QTreds: a flexible LIMS                        for omics laboratories                               NETTAB 2012            ...
CRS4       ✦ CRS4 founded in 1990 by        C.Rubbia and P.Zanella       ✦ Sardinian Technology Park                  • Fo...
Overview                              ✦   Introduction                              ✦   Motivation                        ...
Motivation          ✦ High-throughput technologies and data           explosion          ✦ The development of complex lab ...
QTreds and CGSP       What is it               QTreds is a LIMS                                                   5Wednesd...
QTreds and CGSP       What is it               QTreds is a LIMS                                                   5Wednesd...
QTreds for:           ✦ Tracking and monitoring lab activities           ✦ Quality control and error tracking           ✦ ...
Our approach                              An anthropological approach                                                Broni...
Building new habits                                                    8Wednesday, 21 November 2012
Building new habits                                                    8Wednesday, 21 November 2012
Building new habits                                                    8Wednesday, 21 November 2012
Related issues                     ✦        Data Sharing                     ✦        Scalability                     ✦   ...
Dealing with complexity                                                        10Wednesday, 21 November 2012
Managing complex                              protocols                 DNA Library Preparation                       Exom...
From this                                          12Wednesday, 21 November 2012
From this                                          12Wednesday, 21 November 2012
to thisWednesday, 21 November 2012
QTreds overviewWednesday, 21 November 2012
MVC pattern                                     MVC divides the work                                     of the applicatio...
Development tools          • Web-based application          • The Ruby programming language          • The Rails framework...
QTreds functional                                      blocks                               Workflow Generator    Sample H...
Workflow generator      •Key point: Protocol definition      •Protocol: the sequence of steps of an       experiment        ...
Protocol syntax     • Each experimental protocol is defined as XML      document     • XSD to define:       – structure     ...
Long and boring task        <protocol name=Exome Library Preparation xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance  ...
Visual Tool                                            21Wednesday, 21 November 2012
Sample handling        • Qtreds records:          – the path of each sample - chain of custody        • Storage Location M...
Inventory Management    • Reagents, lab glassware and consumables easily     added through their barcodes    • Minimum sto...
Inventory Modules                                                  24Wednesday, 21 November 2012
Inventory Modules        Catalog where all categories of items        have to be inserted                                 ...
Inventory Modules           Stock to register all consumables in the           lab                                        ...
Inventory Modules           Topology a virtual representation of the           lab to keep track of the locations         ...
Inventory Modules                                         Personal                                         Stock a sort   ...
Roles and Privileges              Centralized Authorization Function              User       Request       Role           ...
Multiple roles                                               26Wednesday, 21 November 2012
Multiple roles            ✦      Admin            ✦      Supervisor            ✦      Inventory manager            ✦      ...
Multiple roles            ✦      Admin                  A user can            ✦      Supervisor             have different...
Multiple roles            ✦      Admin                  A user can            ✦      Supervisor             have different...
Other features        ✦ Internal Messaging System a collaborative         tool to allow users to interact with each       ...
Conclusions        ✦ QTreds and the CRS4 Sequencing and         Genotyping Platform (CSGP)        ✦ Different kinds of exp...
Collaborations               Chemistry     Proteomics                                        Genetics                     ...
Future perspectives      ✦ New version early 2013      ✦ New features:           - Plugin system to directly interface    ...
DS3 group              Personnel                  Expertise               Patricia Rodriguez-Tomé   Bioinformatics, Seismo...
The End                                        32Wednesday, 21 November 2012
The End                              Thanks for your attention!                                                           ...
The End                              Thanks for your attention!                              http://qtreds.crs4.it/demo   ...
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Qtreds

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QTreds is a flexible LIMS developed to address the needs of -OMICS laboratories

