1. Configuring the Main Admin Panel
Core LIMS Training:
Configuring the Main Admin Panel
Here are just a few slides that highlight key concepts for configuring objects in the LIMS. Click on a slide whenever you are ready to move to the next page.

2. Review: LIMS Architecture
Super Types: The highest-level concept for objects that are tracked within the LIMS. Essentially, a broad category that relates Entity Types together.
Examples: Container, Assay, or Sample.
Entity Types: Sub-categories or record types that can be differentiated by the data fields (or attributes) that are defined for each.
Examples: 96 Well Plate (Container), Biochemical Dose-Response (Assay), or Small Molecule (Sample).
Entities: An individual record that stores the actual data values. Entities are unique and are each assigned a specific barcode.
Examples: Microtiter Plate #1 (Container), Receptor Target X Dose-Response (Assay), or Small Molecule #1 (Sample).
As a quick review, you need to understand that Core LIMS is built on 3 types of objects organized into a hierarchy. There are Super types which are the highest objects. These are really an object category. Under each super type you can have one or more Entity types. Another way to describe these objects is to call them the record types. We define the data that needs to be collected for the records on the entity types. The lowest objects are the entities, or individual records. Here is where we collect the data values for each record.
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3. Review: Key Terms
Application: a logical unit of objects and functions grouped together by a set of menus and a dashboard home page; users can access them from tiles on the home page or from the application menu if they have permission
Attributes: these are the data fields that collect values for each record; they are defined on the entity types
Associations: these are links to other records in the system that already contain some relevant data; these relationships are defined on the entity types
A It is also important that you have a solid understanding of these 3 key terms. We will discuss how to configure applications in a future lesson. This lesson will go into detail about how you can configure attributes and associations on entity types. Attributes are the data fields that are collected for each record. The LIMS also allows you to hyperlink related records together with associations.
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4. Relations for Common LIMS Objects
This reference diagram shows the relationships (or associations) between several key Super types in the LIMS. Many of these associations are hard-coded. For example, when you create a new sample type the LIMS will automatically create the related sample lot type. The attributes on each Entity type underlying the Super Types displayed are stored in an Attributes table in the database. Values are the data that is captured for each attribute and are stored in a separate table.
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5. What is Configuration?
Changes made to objects in the LIMS by a system administrator
Does NOT require new software code or builds
Most changes are performed through creating or editing records in the Main Admin Panel
Most changes are implemented instantaneously after they are saved – you do not need to restart any servers
Core LIMS allows you a LOT of flexibility to configure many things in the system which enables easy customization and makes the system very powerful
One of the strengths of Core LIMS is its extensive customizability. LIMS administrators can perform many changes by simply creating and editing records in the system without any coding skills. Because there is so much that you can do through configuration, it is easier to tailor the LIMS to work with your business workflows, even as they evolve and change.
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6. Configs Admins Can Do Add or remove new data fields to a record
Reorder the data fields on a record
Define a controlled vocabulary for a data field
Make a data field editable and/or mandatory
Set a default value, add conditional formatting, or set rules for allowable values for a data field
Create and edit new entity types and super types
Create applications
Modify menus and some hyperlinks on records
Tip: Do NOT modify custom attributes that Core created for you without asking first or else you may break your custom functionality!!
A Here is a list of common configurations that LIMS administrators can do. This lesson will focus mainly on the basic configurations that are performed by editing records in the Main Admin Panel
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7. Configs Admins CAN’T Do
Can’t delete records (but can deactivate them)
Can’t delete attributes (but can remove them from entity types)
Can’t delete entity types or super types (Core will do it for you)
Can’t edit entity type names (but can edit super type names you added)
Reset a barcode sequence (but can select starting sequence or enable user supplied barcode)
A Even though you can do many powerful configurations, there are a still a few configurations that you will not be able to do in the LIMS. In some cases, Core Informatics will be able to do those modifications on the backend for you, if required. This is mostly to ensure that you do not unknowingly damage your data structure and integrity.
