Many aspects of GNomEx are configurable through dictionaries. To edit dictionary entries, click on the 'Configure…' link in the navigation bar and select the 'Add/Edit Dictionaries' link. The dictionary editor displays all of the different dictionaries in a tree. Click on the folder to see a detailed list of the dictionary entries. Click on an individual node in the tree to edit a particular entry. Use the + and — buttons to add or remove a particular dictionary. If the dictionary entry is used by any reference tables, foreign-key constraints in the database will prevent it from being deleted. Instead, you will need to uncheck the isActive flag on the dictionary entry.

The following sections describe key configuration points accomplished through dictionary editing.

System Wide Properties

There are a number of configurable properties that you need to set for your installation. Scroll in the left-hand tree to find the node called 'Admin — Property'. Review the entries and make sure you modify the following properties to match your environment.

General installation properties:

1. production_server: The DNS name or IP address of the production app server.
2. core_facility_name.
3. contact_email_core_facility: The email address that appears on the about page is used as the sender email for auto-generated emails.
4. contact_name_core_facility
5. contact_phone_core_facility

These are all of the directories on the file system for storing GNomEx data.

1. experiment_directory
2. analyis_directory
3. flowcell_directory
4. lucene_index_directory
5. lucene_experiment_index_directory: This is the directory that will contain the lucene experiment index.
6. lucene_analysis_index_directory
7. lucene_protocol_index_directory
8. temp_directory

A number of properties are used to configure the instructions that appear on the 'Submit Request' window:

1. qc_instruction
2. workauth_instructions
3. illumina_barcoding_note

Application Theme

For Illumina Seq experiment orders, the submitter will need to specify the kind of sequencing application performed (example: RNA Seq, ChIP Seq, etc.) Since there are many sequencing applications, the application theme is a way to group similar sequencing applications together.

Billing Period

These define each billing period in your system. The default install comes with a billing period for each month. If you intend on using the GNomEx Billing, please make sure that all of the billing periods for the upcoming year are specified.

Billing Category for Microarray Product

This is a way to categorize microarray slides for billing so that the prices can be defined for a certain category of microarray slide. These categories appear in a dropdown on the Slide detail window.

Billing Category for Microarray Analysis

Use this dictionary to categorize the charges for microarray analysis. For example, there may be a standard microarray analysis charge for expression arrays and a different charge for CGH arrays. These categories appear in a dropdown on the Slide detail window.

Core Facility

You can create multiple core facilities in GNomEx. Go to Manage Dictionaries (Menu item Config -> Manage Dictionaries). Click on the 'Admin — Core Facilities' folder. GNomEx ships with a default core facility. You can add other core facilities here. The next release will allow you to name these whatever you want, but for now, there are only 2 names that are supported:

1. Microarray and Genomic Analysis
2. DNA Sequencing

You have to use these names to get the base functionality to work for the supported workflows.

1. Microarray and Illumina workflows are supported under the 'Microarray and Genomic Analysis' core facility.
2. Capillary Sequencings, Fragment analysis, Mitochondrial DLoop Sequencing, and Cherry Picking are supported under the 'DNA Sequencing' core facility.
3. Coming in the next few months is support for the iScan and Ion Torrent workflows. Soon to follow will be support for the Sequenom MassArray platform.

Illumina Oligo Barcode

1. Illumina Barcode Scheme: Define a group of barcode tags (of same length) to be used to multiplex runs.
2. Illumina Barcode: Define each unique barcode (sequence) tag.
3. Illumina Barcode Scheme Allowed Platforms: Define the experiment platforms that can utilize the barcode scheme.

Instrument

Define your different HiSeq and MiSeq Illumina instruments here. When a flowcell is created in GNomEx, a dropdown will list these instruments so that GNomEx can keep track what instrument the sample was sequenced on.

Sample Bioanalyzer Chip Type

If your site uses Bioanalyzer assays for Sample Quality, define the different chips offered.

Sample Concentration Unit

Define the different unit of measures for sample concentration here.

Sample Source

Deprecated. Please configure a sample annotation instead.

Submission Instructions

If you have a instruction pages that should print with the order form, use this dictionary to define what document should be attached to certain kinds of experiments. For example, you may want to have instructions for Illumina HiSeq experiments that are different than the submission instructions for Microarray experiments. You will need to create HTML documents that are places in the doc directory of the gnomex web application that correspond to the documents defined here.