LIMS Implementation
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Transcript of LIMS Implementation
© 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
© Robin Emig 2015, 2016
What LIMS are for?
© 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
© 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 >>>>
© 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
© 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”
© 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!
© 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
© 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
© Robin Emig 2015, 2016
Data Factories produce better data, faster
○ Efficient scheduling of resources
Mon ThurTues FriWed
© Robin Emig 2015, 2016
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
© 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
© Robin Emig 2015, 2016
Implementing LIMS
© 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 >>>>
© 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
��
© 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
© 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
© 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
© 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
© 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
© 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”}
© 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?
© 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
© 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?
© 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 AssistantData Validator
Lab Processor
Media Prep
Lab
Man
ager
Custom
er
© Robin Emig 2015, 2016
SuperUsers are Important for Success
● They know the systems
● They benefit
○ Get a promotion, bonus, etc.
○ Experience on resume
© 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
© 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
© 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
© Robin Emig 2015, 2016
Key LIMS Functionality
© 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
© Robin Emig 2015, 2016
Plates, Arrays, Tubes, Oh My!
© Robin Emig 2015, 2016
Plate and Sample Management Features
View a plate
Fix plates (ie flip/re-orient)
Duplicate
Support mixed samples
© Robin Emig 2015, 2016
Functions For Creating New Plate
● Fill macros● Templates
○ Preset Data○ Limit what goes where
● Drag and drop
© Robin Emig 2015, 2016
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
© Robin Emig 2015, 2016
Functions for Re-Array Plates
Simple Hit Picking
OR
+ Fill script =
+ Fill script =
© 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
© 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
© Robin Emig 2015, 2016
Features for Stock Management
● Media Labs● Master mixes
● How much is left● How many freeze thaw
© Robin Emig 2015, 2016
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
© 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
© 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?
© 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
© 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?
© 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
© Robin Emig 2015, 2016
Integrating With External Reporting Systems
● Spotfire
○ Integrated reporting (embed in web page)
○ Combined with webservice to writeback?
● Tableau
● Datawarehouses
○ Talend
© Robin Emig 2015, 2016
AcknowledgementsSome images shown from:
EnvironmentalQA
ClarityLIMS
GoogleMaps API
http://www.esoft.co.za/CaseStudies/CaseStudy-LIMS.aspx
http://www.labcyte.com/
bikalims
www.bioxing.com