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

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

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© 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

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





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