- Welcome
- Introduction
- Publications and presentations
- Signing in
- System requirements
-
How To
- Logging into GNomEx
- Submitting an experiment request
- Submitting a microarray hybridization request
- Submitting a sample quality request
- Submitting a sequencing request
- Requesting that microarray hybridization or sequencing be performed on samples previously submitted to sample quality testing
- Adding lanes to a previously submitted sequencing request
- Registering an external experiment in GNomEx
- Finding and viewing a summary of an experiment
- Editing an experiment
- Downloading experiment results
- Linking the samples from an experiment to their BST sample
- Viewing analyses
- Downloading analyzed data files
- Viewing a description of the materials and the methods used during processing of a specific kind of experiment
- Performing a search for experiments and analyses meeting a specific type of criteria
- Submitting a work authorization
- How pricing and billing works in GNomEx
- Adding a new price criterion
- Creating a new price sheet
- Creating a new price category
- Modifying an existing price sheet
- Modifying an existing price category
- Modifying an existing charge item
- Preparing and sending out invoices for clients
- Generating general ledger interface data for automatically billing university accounts
- Window, Tab, and Field Descriptions
-
GNomEx Error Messages and Information Windows
- Are you sure you want to delete all the hybridizations?
- Are you sure you want to delete all of the samples?
- At least one non-empty file must be selected in order for download to proceed.
- Please enter all of the required fields for the hybridization.
- Please enter all required fields for the samples.
- Please enter at least one search criterion.
- Please select a price category.
- Please select a price sheet.
- Remove all hybs currently showing in the list?
- Remove all samples currently showing in the list?
- The number of samples to setup has changed. Do you want to clear out the existing samples?
- The request has not been saved. Are you sure you want to quit?
- The request is now assigned to project.
- The webpage you are viewing is trying to close the window.
- Unable to generate GL interface. Cannot find approved folder.
- You are no longer logged on. Please logon again.
- Your changes have not been saved. Are you sure you want to exit?
-
Working With the List of Samples Submitting for Microarray Hybridization
- Adding a Sample to the List of Samples You Will Be Submitting for Microarray Hybridization
- Adding a sample to the list of samples you will be submitting for microarray hybridization that is similar to another sample already in the list
- Deleting a sample from the list of samples you will be submitting for microarray hybridization
- Deleting all of the samples currently included in the list of samples you will be submitting for microarray hybridization
-
Working With the List of Hybridizations By Requests
- Adding a hybridization to the list of hybridizations you will be requesting
- Adding a hybridization to the list of hybridizations you will be requesting that is similar to another hybridization already in the list
- Deleting a hybridization from the list of hybridizations you will be requesting
- Deleting all of the hybridizations currently included in the list of hybridizations you will be requesting
- Editing a hybridization from the list of hybridizations you will be requesting
- Working with the list of hybridizations you will be requesting
- The hybs tab (submit microarray hybridization request window)
- The submit microarray hybridization request window
- Submitting a microarray hybridization request
- Microarray hybridization requests
-
Specialized Role Topics
- Uploading a sample sheet
- Setting/changing the prices of a charge item
- Setting/changing the experiment type(s) associated with a price sheet
- Setting/changing the criteria by which a charge item will be applied to billing for an experiment
- The sample view tab (new experiment module)
- The hyb setup tab (new experiment request module)
- The hyb view tab (new experiment request module)
- The new project window
- The edit project window
- Adding a new project while you are entering a microarray hybridization request
- Editing an existing project while entering a microarray hybridization request
- Adding a new sample characteristic for annotation while submitting a sample hybridization
- Editing an existing sample characteristic for annotation while submitting a sample hybridization
-
Guides
- User Guide
- Experiment orders
- The foundation of GNomEx
- Experiments at a glance
- Submitting a HiSeq or MiSeq experiment order
- ABI Capillary (Sanger) Sequencing
- Checking on experiment progress
- Copy and pasting into samples grid
- Posting outside experiment data
- iScan experiments
- Downloading and uploading your data
- The download files window
- Downloading large data sets
- Downloading chromatograms
- Fast data transfer from the command line
- Troubleshooting guide for downloading
- Launching FDT with Webstart
- Uploading your data
- Annotating your experiment
- Associating experiment files back to the samples
- Sample annotations
- Copy and paste for the samples grid
- Bulk sample sheet import
- Analysis and data tracks
- Create an analysis
- Data tracks
- Disk usage
- Configuring GNomEx
- Context-sensitive help
- Customize the billing account fields
- Dictionaries
- Seq lib protocols and barcode schemes
- Configuring HiSeq rapid mode sequencing options
- Developer Guide
- Installation Guide
- Configuring GNomEx for FDT
- Configuring GNomEx to use LDAP Authentication
- Compiling and Building
- The Database Schema
- GNomEx Open Source
- Developer Documents
- Illumina HiSeq Realtime Info — The Metrix Server
- FAQs
- Demo
The Samples tab on the Submit Microarray Hybridization Request window is used to enter unique details about each of the samples that you are submitting for hybridization.
