- Welcome
- Introduction
- Publications and presentations
- Signing in
- System requirements
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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
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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?
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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
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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
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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
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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 Data Model
The GNomEx Class Diagram reflects the underlying data model. Some of the table and class names are a bit different than the common term — the data base from which GNomEx first originated used different terms and was primarily an experiment order tracking system. Here are a few of the names that diverge from the concept:Request — This is the Experiment class and table. Request was meant to describe the 'order'.
RequestCategory — Experiment Platform.
Application — Experiment Type.
How to Modify the DB Schema
Adding a column to a table (or add a table) in the database
- Add the column from the table in the upgrade sql script: gnomex_db_upgrade_to_##.#.#.sql. Remember that when you add a foreign key, you should be adding a foreign key constraint.
- Modify the CREATE_TABLE statement in gnomex_db_ddl.sql. (Don’t forget the foreign key constraint when you are adding a foreign key column.)
- If your feature depends on data being populated, add to the upgrade script (#1) and also add to gnomex_db_populate.sql
- (FOR HCI DEVELOPERS ONLY) Make the schema changes to hci-dbdev-08. Remember that when you are adding a column to add the column to the audit table. If you don’t have schema write permissions, you can email Tarik Courdy ( tarik.courdy@hci.utah.edu) or Andy Hofer ( andy.hofer@hci.utah.edu) if I'm not around and you need the column added to hci-dbdev-08.
When removing or renaming a column or table in the database
- Follow the steps provided above. If your transformations are more involved that a simple rename or remove, the upgrade script must be able to conserve the data already in production. The usual technique for this is to add new tables and then using a INSERT with SELECT to populate the new table before deleting the old one.
- These changes must be carefully coordinated with the deployment. So please add a note to the RELEASE_NOTES describing the schema changes that must take place during the deployment.
Syncing the test and production databases (FOR HCI DEVELOPERS ONLY)
When we are ready to deploy to production, I ask our DBA’s to compare the schemas on test and production. They have this cool tool that allows them to apply the changes to production. If these are new columns or tables, they can make this change during the day. If we are removing or renaming columns or tables, the changes have to occur when the server is down and we are ready to deploy. That is where the upgrade (gnomex_db_upgrade_to_##.#.#.sql) script comes in handy. I can look over the changes in the script to make sure that all of the schema changes are performed on the production db.