1. Getting Started with Core Informatics
This tutorial will introduce some key terms and concepts of the Core LIMS before taking a look at the user interface for users in non-administrative roles.

2. What is Core LIMS? Laboratory Information Management System (LIMS)
Manages information for the entire discovery process
Sample Registration
Automated Data Capture & Reduction
Experimental Results Management
Enforcement of Laboratory Workflow & SOPs
Interface with Instrumentation & Robotics
Project Management
Barcoding & Inventory Management
Core LIMS can be easily customized to any scientific area through simple configurations
Core LIMS has a web-based client that can be accessed anywhere with internet access; the server can be stored on the cloud or on premises
Core LIMS is a Laboratory Information Management System that can manage data for the entire discovery process, from sample registration, assay data processing and capture, inventory management, work request systems, and much more. What makes the Core LIMS unique is that it is highly customizable through simple administrator configurations. The LIMS has been successfully implemented for a very diverse set of scientific industries and can be tailored to specific workflows. Another strength of the Core LIMS is that it is a web-based system. This means there is no software to install or maintain on each user’s computer. Instead, users can access data from anywhere or on any mobile device that has internet access. The main server can even be stored in the cloud.

3. Core LIMS is Web-Based Some general tips about web pages:
Full Screen View
Web pages are not limited by screen size and often involve scrolling to see everything
Window size can be increased by utilizing full screen mode in a browser
New Windows or Tabs
New tabs or windows can be opened (using right mouse click) to keep information entered on a web page so users do not have to re-type it later, or to see results on a new page
Note: There is no maximum to the number of windows that can be logged in to the LIMS simultaneously, but if a window is inactive for more than twenty minutes, a re-login will be necessary
Use web caching to reduce redundant typing
Google Chrome is the recommended browser
Since Core LIMS is web-based, users can take advantage of some of the features of current internet browsers for a better user experience. Since web pages are not hard-coded to a specific size, it might be necessary to scroll right or down to view all information on a page. To reduce scrolling, the browser can be set to full screen mode or the page resized. Another advantage of web-based software is that multiple new tabs or windows can be opened in order to easily toggle between information on different pages. If the browser is set to cache previously entered values, time can be saved when entering similar data.

4. Examples: Container, Assay, or Sample.
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).
Core LIMS is built on three types of objects organized into a hierarchy. The highest level of the hierarchy are the Super Types. These are really a conceptual object category. Under each Super Type, are one or more Entity Types, which can also be referred to as record types. Data that needs to be collected for the records is defined on the Entity Types. The lowest objects are the Entities, or individual records. Entities are where data values are collected for each record.
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).

5. 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 few other key terms used within the LIMS are shown on this slide. Each system will have at least a few different applications, although which specific applications are available will vary. Applications will have their own set of menus and their own home page. Administrators can configure as many applications as they want, and give each user access to just the applications they need. Attributes are the data fields that are collected for each record. The LIMS also allows users to hyperlink related records together. These are called Associations.

6. Key Core Concepts
Every record in the system must have a unique name and a unique barcode
The barcode cannot be edited, but the name can be changed later
Every record in the system needs to be associated to one or more projects
Users can never delete records, but they can edit or deactivate them if they have permission
Files or comments can be attached to any record type in the system
The LIMS timestamps and tracks the user performing all major events for every record (creation, edits, etc.)
The LIMS is highly configurable and every system will look slightly different
Some basic concepts for the system are shown on this slide. Every record must have a unique barcode, name, and at least one project, although the name or projects can be edited later. Users can never delete records, but can deactivate them to remove them from view. Files or comments can be attached to any record. The LIMS will track all major events. Another key idea to remember is that every system will probably look slightly different than the generic system used for training since systems are configured to more closely match customer workflows.

