This document discusses key considerations for implementing a Laboratory Information Management System (LIMS). It begins by explaining how LIMS can help manage larger volumes of data and samples compared to tools like Excel. The document then outlines common stages of LIMS implementation from basic databases to more advanced custom systems. Key functionality that LIMS can provide is explored, such as sample tracking, integration with other systems, and security management. Important factors for a successful LIMS implementation are also summarized, such as defining business needs, customization costs, and user training.

1. © Robin Emig 2015, 2016
Laboratory Information
Management Systems (LIMS)
What is a LIMS How and when to implement them The most important features to look for
Robin Emig
Medium Deck

2. © Robin Emig 2015, 2016
What LIMS are for?

3. © Robin Emig 2015, 2016
LIMS Manages Data
● Could be build using Excel, word etc
○ Many initial iterations are
○ These tools start to break down as requirements change
■ People Scale
● Think 3 people all trying to edit the same Excel Doc
■ Data Scale
● Excel can handle many rows, but finding what you want gets harder
■ Auditing and Security Required
■ Data types change
● Imaging, massspec, sequencing files

4. © Robin Emig 2015, 2016
Stages of “LIMS” Implementation
No LIMS
Data in
notebooks
Excel,
documents
Access/Filemaker
(Database)
Basic web interface Custom LIMS
21CFR part 11 LIMS
>>> Users, Capacity, Complexity, Cost >>>>

5. © Robin Emig 2015, 2016
LIMS Enables Increased Capacity and Scale
● Moving from 10-100 plates to 1000’s of plates
● Moving from 10’s-100’s of samples to 10,000s

6. © Robin Emig 2015, 2016
LIMS Enables Increased Capacity and Scale
● Enables moving from a few types of samples to 100’s
● Enables moving from 1-2 people to hundreds
● Moves away from 10’s of excel files
○ avoid the “can you close file X email”

7. © Robin Emig 2015, 2016
Lims can Reduce Error and Improve Accuracy
● The right sample tested the right way
● The right sample delivered to the right customer
● Don’t lose that important sample!

8. © Robin Emig 2015, 2016
LIMS Enables Data visibility and Improved Analysis
● Data visibility
○ Reporting enabled across tests, people, labs, sites
○ Standardized handoff of data to other labs/systems
○ Dashboards to help understand data at a glance
● Improved data analysis
○ Standardized data columns
○ Automated analysis
○ Statistical Quality control

9. © Robin Emig 2015, 2016
FDA Requires Data Auditing
● Must implement data access controls and audits
○ system validations
○ audit trails
○ electronic signatures
○ documentation for software and systems
● Hard to audit Excel documents [because modifications must be signed and time-stamped]
● Many LIMS have these features built-in from the get-go
● for more Info see: https://en.wikipedia.org/wiki/Title_21_CFR_Part_11

10. © Robin Emig 2015, 2016
Data Factories produce better data, faster
○ Efficient scheduling of resources
Mon ThurTues FriWed

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Data Factories produce better data, faster
Workflow and workflow decisions
● Standardization of steps and data
● Enables re-configurable workflows
● Enables automated workflows
● Many people can contribute to different parts
of the final data assembly
● Everyone has a better understanding of what
the data means

12. © Robin Emig 2015, 2016
Different things Called LIMS
● Notebooks (paper or ELNs)
○ Excel Files
○ Excel Systems
● Microsoft Access/Filemaker Pro/Sharepoint
○ Ie actual databases
● Wiki’s
● Off the Shelf fixed systems
● Off the Shelf Customizable
● Pure custom development

13. © Robin Emig 2015, 2016
Implementing LIMS

14. © Robin Emig 2015, 2016
Stages of “LIMS” Implementation
No LIMS
Data in
notebooks
Excel,
documents
Access/Filemaker
(Database)
Basic web interface Custom LIMS
21CFR part 11 LIMS
>>> Users, Capacity, Complexity, Cost >>>>

15. © Robin Emig 2015, 2016
Most LIMS are considered failures
● All LIMS will fail
● LIMS are often architected and created at a point in time
● Then frankensteined every iteration of the business
● Not all people benefit from LIMS
● Those that don’t often consider it a failure

16. © Robin Emig 2015, 2016
LIMS Implementation Process
● Determine need for a LIMS
○ GLP/GMP/etc
○ Throughput
● Determine who needs what data
○ What questions will they have
○ How will they need to see it
● Determine any Value proposals
○ Ie mislabeling means we lost FDA approval vs 1 lost day of work
○ Everyone is X% more efficient because they don’t have to spend all day looking through freezers
○ Samples last X% longer because the freezers are accessed more quickly