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8. Navigating to the Main Admin Panel
From a gadget
From the LIMS menu in the LIMS administration application
From the Main Admin Panel menu
You can navigate to the Main AdmTin Panel in one of 3 ways: using a gadget, the Main admin panel menu shortcut in your user menu, or you can use a menu under the LIMS main menu in the Lims Administration application.
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9. Main Admin Panel
The admin panel lists all the Super Types in the System (black are hard-coded, blue were configured and are editable)
Click on the List All Types to find the Entity Type record you want to edit
Administrators can add other new Super Types here
Here is the main page for the Main Admin Panel. It lists all of the Super Types in the system. You can create your own Super types at the bottom of the page. If you create your own it will be a blue hyperlink so you can change the name later.
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10. List All Entity Types
List All will show you a summary table of all records of this type (may be slow if there are lots!)
Edit Attributes link lets you modify Attributes - use this to configure changes to the system
Details link lets you view Attributes
Other Common Actions:
New = Create a new record
Query = Search by attributes of this record type
Edit Associations = Modify associations with other entities
Edit Security = Change access for entity
Load Entities = Way to batch insert or update records from a spreadsheet
Conditional Formats = Add coloring based on thresholds
If you click on the List all Entity Types hyperlink by one of the Super types you will get a list of the underlying Entity types. There will usually be one Entity Type that has the same name as the parent Super type. This Entity type often does not have any records beneath it, but it is required for certain features to work. This Entity type does not need to be visible to end users. You can create as many new Entity types as you need to.
There are also hyperlinks with actions list next to each Entity type. The Details hyperlink gives you a Read Only view of the attributes and associations that are configured for the Entity type. You can modify these settings using the Edit Attributes or Edit Associations hyperlinks. .
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11. Configuring an Entity Type
Track Versions allows you to compare values between user edits
Require Signature makes users provide their password before making an edit
Note: Do NOT use special characters in attribute names (underscores are OK)
Fill in any general info at the top
Look for attributes you can re-use at the bottom and select them
Add any new attributes you need
Select Update Attributes to save changes
This slide shows you the Edit Attributes page. Here you can add, remove, or modify attributes on an Entity type. The current attributes will be listed towards the bottom of the page in a table. To track a new data field, type in an attribute name in the Add New text box shown above the current attributes and fill in the rest of the options. Be sure to check the select box at the far right and click the Update Attributes button when you are done to save the changes. You can only add one new attribute at a time. There is currently no way to load multiple attributes from a spreadsheet.
You can also change options for the current attributes if needed.
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12. Attribute Properties
Attribute = Give the new attribute a database name
Data Type = Choose what type of data to collect (some data types can be edited later)
Units = Provide any standard units (optional)
Column Header = Display name of attribute (if blank will use database name)
Default Value = Leave a default if value commonly the same
Tabs = If you want to split attributes onto separate tabs, list the tab names
Display Seq = List the order the attributes are displayed on page
Call Seq = Order the attributes are processed (matters for user equations)
Editable = Whether a user is allowed to change the value later
Mandatory = Whether a value is required to save the record
Sort = Direction of sort
Multi-Select = Whether users can enter more than one value in a pull-down
Select = Checkbox must be checked for attribute to be displayed and stored
Integrity = Check the box if you expect the data to be unique and you want to check for duplicates before creating the record
This slide defines all the columns in the attributes table. It also gives you a feel for just how much you can configure in the LIMS. For example, you can select whether an attribute is required to save a record, can be edited after the record is saved, or whether to allow new records with a duplicate value for an attribute to a previous record to be created.
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13. Adding Associations
Just like Attributes, you select Edit Associations to add or edit current associations
Associations are used (instead of an Attribute) when your data field for a record is the same as an Entity Type or a Super Type. When you have an attribute with a controlled vocabulary that you want to use across many Entity Types, it is better to change the attribute to an Entity Type and create an Association.
