Project and Sample Set Up

Instrument Configuration and Project Options

Results Analysis

Fragment Collection

File Storage and Archiving

Other Features

Project and Sample Set Up

Open the project in WAVEMAKER Software and then select the Clear Results button on the toolbar. A message will warn you that you are removing results from the project. Press OK. Do not select the Save icon or use the File | Save command or the old project will be overwritten. Select the Save As command from the File menu and enter a new name before selecting OK.

There are three sets of default gradient parameters used for new samples. These are selected by 'Caution Level' and they are labeled Fast, Normal and Cautious. The parameters associated with each caution level are determined from the Gradient tab on the Project Options dialog. To change the defaults for your project, enter the new values and press OK. Samples created from now on will have the new defaults. Remember that the caution level selected when the Project Options dialog is closed becomes the default caution level for new samples. To use the defaults for all new projects, select the Save as Project Default box before pressing the OK button.

This depends on how the individual samples differ. For screening of large numbers of identical samples, i.e. mutation detection in the same fragment, a single method can be created and saved to disk. This method can then be set for a large number of samples by filling the Method Name column. The Sample Name can be specified before filling with the Method. The Sample Name can also be filled. See the on-line help and the user manual for more information about Sample Table editing features.

Click on one of the cells in the Sample Table to give it the focus. You can then move from cell to cell using the cursor (arrow) keys. When you move to a drop-down list, a button with a down arrow appears. Pressing Alt + down arrow drops the list and you can then select an item using the up and down arrows. To select the entire row, press Shift + left or right arrow. To select a group of rows, press Shift + up or down arrow. Pressing F2 will open the context menu for copying and pasting or filling. See the on-line help or user manual for more keyboard functions and tips on setting up samples.

The Instrument Configuration dialog shows which detectors are physically on the instrument. These settings should not be changed unless the detector is actually disconnected. The Project Options dialog allows you to disable a detector for the present project. The detector may be connected and powered up, but data will not be collected from a disabled detector. It is possible to mix samples using different detectors within a single project by changing the individual sample settings on the Run Information page. Select the specific sample in the Sample Table and switch to the Run Information page to review the settings. Press Apply after making changes.

The best way to set up a table of samples without being at the instrument is to use the Desktop version of WAVEMAKER 4.0. The Desktop version creates the same project files used in the System version. Otherwise, it is possible to copy the Sample Table from WAVEMAKER Software into a spreadsheet program and make changes in most fields. Care should be taken when changing the information in the drop-down lists, i.e. Application Type, Sequence Name and Method Name. The spreadsheet can be saved and used as a template for new tables by copying it back into the Sample Table.

Assuming you have checked the Edit Table box to allow changes to the gradient table, you must press the Apply button to confirm the changes. If you uncheck the Edit Table box before pressing Apply, the gradient parameters (gradient duration, equilibration duration, etc.) will be reapplied to the gradient.

It may not have been properly entered before the cursor was moved. Normally, moving to another cell of the Sample Table confirms the entry. To ensure the correct value, press the Enter key.

Instrument Configuration and Project Options

The Project Options determine if the detector enabled boxes on the Run Information page can be changed. If a detector is disabled from the Project Options dialog, that box will be grayed out in Run Information. If the method originally had the detector enabled and then the project options are used to disable the detector for new samples, the box will be checked and disabled. Enable the detector in the Project Options and then uncheck the box on the Run Information page before disabling the detector again.

Results Analysis

The display scales for each chart can be set differently. To change the default values, right-click on the chart and select Chart... to open the Chart Options dialog. Select the Axes tab and enter the values. Check the Save As Default box and press OK. The defaults will be used for all projects. Be aware that the Autoscale to Data option on the Results Options dialog overrides the axes defaults if it is checked.

If a sublist has any data loaded, it will be added to the Sublist Reports whether it is shown on the Results page or not. To remove it from the reports, close the Print Reports dialog and clear all the data from the other sublist before returning to print the reports.