7. Samples, Lots, & Containers
Parent level concept of entities that can be registered, tracked, and utilized in experiments.
This is a the “blueprint” for the house or the “recipe” for a type of soda.
Lot
A distinct child of a sample that can be associated to containers and used in experiments.
This is each physical construction of the house from the same blueprint, or different batch of soda made from the same recipe.
Container
Object that can store sample lots and contains one or multiple container cells. This is the land plot that holds the house, or the can that holds a particular batch of soda.
It is important to realize that there are three key Super Types involved in registering the samples that are tested in experiments. Samples are the parent level idea of what will be tested. For example, a Sample might be the blueprint of a house to be built or a recipe for a specific type of soda to be made. A Lot is a specific instance or batch of a sample. This is equivalent to a physical construction of a house made from that blueprint, or a batch of soda made from the recipe. Containers are yet another type of record that has the information about what physically holds the Lot. For example, this might be equivalent to the land plot that the house is built upon or the can that holds a particular batch of soda. There can be many Lots for a single Sample, and many Containers to hold a single Lot.
Samples, lots, and containers are all equivalent super types
There are separate records for each of them, but related records can easily be found through hyperlinks
There can be one or more lots for a given sample
A given lot can be stored in one or more containers

8. Assays, Experiments, & Protocols
One or more experiments that are tracking the same set of result data types.
This is the inspection for the house, or a taste test for the soda.
Experiment
Process execution or instance/event in which data is collected for a set of samples.
This is each part of the inspection (foundation, septic, electric, etc.), or each time the test is executed for a batch of soda.
Protocol
Description of conditions associated to an experiment. These are the steps to follow during the inspection, or the instructions for giving the taste test.
Similarly, assays, experiments and protocols are closely related concepts that are all Super Types in the LIMS. Assays are similar to Samples – they are the parent idea. What types of data are collected for a group of the same experiment type will be defined on the Assay. Experiments are like lots – they are the specific instance or group of sample lots tested on the same day under the same set of conditions. Protocols are the set of conditions under which the experiment is run. The associations between these records are defined on the experiment.

9. Assays, Experiments, & Protocols
Assays, experiments, and protocols are all equivalent super types
There are separate records for each of them, but related records can be easily found through hyperlinks
The associations between objects are stored on the experiment
There can be one or more experiments for a given assay
Multiple sample lots can be tested in the same experiment
Different experiments can run the same assay using different protocols
Data for the same lot that is tested in the same assay using the same protocol can be aggregated together

10. Logging In
Users will receive a web address to access their system from an internet browser – it is a good idea to bookmark the site in the browser favorites list
An initial username and password may either be set up by the system administrator or Core, and may be integrated with an LDAP database that contains a corporate username and password
When users first launch the hyperlink provided, they will be directed to a log in page. It is recommended that users bookmark this page in their browser so that they can easily return whenever necessary. The user should enter their username and password – the password will enter as encrypted text for a secure login. The system may be set up to integrate with a corporate password system, or the LIMS can manage its own account passwords. The user should then click the Login button when done.

11. To return to this system home page from any page, select the Core icon
Once credentials have been verified, users will be taken to the main System Home Page. Users can always return to this page by clicking on the Core icon in the upper left corner from any page in the system.
Users will have access to one or more applications, and can transfer between these applications from the colored tiles in the main window, or by selecting them from the application pull down menu in the upper left corner underneath the 3 by 3 grid icon. Each application has its own separate home page with different menu items containing different functionality. Application pages may also contain gadgets which direct users to other pages within the system that contain key functionality. Users can also rearrange the order of how these application tiles are laid out by clicking on the orange “Edit” button in the upper right. The upper left corners of each tile will be highlighted white, and tiles can then be dragged and dropped where desired. Once completed, clicking the orange “Save” button will lock the new positions. The System Home Page is the only page that all users will have permission to edit in order to create their own personal view.
From the home page, there will be tiles representing all the applications which can be accessed
Click on any tile to go to that application home page
Tiles can be reordered on this page if desired
CONFIDENTIAL

12. Common Navigation Elements
Application-Specific Menus – will change depending upon which application the user is currently in
Application Menu
Location Menu
User Menu
Help Menu
Before moving on, let's take a second to identify some of the common navigation elements on the home page as well as on most other pages in the system.
The Application Menu icon is in the upper left corner and looks like a 3 by 3 grid. It provides the user with a drop down list of those Applications that the user has access to.
Depending on the Application selected, the appropriate Application-Specific Menus will display on the page accordingly.
The Quick Find Tool provides the user with a quick way to locate any record within the LIMS.
The Location Menu icon will open up a hierarchical list of Locations to view.
The User Menu dropdown list provides the user with the ability to log out, access their own employee details page, and, if they are an administrator, access the main admin panel.
The Help Menu dropdown list provides various forms of help to the user and will be explained in greater detail shortly.
The Center Pane is the area of the page that is dedicated to displaying records and dashboards
And finally, the Page Title helps to identify the page that is currently being displayed.
Page Title – indicates where the user is in the system
Center Pane – where records and dashboards will be displayed
Quick Find

