QTreds : a flexible LIMS for omics laboratories Piergiorgio Palla CRS4 - DS3 Program email: [email protected] 1 NETTAB 2012 16th November, 2012 Wednesday, 21 November 2012
Jul 12, 2020
QTreds: a flexible LIMSfor omics laboratories
Piergiorgio PallaCRS4 - DS3 Program
email: [email protected]
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NETTAB 2012 16th November, 2012
Wednesday, 21 November 2012
CRS4
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✦ CRS4 founded in 1990 by C.Rubbia and P.Zanella
✦ Sardinian Technology Park
•Focus Areas:– Data Fusion– Information Society (ICT)– Energy and Environment– Biomedicine
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Overview
✦ Introduction✦ Motivation✦ Core Modules✦ Conclusions✦ Future perspectives
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Motivation
✦ High-throughput technologies and data explosion
✦ The development of complex lab procedures✦ A LIMS to efficiently handle these issues✦ What is a Lims?
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QTreds and CGSP
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What is it QTreds is a LIMS
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QTreds and CGSP
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What is it QTreds is a LIMS
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QTreds for:
✦ Tracking and monitoring lab activities✦ Quality control and error tracking✦ Access control policy✦ Sample handling
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Our approach
Bronislaw Malinowsky
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An anthropological approach
“to grasp the native’s point of view, his relation to life, to realize his vision of his world”(Argonauts of the Western Pacific, 1961)
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Building new habits
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Building new habits
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Building new habits
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Related issues
✦ Data Sharing✦ Scalability✦ Access Control✦ Data Integrity Loss✦ Data Redudancy
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Dealing with complexity
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Managing complex protocols
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DNA Library PreparationExome Enrichment
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From this
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From this
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to this
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QTreds overview
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MVC pattern
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MVC divides the work of the application into three separate but closely cooperative subsystems
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Development tools
• Web-based application• The Ruby programming language• The Rails framework
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QTreds functional blocks
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Workflow Generator Sample Handler
Inventory Management System
User Management System
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Workflow generator
•Key point: Protocol definition•Protocol: the sequence of steps of an experiment
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Sonication PCRAdenilation
Workflow
.....
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Protocol syntax
• Each experimental protocol is defined as XML document
• XSD to define:– structure– elements– attributes– constraints
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syntax
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Long and boring task
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<protocol name='Exome Library Preparation' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:noNamespaceSchemaLocation='/LimsDemo/db/migrate/dev_data/protocols.xsd' locksources='no,yes' output='P,S' version='1' input='U'> <activities> <activity name='Sonication' id='1'>
<instrument name='Covaris S-Series' required='true' category='sonicatore' default='Covaris -1p' id='1.1'> <input name='Device parameters' id='1.1'> <attribute type='decimal' key='duty cycle'>8</attribute> <attribute type='decimal' key='intensity'>3</attribute> <attribute type='decimal' key='cycles per burst'>200</attribute> <attribute type='decimal' key='second frequency sweeping'>60</attribute> <attribute type='decimal' key='number of cycles'>2</attribute> </input> </instrument> <input name='Note' id='1.2'> !<attribute type='textarea' key='note'/> </input> <comment title='Alternative procedure'/> </activity>
<activity name='End repair' id='2'>
<input name='Schema Multiwell-Samples' id='2.1'> <attribute type='file' key='Path'/>
</input>
List of:• activities• instruments• reagents• items ...
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Visual Tool
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Sample handling
•Qtreds records:– the path of each sample - chain of custody
• Storage Location Management •allows to handle:
– One sample at a time– Multiple samples
• Multiple samples can be combined into one entity (Pooling)
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Inventory Management
• Reagents, lab glassware and consumables easily added through their barcodes
• Minimum stock levels can be handled to avoid shortages of essential products
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Inventory Modules
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Inventory Modules
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Catalog where all categories of items have to be inserted
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Inventory Modules
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Stock to register all consumables in the lab
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Inventory Modules
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Topology a virtual representation of the lab to keep track of the locations
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Inventory Modules
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Personal Stock a sort of “shopping cart”
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Roles and Privileges
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Centralized Authorization FunctionUser Request Role
F(U, R, R[])Access rights
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Multiple roles
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Multiple roles
✦ Admin✦ Supervisor✦ Inventory manager✦ User✦ Analyzer
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Multiple roles
✦ Admin✦ Supervisor✦ Inventory manager✦ User✦ Analyzer
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A user can have different roles
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Multiple roles
✦ Admin✦ Supervisor✦ Inventory manager✦ User✦ Analyzer
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A user can have different roles
F(U, R, R[])
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Other features
✦ Internal Messaging System a collaborative tool to allow users to interact with each other
✦ REST API to allow an automated access to information
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Conclusions
✦ QTreds and the CRS4 Sequencing and Genotyping Platform (CSGP)
✦ Different kinds of experiments:- DNA Library Preparation- Exome Enrichment- Sequencing
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Collaborations
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MetabolomicsGenomics
Proteomics
Chemistry
Genetics
Virology
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Future perspectives
✦ New version early 2013✦ New features:
- Plugin system to directly interface instruments to QTreds
- Ad-hoc reporting visual tool to create your own reports
- ”Calendarization” system to schedule the activities and the workload balancing
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DS3 group
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Personnel Expertise Patricia Rodriguez-Tomé Bioinformatics, Seismology (HEAD)
Giuliana Brunetti Biology, Science dissemination
Gianfranco Frau Computer Engineering
Elisabetta Marras Statistics
Piergiorgio Palla Computer Engineering
Luana Vargiu Biology
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The End
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The End
Thanks for your attention!
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The End
Thanks for your attention!
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http://qtreds.crs4.it/demouser: labuserpsswd: qtreds
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