17. © Robin Emig 2015, 2016
Prevent a LIMS disaster
● Figure out your lab process first
○ Know what aspects of the lab work are tracked in the LIMS.
○ Code/modify/debug as you go will be costly and possibly dangerous to data integrity
● LIMS will not help you figure out your process
○ Out of the box solution may force you into best practices
■ Is this the best way forward for you?
● Involve someone who understands what LIMS brings to the table

18. © Robin Emig 2015, 2016
Hiring the Right People for LIMS Implementation
● Hire people with LIMS experience
● Highly technical (IT) Lab personnel are good for BA/Testing/Configuration
○ can also do minor coding
● Need workflow? Hire people with workflow system experience.
○ can be LIMS workflow or CRM/etc

19. © Robin Emig 2015, 2016
Hiring the Right People for LIMS Implementation
● Hire people with experience with the LIMS you are implementing
○ Especially true for customization
○ They can help you choose the LIMS as well
● Consider a mix of contractors and FTE
○ Builds in house talent, and system is delivered sooner
● Build a relationship with LIMS contractors
○ Enables you to bring them on for short projects over the years
○ Helps to have a consultant for the next version, or other LIMS systems

20. © Robin Emig 2015, 2016
Important Considerations for LIMS Evaluations
● What will be configuration? ie barcode label formats
○ Simple to do, usually looks like a settings dialog
● What will be customization? ie new entities, business logic
○ More involved, there may be a “tool” or “development environment”
● Understanding the difference will reduce costs and time to release

21. © Robin Emig 2015, 2016
What to ask about “User Configurable” LIMS
● Usually this means no programming required, mostly settings changes
○ Many will say their system is “fully configurable”
○ Pick your most complex request and ask them to demo it
● More configurable = harder to understand raw data model
○ User sees: ID, Name, Volume, Site, Trashed
○ Database has: ID, Name, Volume, customField1, customField2 or
○ Entity-Tag-Value ie {S00285, Name, “InitialSample”} {S00285, Site, “PaloAlto”}

22. © Robin Emig 2015, 2016
What to ask about Customizable LIMS
● Usually this means at least some programming (Scripting, 4g, or other)
● Can you do the work, or just the LIMS company?
● Is the customization done through their “development tools” or standards (ie Visual Studio)
● Look for Inheritance or “user” tables to help isolate your work from core
● Can it be on a Dev system and then moved to QA/Prod?

23. © Robin Emig 2015, 2016
Customizable LIMS Upgrades and Releases
● How are releases done?
○ same as install?
○ custom scripts?
● If the LIMS company upgrades, will your custom code still work?
● Beware of data model changes locking you into a version
● Look for Inheritance or “user” tables to help isolate your work from core

24. © Robin Emig 2015, 2016
Determine Business Entities Early on
● A strain is a base bacteria? A bacteria + a plasmid?
● A plasmid is a plasmid or a gene?
● A cell line is a base genome + a plasmid with CRISPR guide RNA? just the base genome?

25. © Robin Emig 2015, 2016
People are more Important than Software
● Who is going to use the system
○ Enter data
○ Run automation
○ Update tracking information
● Who is going to directly benefit from the system
○ Managers
○ Executives
○ Users
■ Customers
Sample Coordinator
Customer
QC Lab Assistant
Data Validator
Lab Processor
Media Prep
LabManager
Customer

26. © Robin Emig 2015, 2016
SuperUsers are Important for Success
● They know the systems
● They benefit
○ Get a promotion, bonus, etc.
○ Experience on resume

27. © Robin Emig 2015, 2016
LIMS Licensing and Customization Costs
● Depends on licensing
● More customization = More Co$t
● Software rules…
○ Don’t build anything you can buy
○ Don’t buy anything you can get for “free”
○ Keep in mind “free” may cost you more than building it

28. © Robin Emig 2015, 2016
LIMS Licensing Costs
● Per concurrent user
○ usually more expensive ($1.5K- 15K/ year)
○ good for a large number of infrequent users
● Per user
○ usually less expensive ($200-$2000/year)
○ watch out for per user/per computer
○ and auditing (ie 50 people using the same account)
○ good for a few frequent users
○ many cloud companies are now per user/month ($20-$200/month)
● Enterprise
○ Usually expensive ($250K-$600K/year)
○ good for large installations (25 - 250 users)
○ watch out for “data units” or “function unit” charges
○ not a bad thing, but something to be aware of