13. Common Navigation Elements: System Home Page Panels
The Updates tab shows the activities of any user that is being followed
The Favorites tab shows any records that a user has “liked”
Recent Items displays a list of items visited within the last two weeks
On the main System Home Page, to the right side of the page, there are three tabs each opening an individual panel.
The first is the "Updates" tab, which is like an RSS feed of the activities of any user being followed. Any user can follow a colleague by navigating to their user record and clicking on the Follow icon. Then, when the followed user creates new records, publishes experiments, or makes announcements in the Share box at the top of this panel, the follower will see those activities in their updates panel. Users can easily click on the hyperlinked records in this panel to jump to the exact record and view the details. This is a nice way to see right away what colleagues are working on. Users will not see any records that they do not have permissions to view!
The second tab is the "Favorites" panel. This will show all of the User Favorites. Favorites are those items within the LIMS that the user 'Likes'. The Core LIMS allows a user to "like" certain items within the LIMS. Those items get added to this Favorites Panel for easy access in the future. This is a convenient way to bookmark key records that users need to navigate to frequently.
The third tab is the "Recent Items" tab. This Panel shows all records that the logged in user has visited in the last two weeks. This again provides another nice shortcut for the user to quickly find pages that they have been recently working with.
Click here to expand Entity Type

14. Common Navigation Elements: Application Menu
Core LIMS is divided into several applications which have toolbars with functionality related to those specific applications
Applications can be accessed from the application menu located in the upper left corner of every page
This menu is customized to each user and will only display accessible applications for that user
It can be used to navigate between applications directly (without having to go through system home page tiles)
Changing applications will automatically change the Application-Specific menus on the top of the page
LIMS administrators can set the default application by editing the Employee Details record
Let’s take a more detailed look at some of the navigation elements we introduced earlier.
Core LIMS is divided into many applications. An application is a logical unit of objects and functions grouped together by a set of menus and a dashboard home page. Applications may be created by Core Informatics, or created by an administrator so that they are customized to business workflows. Administrators can control which applications users can view to make it easier for them to find the pages they need to enter and view data. In the upper left corner of every page, users will find a 3 by 3 grid icon that contains the Application Menu drop down list. This list contains all of those applications that the logged in user has access to. Clicking on any menu item will take the user directly to that application's home page as well as update the application-specific menus along the top of page next to the Core icon. This drop down list acts as a shortcut for navigation between applications so users do not have to navigate to the System Home Page to switch between applications using the tiles.

15. Common Navigation Elements: Quick Find1 2
Scan/type the barcode OR enter the record name (case sensitive)
Click on the magnifying glass to start the search
The desired record will be opened in the center pane
The Quick Find tool is located in the upper right screen of all pages within the LIMS. The easiest way to use it is to type or scan a barcode of a record into the text box and click on the magnifying glass icon to initiate the search. Since the search should only find one match, it will automatically take the user directly to the record. If a record has a different name than the barcode, users can also use that name to find the record. Note that a name search is case sensitive by default.

16. Common Navigation Elements: Help Menu
The Help Menus are next.
There is a Help question mark icon located in the upper right corner of every page. If a user opens the pull down menu underneath the icon, there is a link to the online documentation. Within the documentation, users can search for a specific character string or can browse for a topic using the Table of Contents. On some pages there may be alternative ways to access the online documentation. There may be gadgets that contain links to key documentation or supporting tutorials in a dashboard page. Some pages also contain orange question marks that can be selected to take users directly into the help documentation for additional help with the activity currently being performed.
The Help menu also contains a link to the online support login, allowing Administrators to log in to the Customer Support Help Center to submit a support issue. New customers will get access to this system after their initial development phase of the project. The third Help Menu item will provide specific information regarding the version and build of the LIMS that the user is running. In a multi-tenant environment, the name of the account is specified here.
Located in the far upper right corner of every page
Access to Online Documentation and the Core Support Center where LIMS admins can submit support tickets
Orange question mark icons on pages also open documentation