The Edit Associations page is very similar to the Edit Attributes page. The general settings at the top of the page are the same and the current associations are listed at the bottom with a row to add a new association. The columns in the table are slightly different than Attributes table. An association allows users to forge a hyperlink between 2 related records. The association can be configured on either of the 2 Entity types that you are trying to link.
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14. Association Properties
Context - should be all in capital letters. This is the database name of the association
Display – this is the text that will be displayed on interfaces for this entity type (i.e. text should be similar to the selected Entity Type)
Reverse-Display – this is the text that will be displayed on interfaces for the selected Entity Type (i.e. text should be similar to the current Entity Type)
Entity Type – select the desired Entity Type from the pull-down menu to associate with; users must then select a valid record from that Entity Type to use that field
Sequence – this is the order that the association will be displayed in the Associations section
Association Interface – what type of field (pull-down menu, etc.) will be displayed to enter the data
Show on Create? – whether the association will be displayed when creating new records of this entity type
Editable = Whether a user is allowed to change the value later
Mandatory = Whether a value is required to save the record
Show on Details? Whether the association will be displayed on the Entity Details page
Show on Query? Whether you can use that associated Entity Type as a filter for queries
Multi-Select = Whether users can enter more than one value in a pull-down
Select = Checkbox must be checked for attribute to be displayed and stored
This slide defines all the columns in the associations table. It is very similar to the attributes table. Context is the database name of the association and should be in all capital letters. You also need a display name for the record as well as a display name on the record that you are linking to. If you want to link to an Entity type that is not listed as an option, you will need to associate it to the Super type first. See the documentation for more details.
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15. Viewing the Configured Entity Type
Once the Entity Type record is updated, the new attributes and associations will be visible immediately in all relevant pages
Historical records previously entered will display the new attribute, but have no data
Click on the Create (or Add/Remove) link to enter a controlled vocabulary list
Once you have completed your modifications to the Edit Attributes or Edit Associations pages, you will be automatically be directed to the Details page where you can confirm that your changes are now saved. This is a read only view of the Entity type record.
On the Details page, there is an additional column displayed in the attributes table called Vocabulary. In this column you can add or modify a controlled vocabulary.
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16. Defining a Controlled Vocabulary
A controlled vocabulary will limit the users to the items in this list
The items will be displayed in a pull-down menu
This will speed data entry for end users by limiting manual typing
This will also improve search results by minimizing typographical errors
To add new terms, type them in the add box and select Add to List
Click on the hyperlink below the barcode to remove items
The list will be displayed in alphabetical order
Tip: There is an Add button on the Create New page that will let admins add to the dictionary without going to the Main Admin Panel
A controlled vocabulary is when you give users a limited pull-down list of options instead of an unstructured text box where users can enter any value. This is useful way to speed data entry and improve searching across multiple values that are essentially the same. You can add to a dictionary from the Details page or you can also add from an Add button on a Create or Edit page. You can only add one item at a time from the Main Admin Panel, but you can paste a list of multiple items using the shortcuts from the Create or Edit pages.
You can set whether one or more dictionary items can be selected in the Attributes table when you Edit Attributes.
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17. Removing an Attribute
From the Main Admin page, navigate to the Entity Type you want to edit
Select the Edit Attributes hyperlink
For attributes, deselect any unwanted attributes
Click OK through warning message
Click Update Attributes when done
Any data stored in removed attribute is cached and returned if you later add that attribute back in
Attribute still exists in the LIMS, it is just not associated to your entity type
If you no longer want to have values collected or displayed for an attribute on an Entity type, you can remove it from the Entity type. Even though it will be not publically displayed, the attribute (and any data values that were stored for it) will still exist in the LIMS and can be restored later if desired. Go to the Edit Attributes and uncheck the Select box to remove the attribute.