Both a chart title and comments for each result trace are available. To add a chart title, right-click on the display to open the context menu and select Chart.... The Chart Options dialog will open and the chart title can be entered on the Chart tab. To add comments for each trace, type the text into the Comment field in the Results grid. The Comments field may be hidden until you scroll the grid to the left. The comments can be used in place of the sample name when the chart legend is enabled. Open the Chart Options dialog and select Comments instead of Sample Name, check the box to show the legend and press OK.

If one of the dialogs, such as the Project Options dialog, is still open when an injection is completed, the results for that sample will not be added to the Results page until the dialog is closed. It is recommended that the instrument configuration and project options be reviewed and changes made before starting to run samples.

Fragment Collection

Saving the project also saves the fragment collection job file. The job file contains all of the collection tables and all of the result tables for the associated project.

Select the line using the mouse and press the Delete key. If the line was created with one of the multi-vial modes, the following vials will be renumbered but the other settings will be unchanged.

The data trace in the chart will have a blue highlight between the markers when WAVEMAKER Software determines that the region can be collected using the event parameters. If a blue highlight is not visible, the event will not be added to the table. For Threshold detection, make sure the threshold line is below the region to collect. For Peak, Leading and Trailing edge detection, check the slope value selected. The value may be too high for the desired peak. Press Update Chart after changing the value.

File Storage and Archiving

The location of the sequence file depends on where the project file has been saved. If the project file has never been saved, a new sequence entered into WAVEMAKER Software is saved into the Sequences folder under the WAVEMAKER 4.0 folder by default. If the project has been loaded first from disk, the new sequence file is kept in memory and then saved with the project file the next time the project is saved. Note that when the project is saved, any sequences opened into the project from other folders are also saved to the project location.

A sample must be completely specified for it to be saved into the project. At minimum, an application type must also be set after the sequence is entered for the sample to be complete. If only a sequence is entered for the sample row, it will be cleared when the project is reloaded. The new sequence file will still be saved with the project when the project is saved, but it will not be added to the Sequence File drop-down list when the project is reloaded unless the sample is completed. The sequence can still be opened into the project for later use and it will then be added to the Sequence File list.

Methods are saved to the same folder where the current project file is located. If a new project file has not been saved, the method will be saved to the location of the last project file opened in WAVEMAKER 4.0. This behavior is provided to make it easier to keep methods and projects for a specific application together. To save the method in another location, select the desired folder while using the Save Method dialog or save the new project to the desired folder before saving the method.

Methods are saved to the same folder where the project file is located by default. If the project file has not been saved, the method will be saved to the last project file opened in WAVEMAKER 4.0. The method can be saved to another location by selecting the desired folder in the Save Method dialog. If the method is saved to a location other than the default folder, it will not appear in the Method Name list on the Sample Table or in the View Methods dialog as these tools only look in the default location. Open the method from the File menu to copy it to the default location and bring it into the project.

When a project has been archived or moved to a new location, method and sequence files used in the project should be archived to the same location also. When a project is loaded, it is assumed that any saved methods have been saved with the project. Sequence files can be located either with the project or loaded from the Sequences folder in the WAVEMAKER 4.0 folder. Transgenomic, Inc. recommends that the project file be saved in the Application Folder used for the project. The project and its associated methods can be more easily archived this way.

Place the sequences into the Sequences folder under the WAVEMAKER 4.0 folder and they will be added to the Sequence File list for all new projects automatically. Note that if the project files are saved to different locations, the complete set of sequences will also be saved with the project. This can result in a large number of duplicate copies unless the projects are being saved into the same folder.

This can be done if projects are kept in a single folder. Place the method files in the folder and they will be added to the Method Name list for all new projects automatically. If the methods do not appear in the Method Name list, open a project from the folder before pressing New Project. Transgenomic, Inc. recommends that the project file be saved in the Application Folder used for the project. The project and its associated methods can be more easily archived this way.

Other Features

Select any vial on the plate diagram and the vial position will be indicated in the status bar at the lower left. The format is row & column: vial number.

The Estimated Run Time is adjusted as samples are run depending on the type of sample and options such as equilibration, etc.