17. Common Navigation Elements: User Menu
Located in the upper right corner of every page next to the Help Menu
Users can logout here or can just close their web browser
Access to My Account page – this is the Employee Details page that contains some features of interest to users
The Main Administration Panel link will only be available to Admins
The User Menu is located just to the left of the Help Menu, underneath the Headshot icon.
The User Menu contains a menu to log out of the LIMS. If a user closes the web browser, the system will eventually automatically log them out, but users will be logged out faster if they specifically click on the Logout option in the User Menu. This is most important to customers who are using a concurrent license model and want to free up the license for the next user sooner. The My Account menu option provides the user with access to their own user record so they can make changes to their employee record if needed. Users cannot change their permissions, but they can change their password here. We will look at this page in greater detail shortly. If the user is an Administrator, the User Menu will also contain a link to the Main Admin Panel. The Main Admin Panel is where much of the LIMS Configuration is done, and is therefore restricted to Administrators only.

18. Page Elements: My Account Page Elements
Title tells users where they are in the system
Links to related pages or reports are customizable
Main Tool Bar
Record
Identifiers
Barcode
Clicking on the My Account link from the User Menu will bring the user to their user record, which is an Employee Details page. This page will allow the user to change their password (unless passwords are set up to be managed by an external LDAP system). Users will not be allowed to edit their own user permissions. This page also is a good example record that demonstrates the basic features of most pages within the Core LIMS. It includes the page title and a main tool bar where the user can perform common operations on the record. We will look at the tool bar in more detail in a minute.
Fields that are common to all records will be located in the top Details section. Every record in the LIMS will have a unique name and a unique barcode. Often the name and the barcode are the same, but they can be different. Users can edit the name after a record is created, but cannot edit a barcode later, however they can use their own external barcodes, if needed. All records will be assigned one or more projects.
Data fields that are specific to that record type will be listed below in the Attributes section. These fields can be configured by an administrator.
The page will also contain functions. Functions can be configured by an administrator and will change depending upon what type of record it is. Typically functions are links to reports or pages with specific functionality. These can be configured as a drop down list, as shown on this page. "My Experiments," "My Assays," or "My Samples" are functions specific to employee records. Functions may also be configured to be buttons instead of menus.
When users first navigate to a page, it will be in a read only view and the data cannot be modified. A user can go into an edit mode at any time to edit the data that they have permission to edit using the Edit icon on the main tool bar.
General attributes (common to all records) are in the top Details section
Attributes (data fields) that are specific to a record type are listed below

19. Page Elements: More Common Elements
Associations are links to other existing records
Each association can be expanded to view the data from the linked records
Looking at the bottom of the Employee Details Page, users will find the Associations section. This is a very common page element that is found on many pages within the LIMS. Associations are links to other common records in the system. Associated records will be grouped together by record type in panels that can be collapsed or expanded using the arrows at the right of the panel. Users can view a summary of the data of the linked record in the table, or can click on a hyperlink to view the linked record directly.
At the bottom of every record is the Events section. When expanded, this will show the user an historic list of activities on that specific record: this is typically the date it was created and any edits from that day forward. Other key events, such as when an experiment is published or unpublished or when objects are moved, are also displayed here. The user who performed the action and the time it happened is also recorded. This is a great way to view the history of a record.
Record history is listed in the Events section

20. Page Elements: Main Tool Bar
Edit
Will unlock the editable fields for editing (if user has permission)
Copy
Quick way to pre-populate a new record with similar data to reduce data entry effort (not supported for all record types)
Files
View or attach any type of electronic document related to the record; it will be colored orange and list a number if there are currently files attached to the record
Follow/Like
Follow icon (eye) shows on employee records; Like button (heart) on other records; Follow turns on RSS Updates feed, while Like bookmarks records for the user’s Favorites tab on the System Home Page
Locate
Shows the location history of the record; most useful for record types that users want to track the location for (such as containers)
Comment
Allows the user to add or view comments associated to this record
Search
Will open a search page with fields that are relevant to the type of object being viewed
Moving our focus back to the top of the page, let’s take a look at the specific functions within the main tool bar. The main tool bar allows the user to perform basic activities on a record.
The left and right arrow icons allow the user to browse to the next or previous active records of that record type.
The pencil icon is an Edit button that switches the record from a view only mode into an editable form so the user can update the data.
The magnifying glass icon is a Search button that will open a search page with query fields that are relevant to the type of object being viewed.
The paper clip icon is a Files button that will allow users to view or attach any type of document that might be relevant to that record. If there are any files attached, an orange number will display the number of files currently attached to that record at that time.
The page icon represents the Electronic Lab Notebook button and allows the user to link the record to an electronic laboratory notebook.
The Copy button provides a quick way to pre-populate a newly created record with similar data. This operation is not supported for all record types, but it will be grayed out if it cannot be used on the current record.
The Locate button will show the location history of the record, which is most useful for tracking things like containers. Note that although it has the same icon as the Location menu in the Quick Find Tool, it has a different function when it is called from the main tool bar.
The speech bubble icon is a Comments button. Users can click on this button to view all current comments and add new ones. The adjacent number indicates the number of comments currently attached to this record.
The eye icon is the Follow icon. This icon is only on Employee records and allows any user to follow that employee so that they can view the activities of that employee in the Updates tab on their System Home Page. To follow an employee, click on the button and the number will increment by one to show the total number of users following this employee. Click on the follow button again to turn it off.
On every other record type beside employee records, there is a heart icon in this position in the main tool bar. This is the “Like” button where users can bookmark records that they want to see displayed in their Favorites tab on the System Home Page. Click on the button to turn it on and click a second time to remove the bookmark.
ELN
Links record to an electronic laboratory notebook

