Edit Window, right-click over the Edit window area to open the context-sensitive menu and select [Export As]->[export format].
To export a list in the List Selector, highlight the list from the List Selector. Right-click over the List Selector area to open the context-sensitive menu and select [Export As]->[export format].
In both cases, you will be prompted with a file dialog box to specify the destination of the file.

Print a list
To produce a print-out of a list, use the menu item [List]->[Print]->[Print Option...]

Close Edit Window content
To close the list loaded in the Edit Window, use the menu item [List]->[Close List]->[Edit]. Alternatively, you can right-click on the Edit Window area to open the context-sensitive menu and choose [Close List].


View Germplasm Characteristics

The germplasm characteristics of list entries can be displayed to be able to see the complete information on the germplasm.
To do this, tag entries then right-click and select [View Characteristics].

Click on the "Play" button for a demonstration


Select Germplasm

Whenever a germplasm name is specified and multiple records are found in the database, the "GMS Search" form will appear. To select the germplasm that perfectly describes the name you specified, click on the record and click on the "Select" button.

Click on the "Play" button for a demonstration


Select Location

Location Selector Window

A location can be specified when specifying characteristics of a cross or line, or when changes to a germplasm record, i.e., edit, delete, or replace, are made. A location can be specified in a window where a button appears beside a location field. To specify a location, click . A window, similar to Figure 1.4.7 appears. The locations displayed in the listbox are the locations of a specified country. The four most recent locations selected are displayed in the shaded box below the listbox. To retrieve locations, select the desired country from the country pick list. If the location ID of the desired country is known, it can be selected from the location ID pick list instead. Locations in the selected country are displayed in the listbox with the country itself as the default. To select a different location, scroll the list with the scroll bar, or type the name of the location in the location field. Typing a name will cause the highlighted value to change to the one nearest the typed value. There is no highlighted value if no locations match a typed name. To select a location, follow any of the steps described below: (1) Double click on a desired location in the listbox; or (2) Highlight a desired location and click ; or (3) Type the complete name and click . [Note: A location name which has been typed must match exactly a location in the listbox. Otherwise, an error message appears.]; or (4) Select from the list of recent locations by double clicking on the desired location in the box; or (5) Change a specified location to an unknown one. Clear the location field and click . The previously specified location is removed.