PG P Barcode Initiative November The NEBC barcode database

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					                                PG&P Barcode Initiative
                                  1st November 2005




    The NEBC barcode database
         and labelling hardware

                    Tim Booth
http://darwin.nox.ac.uk/pgp-wiki/index.php/Barcodes
                tbooth@ceh.ac.uk
                                                PG&P Barcode Initiative
                                                  1st November 2005


                            Welcome
10:00 - 10:30 : Welcome and coffee

10:30 - 11:15 : Overview and demonstration of the barcode software
and hardware (Tim Booth)

11:15 - 12:05 : Explanation and demonstration of hardware and
software in use by Steve George's group (Carolynn McKenzie)

12:15 - 12:30 : Presentations from groups on the types of samples they
handle, and typical workflows. (Anna Law, others??)

12:30 - 13:30 : Lunch

13:30 - 16:00 : Afternoon – discussion comprising first meeting of the
barcode working group.
                                                PG&P Barcode Initiative
                                                  1st November 2005


                            Welcome
10:00 - 10:30 : Welcome and coffee

10:30 - 11:15 : Overview and demonstration of the barcode software
and hardware (Tim Booth)

11:15 - 12:05 : Explanation and demonstration of hardware and
software in use by Steve George's group (Carolynn McKenzie)

12:15 - 12:30 : Presentations from groups on the types of samples they
handle, and typical workflows. (Anna Law, others??)

12:30 - 13:30 : Lunch

13:30 - 16:00 : Afternoon – discussion comprising first meeting of the
barcode working group.
                                          PG&P Barcode Initiative
                                            1st November 2005


             Timeline of Events
• Barcoding was first proposed by Mar. Met. consortium, 22nd
  March 2005.
• Fish Tox. grant joined the proposal on the 16th August.
• NEBC receives funding for project: 31st August.
• Tim initiates work on pilot project: 2nd September.
• Pilot database published to web for feedback: 3rd October
• First labelling equipment available to Tim: 10th October
• First meeting of working group, with finalisation of barcode types:
  1st Nov
• Version 1 of the system ready for full deployment: 1st December
  2005
                         PG&P Barcode Initiative
                           1st November 2005


         Proposed system
• Develop a basic, in-house solution
• Allocate barcodes centrally
• Have a central database
• Allow data about the codes to be
  recorded
• Provide for both short term (active
  phase) and long term (archive phase)
  use
                               PG&P Barcode Initiative
                                 1st November 2005


            Working Group
• Policy decisions
• Communication and training
• Evaluation
• Further development
• Publication

  Tim Booth             Dawn Field
  Josh Neufield         Jack Gilbert
                                                   PG&P Barcode Initiative
                                                     1st November 2005


                   Design Rationale
• All stored samples will have an identifying code which can be checked in a
  central online database.
• The database will also make reports available online, which can be linked to
  EnvBase records.
• All sequences, microarray results etc. produced from these samples will
  reference the original source, and the core facilities will have access to the
  barcode database.
• Clone libraries will reference the original environmental sample, and subclone
  libraries the original clones etc. within the database.
• The printed labels will be clearly legible and able to withstand long-term
  freezer storage.
• Labels will be printable on site or available from a central printing location.
                           PG&P Barcode Initiative
                             1st November 2005


     The Barcode Database
• Centralised PostgreSQL database,
  shared via web front-end
• Input via spreadsheet (Excel, Calc) and
  upload to database
• Easily customisable - different types
  defined by creating tables in the
  database
                         PG&P Barcode Initiative
                           1st November 2005


      Lifecycle of a barcode
• Unallocated
• Allocated
• Data entered
• Update, update...
• Dispose (maybe)
• Archive or Publish via EnvBase
                                         PG&P Barcode Initiative
                                           1st November 2005


       Lifecycle of the database
           1,000,000 potential codes per group

                   All allocated codes

                  Codes actually used
Time




                Samples kept in storage

                   Logged in EnvBase            Publication phase

                       Sample
                       repository               Export to repository
                                                catalogue
                         PG&P Barcode Initiative
                           1st November 2005


        Barcode Labelling
• Hardware budget for printers and
  scanners for all sites that want them
• Thermal transfer onto high-tack labels
• Wand scanner
• You need a computer with an internet
  connection, preferably a BL machine and
  preferably in the lab
                     PG&P Barcode Initiative
                       1st November 2005


          Barcode Hardware
                   £119.00


£232.00
                                 £23.20
                                 per roll of 2,000
                                 + £5.95 ribbon
                            PG&P Barcode Initiative
                              1st November 2005