21. Navigating to a Create Page
There are multiple ways to navigate to a Create Page
Users can navigate to a Create New Page from a Create menu item
Users can navigate from a hyperlink on a gadget tile
There are multiple ways to navigate to a create page.

22. Creating a Single Record
If only a single record is needed, it is easiest to use the create new page. Every object type will have its own create page that will provide data fields for the attributes and associations that are defined for that object type. For example, this create employee page provides spaces to enter all the information needed to create a user account in the system. However, there are some basic similarities for all create pages in the LIMS.
Create Pages are used to enter new records
The page may vary slightly depending on the type of record being created

23. Common Create Page Features
Title
Indicates the type of record being created
Name
Optional and can be edited later
Important if used in pull down menus
If left blank or not unique, system will usually assign the barcode as name
May be configured with an auto-naming formula
Project
All records need at least one project
If one is not selected, as a default it will be set to ‘General’
Location Barcode
Can be scanned in or typed in
Can be selected or dragged and dropped from the Location Menu
Attributes
Will vary depending on the record type
Text boxes, calendar pickers, pull down menus, etc.
Can be mandatory or optional
Associations
Links current record to other records in the system

24. Details Page
Once the record is saved, the Details Page provides a “read only” view of the record

25. Edit Page
Clicking the Edit icon on the Details Page opens the record in an editable format

26. Deactivating a Record Records cannot be permanently deleted
Records are “deactivated” by clearing the Active checkbox when in Edit mode
Deactivating a record will prevent that record from showing up in common queries, reports and views

27. Functions available vary depending on the record type
List Functions Page
List Members section
Functions available vary depending on the record type
The List Functions Page can be used to edit multiple records (plus many other operations)
Records can be pasted into the page directly or forwarded
Various functions are available which are determined by record type
Does not require administrative privileges

28. Navigating to a List Functions Page
Manually type or paste bar codes here
If the list of barcodes to edit is already known, navigate to the List Functions Page via the drop down menu option
Enter the barcodes manually
Select the function to perform on all barcodes and submit

29. Editing with the List Functions Page
Can deactivate multiple records
Can also update many records with the same value for an attribute or an association
Properties will be set on all barcodes in the List Member section
Prior values will be overwritten with new values entered

30. Forwarding Records to List Functions Page
Usually query results or reports list records in a Smart Table
Select specific items to pass along, or pass all items

31. Interactive Smart Table
The Smart Table is a common element used in many places in the system:
List All menus
Returns from queries
Associations on Details pages
Reports
Columns can be reordered by dragging and dropping or hidden entirely
Data can be filtered on the fly to focus on key records
There is one last important common navigation element to identify. This is the Smart Table. A Smart Table is a common element used on many pages in the system where the system needs to return a list of items to the user. Smart Tables are used to display data whenever a "List All" menu is selected or a query is returned. We saw an example of a Smart Table in the associations section of an employee details page. Smart Tables are also common in reports. Smart Tables are very powerful as they allow the user to dynamically sort the table, filter the table, hide columns, move columns and select specific rows from the table to pass on to other functions in the LIMS.
Highlighted rows can be sent to List Functions pages so that users can perform actions on a set of records