Show me the Samples tab. Most of the tab is taken up by a grid in which are listed each of the samples that are to be submitted (one sample per row in the grid).
Show me the Samples grid.
The number of samples displayed in the Samples grid when you first access this tab depends on the value entered in the first field (A. How many samples will you be submitting?) on the Sample Setup tab.
Show me this field. If you go back to the Sample Setup tab and change this value, then return to the Samples tab, you will be asked if you would like to update the number of samples displayed to reflect this change.
Show me the dialog. If you choose Yes, GNomEx will automatically add or remove the appropriate number of samples to/from the grid to match the current value in that field. However, when it does so, any edits you have made to the sample records already in the grid will also be lost. All of the values displayed for all of the samples in the grid will be reset to match the information entered on the Sample Setup and Annotations tabs.
You can add or delete samples (rows) in the grid independent of the value entered on the Sample Setup tab — see Working With the List of Samples You Will Be Submitting for Microarray Hybridization. Buttons are provided to the left above the grid for this purpose. The Add Sample button adds a new sample using all of the default values established for your samples except for the sample concentration (Conc.) column — see Adding a Sample to the List of Samples You Will Be Submitting for Microarray Hybridization.
Show me the Add Sample button. The Delete Sample button removes a selected sample from the grid — see Deleting a Sample from the List of Samples You Will Be Submitting for Microarray Hibridization.
Show me the Delete Sample button. The Replicate Sample button creates a new sample in the grid, using as its defaults the current values of a selected sample, regardless of whether these values match the defaults entered on the Sample Setup and Annotations tabs or not — see Adding a Sample to the List of Samples You Will Be Submitting For Microarray Hybridization that is Similar to Another Sample Already in the List.
Show me the Replicate Sample button. (These last two buttons will not function if a sample is not selected in the grid.) Another button (Clear All) is provided above the grid to the right to remove all of the samples currently listed in the grid — see Deleting All of the Samples Currently Included in the List of Samples You Will Be Submitting for Microarray Hybridization.
Show me the Clear All button. Sample data can be edited directly in the grid itself by clicking on the appropriate column and making the necessary changes — see Editing a Sample from the List of Samples You Will Be Submitting for Microarray Hybridization.
There are several columns that always appear in this grid. The first column is the Sample Name column. This column is used for entering an identifier for each of the samples being submitted. An identifier must be entered for every sample listed in the grid, as represented by the fact that the fields in this column that do not have a value entered are displayed in pink.
Every required field in the grid that is blank (whether it started as blank or you deleted the value that was in it) will be displayed in this pink color until a value is entered in it.
The next five columns all display values whose defaults are taken from parts B through F on the Sample Setup tab.
Show me these fields on the Sample Setup tab. Despite this fact, each of these columns is editable, meaning if the more general value entered on the Sample Setup tab does not apply to a specific sample, you can change that value here. If you go back to the Sample Setup tab and change a value, all of the samples will automatically be updated with the new value, including any that you had previously edited in the grid, so you should be aware of this if you move back in the wizard to make changes. These five columns include the type of sample being submitted (Sample Type), the kind of Organism the sample was collected from, what kind of organic material was collected from that organism (as the more specific Source of the samples being submitted), the sample concentration (Conc.) in ng/µL, and the nucleic acid purification/extraction method used (Sample Prep Method). These five fields are also required fields, although by default, they should already have a value entered in them when you first access the tab.
The final standard column in the grid is the Description column, used to enter a text description or other applicable note about each sample. This field is optional (meaning it may be left blank). Other columns may also appear in the grid. The appearance of these additional columns depends on the settings selected on the Annotations tab — see The Annotations Tab (Submit Microarray Hybridization Request Window). Of special note is Treatment column which will appear in the grid if any text is entered in the large text field (B. Describe in general terms how the sample(s) differ) in part B of the Annotations tab.
Show me this field. If the column is used, the text entered in that field serves as the default value in the Treatment column for all of the samples in the grid.
There are three buttons along the bottom of this tab. The < Back button in the bottom center of the tab automatically moves back to the Annotations tab — see The Annotations Tab (Submit Microarray Hybridization Request Window).
The Next > button automatically selects the Hyb setup tab, although this button only becomes active if all of the required fields in the grid have a value entered in them — in other words, there are no fields colored pink in the grid — see The Hyb Setup Tab (Submit Microarray Hybridization Request Window).
The Cancel button in the lower right corner of the window closes the window without submitting your hybridization request.
If you click on this button, all of the data entered on the window will be lost. Before closing the window, however, a dialog opens to verify that you really want to cancel your request.
Click Yes on this dialog to verify that you really want to close the Submit Microarray Hybridization Request window without submitting a request or No to return to the window and continue with your submission.