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18. Removing an Association
From the Main Admin page, navigate to the Entity Type you want to edit
Select the Edit Associations hyperlink
For associations, click the remove hyperlink
Click OK through warning message
Data is NOT cached and any associated values will be lost permanently
Similarly, you can remove links between Entity types as well. However, if you remove an association, any data that you had previously created will NOT be restored if you restore the association.
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19. Reusing Attributes
It is good practice to reuse the same attributes on multiple entity types when possible
Less confusing for users when reporting
Less maintenance for administrators, but may be less information when troubleshooting errors
To reuse an attribute not listed at the bottom of the Edit Attributes page, just type the attribute name with the same spelling and data type when editing attributes for an Entity Type. Core will automatically add the existing attribute instead of creating a new one.
It is possible, and also good practice to reuse the same attributes for multiple Entity types. For example, if you have an assay type that collects an attribute called temperature, you may want to use the same attribute to collect temperature in a similar assay type. The advantage is this makes it less confusing for end users to select the correct attribute name in reports and it is less maintenance for LIMS administrators to manage fewer attributes. However, sometimes this may give you less information for someone reading an error log.
To reuse an attribute that has been used in the same Super type, look at the bottom of the attribute list and select the desired attribute. To reuse an attribute that has not been previously associated to that Super type, just spell the attribute name the same way and use the same data type and the LIMS will automatically use the existing attribute.
Look at the bottom of the Edit Attributes page to find attributes that have been used for the Super Type before. Add sequences and select them to reuse
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20. Finding & Editing Attributes
If you don’t know which entity type an attribute is on, you can use the List All Attributes menu to find it (Tip: Use Control F to find the attribute in the table)
You can click on an attribute to modify the attribute name (but, you can modify the display name by editing the attribute on the entity type)
Attribute names must be unique
You can change closely related data types for the attribute
You can not delete attributes, but you can remove them from all entity types
If you need to find where an attribute is located in the LIMS, you can use the LIMS>List All Attributes menu in the LIMS Administration application. The table of attributes can be resorted by clicking on the column headers. It is easiest to use Control F to find what attribute you need on the page.
You can edit the name of an attribute, although it is better practice to edit the display name instead of the database name in case there are triggers or other code that reference the database name that may break. The attribute name must be unique, so you may need to rename an old attribute name if you want to use the same exact name for a new attribute. In some cases, you can also edit the data type to a closely related data type.
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21. System Configurations
In rare cases, you may need to edit system settings (for example, to connect to LDAP or to turn on project security). You can find these from the Lims> System Configuration menu in the LIMS Application.
Just click on the Edit icon to change the values as if you were editing any other record; Do NOT deactivate this record
In some cases you may need to change a system-wide setting. This is done on the System Configuration page which is just a record for the LIMS entity type in the system. This is common for setting up an integration with an LDAP system or turning on Project-based security. These changes are made by just a simple edit of the record. Check all the tabs to find the value you need to change. Do NOT deactivate this record or you will NOT be able to log in.
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22. New Admin Don’t Checklist
You are encouraged to practice with your test system, but a few common mistakes to avoid…
Do NOT deactivate the LIMS record (LM1)
Do NOT modify/deactivate LIMS Admin employee account (EM1)
Do NOT modify/deactivate the General project record (PJ1)
Do NOT modify/deactivate the Trash or No Location records (usually LC1 & LC2)
Do NOT modify/deactivate the No Protocol record (PT1)
Do NOT use special characters (commas, appostrophes, etc.) when creating attributes (underscores are OK)
Do NOT modify custom attributes that Core created for you without asking first – you may break your custom functionality
With the completion of this tutorial you should have enough information to try some configurations on your own to see how things work. It is encouraged that you try on a test system to learn. There are a few records that you should avoid editing in order to keep your system functioning correctly that are listed on this slide. As a general rule, it is a good idea to check with Core Informatics before you try to modify records that you did not create so you avoid problems later.
This concludes this brief tutorial about how to configure objects in the LIMS. Be sure to see the documentation or other tutorials for further information.
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