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Qtreds

  1. 1. QTreds: a flexible LIMS for omics laboratories NETTAB 2012 16th November, 2012 Piergiorgio Palla CRS4 - DS3 Program email: pg@crs4.it 1Wednesday, 21 November 2012
  2. 2. CRS4 ✦ CRS4 founded in 1990 by C.Rubbia and P.Zanella ✦ Sardinian Technology Park • Focus Areas: – Data Fusion – Information Society (ICT) – Energy and Environment – Biomedicine 2Wednesday, 21 November 2012
  3. 3. Overview ✦ Introduction ✦ Motivation ✦ Core Modules ✦ Conclusions ✦ Future perspectives 3Wednesday, 21 November 2012
  4. 4. Motivation ✦ High-throughput technologies and data explosion ✦ The development of complex lab procedures ✦ A LIMS to efficiently handle these issues ✦ What is a Lims? 4Wednesday, 21 November 2012
  5. 5. QTreds and CGSP What is it QTreds is a LIMS 5Wednesday, 21 November 2012
  6. 6. QTreds and CGSP What is it QTreds is a LIMS 5Wednesday, 21 November 2012
  7. 7. QTreds for: ✦ Tracking and monitoring lab activities ✦ Quality control and error tracking ✦ Access control policy ✦ Sample handling 6Wednesday, 21 November 2012
  8. 8. Our approach An anthropological approach Bronislaw Malinowsky “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) 7Wednesday, 21 November 2012
  9. 9. Building new habits 8Wednesday, 21 November 2012
  10. 10. Building new habits 8Wednesday, 21 November 2012
  11. 11. Building new habits 8Wednesday, 21 November 2012
  12. 12. Related issues ✦ Data Sharing ✦ Scalability ✦ Access Control ✦ Data Integrity Loss ✦ Data Redudancy 9Wednesday, 21 November 2012
  13. 13. Dealing with complexity 10Wednesday, 21 November 2012
  14. 14. Managing complex protocols DNA Library Preparation Exome Enrichment 11Wednesday, 21 November 2012
  15. 15. From this 12Wednesday, 21 November 2012
  16. 16. From this 12Wednesday, 21 November 2012
  17. 17. to thisWednesday, 21 November 2012
  18. 18. QTreds overviewWednesday, 21 November 2012
  19. 19. MVC pattern MVC divides the work of the application into three separate but closely cooperative subsystems 15Wednesday, 21 November 2012
  20. 20. Development tools • Web-based application • The Ruby programming language • The Rails framework 16Wednesday, 21 November 2012
  21. 21. QTreds functional blocks Workflow Generator Sample Handler Inventory Management User Management System System 17Wednesday, 21 November 2012
  22. 22. Workflow generator •Key point: Protocol definition •Protocol: the sequence of steps of an experiment Workflow Sonication Adenilation ..... PCR 18Wednesday, 21 November 2012
  23. 23. Protocol syntax • Each experimental protocol is defined as XML document • XSD to define: – structure – elements – attributes syntax – constraints 19Wednesday, 21 November 2012
  24. 24. Long and boring task <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/> List of: • activities </input> • instruments <comment title=Alternative procedure/> </activity> <activity name=End repair id=2> • reagents <input name=Schema Multiwell-Samples id=2.1> <attribute type=file key=Path/> </input> • items ... 20Wednesday, 21 November 2012
  25. 25. Visual Tool 21Wednesday, 21 November 2012
  26. 26. 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) 22Wednesday, 21 November 2012
  27. 27. Inventory Management • Reagents, lab glassware and consumables easily added through their barcodes • Minimum stock levels can be handled to avoid shortages of essential products 23Wednesday, 21 November 2012
  28. 28. Inventory Modules 24Wednesday, 21 November 2012
  29. 29. Inventory Modules Catalog where all categories of items have to be inserted 24Wednesday, 21 November 2012
  30. 30. Inventory Modules Stock to register all consumables in the lab 24Wednesday, 21 November 2012
  31. 31. Inventory Modules Topology a virtual representation of the lab to keep track of the locations 24Wednesday, 21 November 2012
  32. 32. Inventory Modules Personal Stock a sort of “shopping cart” 24Wednesday, 21 November 2012
  33. 33. Roles and Privileges Centralized Authorization Function User Request Role Access rights F(U, R, R[]) 25Wednesday, 21 November 2012
  34. 34. Multiple roles 26Wednesday, 21 November 2012
  35. 35. Multiple roles ✦ Admin ✦ Supervisor ✦ Inventory manager ✦ User ✦ Analyzer 26Wednesday, 21 November 2012
  36. 36. Multiple roles ✦ Admin A user can ✦ Supervisor have different roles ✦ Inventory manager ✦ User ✦ Analyzer 26Wednesday, 21 November 2012
  37. 37. Multiple roles ✦ Admin A user can ✦ Supervisor have different roles ✦ Inventory manager ✦ User ✦ Analyzer F(U, R, R[]) 26Wednesday, 21 November 2012
  38. 38. 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 27Wednesday, 21 November 2012
  39. 39. Conclusions ✦ QTreds and the CRS4 Sequencing and Genotyping Platform (CSGP) ✦ Different kinds of experiments: - DNA Library Preparation - Exome Enrichment - Sequencing 28Wednesday, 21 November 2012
  40. 40. Collaborations Chemistry Proteomics Genetics Virology Genomics Metabolomics 29Wednesday, 21 November 2012
  41. 41. 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 30Wednesday, 21 November 2012
  42. 42. DS3 group 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 31Wednesday, 21 November 2012
  43. 43. The End 32Wednesday, 21 November 2012
  44. 44. The End Thanks for your attention! 32Wednesday, 21 November 2012
  45. 45. The End Thanks for your attention! http://qtreds.crs4.it/demo user: labuser psswd: qtreds 32Wednesday, 21 November 2012

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