  What the barcodes look like
• Numeric for simplicity
• 8 digits to fit on an Eppendorf label

– Larger labels are clearer and can carry
  extra info


– Consider labelling the whole plate,
  rather than each item in it
                            PG&P Barcode Initiative
                              1st November 2005


        Numbering scheme
• Both projects have a database
• First 2 digits identify the database
  – 01 for Marine metagenomics
  – 02 for Fish toxicogenomics

• 6 digits per sample gives a potential 1
  million codes per project
                   PG&P Barcode Initiative
                     1st November 2005
Barcode Database
                   PG&P Barcode Initiative
                     1st November 2005
Barcode Database
                          PG&P Barcode Initiative
                            1st November 2005


      Printing and scanning
• Use the website to generate an EPL file
• Or use the software supplied with the
  printer (Windows only)
• Scan a code to look it up
• Scan a code to jump to line in CSV
• Scan a code to enter into spreadsheet
                   PG&P Barcode Initiative
                     1st November 2005
Barcode Database
       PG&P Barcode Initiative
         1st November 2005




Demo
                         PG&P Barcode Initiative
                           1st November 2005


     What the system is not
• A high throughput tool
• A system for process management (ie a
  LIM system)
• A way to catalogue samples labelled with
  an alternative barcode scheme
• A catalogue for a sample library (though
  it could form the basis for one)
                            PG&P Barcode Initiative
                              1st November 2005


              Data Quality
• Samples with ambiguous or inadequate data

• Sample stored without label
• Labelled samples with no data in database
• Labelled sample with incorrect data

• Sample was moved and move not recorded
• Sample was disposed but disposal not
  recorded (use of EnvBase expiry date)
                            PG&P Barcode Initiative
                              1st November 2005


              Data Quality
• Samples with ambiguous or inadequate data

• Sample stored without label
• Labelled samples with no data in database
• Labelled sample with incorrect data

• Sample was moved and move not recorded
• Sample was disposed but disposal not
  recorded (use of EnvBase expiry date)
                            PG&P Barcode Initiative
                              1st November 2005


              Data Quality
• Samples with ambiguous or inadequate data

• Sample stored without label
• Labelled samples with no data in database
• Labelled sample with incorrect data

• Sample was moved and move not recorded
• Sample was disposed but disposal not
  recorded (use of EnvBase expiry date)
                          PG&P Barcode Initiative
                            1st November 2005


        Training and Policy
• Web interface tries to be self
  documenting
• User guide will appear on the Wiki
• Further training? – on site or in Oxford?
• “Nothing goes in freezer X without a
  barcode”
• “Nothing goes off site without a barcode”
                         PG&P Barcode Initiative
                           1st November 2005


         Publication stage
• All data outputs from the project are
  published via EnvBase
• EnvBase already stores info on physical
  samples
• Rule of thumb is one barcode block
  becomes one EnvBase holding
• EnvBase will then link to reports and
  metadata download
            PG&P Barcode Initiative
              1st November 2005


An EnvBase Dataset
      PG&P Barcode Initiative
        1st November 2005


Linking
            PG&P Barcode Initiative
              1st November 2005


GenQuery Reporting
       PG&P Barcode Initiative
         1st November 2005




Demo
                          PG&P Barcode Initiative
                            1st November 2005


   The NERC Core Facilities
• Eg, Sequencing centre in Edinburgh,
  also Sheffield and Liverpool
• They will be able to query the database.
• All samples sent must have a valid code.
• All results returned must reference said
  code.
                          PG&P Barcode Initiative
                            1st November 2005


       Further Development
• Multi-database query
• Reporting
• Auditing?
• Packaging (and publication)
• Better integration with OOo
• Better integration with MS Office?
                                      PG&P Barcode Initiative
                                        1st November 2005


                 Thanks to
The NEBC in Oxford               CEHOX testers
  – Tim Booth                         – Andy Whiteley
  – Ashley Morley                     – Anna Law
  – Joe Wood
  – Bela Tiwari                  and everyone who
  – Stewart Houten               provided comments
  – Dawn Field                   and feedback

            but not: The Sanger Centre, who never returned my calls.
                               PG&P Barcode Initiative
                                 1st November 2005


                  Roundup
• Interface to be completed 1st December

• Please don't assume anything – only you
  know what you need from the system!
• Please send feedback
• Make use of the barcodes Wiki
http://darwin.nox.ac.uk/pgp-wiki/index.php/Barcodes