29. © Robin Emig 2015, 2016
Initial Costs of LIMS Startup
● Usually license fee (see prior slides)
● An onsite install fee
● $2K-$10K/day
● A Spin up fee (for cloud or simple installs)
● $1K-$10K
● Customization
● “Non programming” $100/hour
● Developer Required $150-$250/hour
● For a large system, plan on 2-6000 hours
● Building your own from scratch?
● plan on 3-5FTE years for a mid size
● 5-10 FTE years for a large system

30. © Robin Emig 2015, 2016
Key LIMS
Functionality

31. © Robin Emig 2015, 2016
Common Features in LIMS Systems
● Sample Tracking
○ Plate, tube, etc
● Label Printing/Scanning
● Freezer/location/Storage tracking
● Security Management
● Process Tracking
● Integration With Other Systems
● Calculations
● Reporting

32. © Robin Emig 2015, 2016
Plates, Arrays, Tubes, Oh My!

33. © Robin Emig 2015, 2016
Plate and Sample Management Features
View a plate
Fix plates (ie flip/re-orient)
Duplicate
Support mixed samples

34. © Robin Emig 2015, 2016
Functions For Creating New Plate
● Fill macros
● Templates
○ Preset Data
○ Limit what goes where
● Drag and drop

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Functions for Creating a New Plate With Multiple Data
● Ability to have and set multiple data points per well/entity
● Selection/Combo List
○ Select 3 types of data
○ each with 4 options

36. © Robin Emig 2015, 2016
Functions for Re-Array Plates
Simple Hit
Picking
OR
+ Fill script
=
+ Fill script
=

37. © Robin Emig 2015, 2016
Considerations for Barcoding
● 2-D barcodes
● alphanumeric text and the barcode versus just numbers
● labels which include additional text
● Preprinted barcodes
● printing directly on the tube or plate
● thermal resistance - chemical resistant - cold resistant
● printing on stakes for greenhouse/outdoors
● Portable bar code printing

38. © Robin Emig 2015, 2016
Considerations for Barcode Scanners
● wireless
● wireless Internet accessible with display
● to the tube scanners scanning from underneath
● keyboard wedge style
● scanning into a webpage

39. © Robin Emig 2015, 2016
Features for Stock Management
● Media Labs
● Master mixes
● How much is left
● How many freeze thaw

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Features for Process Tracking/Workflow
● One path only or multiple paths
● Cycles allowed
○ Does this create new samples or overwrite?
● Dynamic workflows
○ skip/take different paths
○ return to start? ie cycles
● Nested workflows
○ ability to reuse other workflows
● External Triggers
○ new file/modified file
○ Web service call

41. © Robin Emig 2015, 2016
Features for Security Management
● Login
○ Windows Authentication
○ LDAP/Active directory integration
○ Single signon?
○ Sign on/Impersonation of another user
● Group management - ie DNA Lab
● Role Management - ie Lab Admins
● Electronic signatures

42. © Robin Emig 2015, 2016
Granularity Levels for Security Management
● System - simple login or not
● Page/Form - particular interfaces/functions
● Action/Button - particular functions within a page
● Read vs Write - all access for read only? Write access to select few
● Row Level - Write ability, but just to the items that you own
● Workflow Level - Write/Actions to only things in your workflow
● Visibility Level - ie can you see other groups data even if it is the same workflow?

43. © Robin Emig 2015, 2016
Features for Process Tracking and Dashboards
● Basic counting Dash
● Ability to have multiple workflows
● Graphs/Colors within Dash (ie not just numbers)
● Highlighting at risk samples
○ Visual Representation of completion
○ Dashboards per workflow per “project” or “client”
● Linkable to more reports or action

44. © Robin Emig 2015, 2016
Considerations for Integration With Other Systems
● What is the integration path
● Direct database access
○ Beware no-sql or document databases
● Webservices
○ Canned or configurable?
○ Same business logic and security?

45. © Robin Emig 2015, 2016
Integration With Calculation and Statistics Engines
● Make it easier to build dashboards for monitoring capacity or workflow, etc.
● Make it easier for scientists to extract the data they need for an analysis without coding
● R/Matlab/Sas Integration
● IPython/Jupyter Notebooks Integration

46. © Robin Emig 2015, 2016
Integrating With External Reporting Systems
● Spotfire
○ Integrated reporting (embed in web page)
○ Combined with webservice to writeback?
● Tableau
● Datawarehouses
○ Talend

47. © Robin Emig 2015, 2016
Acknowledgements
Some images shown from:
EnvironmentalQA
ClarityLIMS
GoogleMaps API
http://www.esoft.co.za/CaseStudies/CaseStudy-LIMS.aspx
http://www.labcyte.com/
bikalims
www.bioxing.com

48. © Robin Emig 2015, 2016
End
Contact Robin Emig @ robinemig@gmail.com or on LinkedIn