Uploaded image for project: 'LIMS'
  1. LIMS
  2. LIMS-3183

Processing bulk Dairy Samples 1. Configuration

    Details

    • Type: Story
    • Status: Resolved
    • Priority: Major
    • Resolution: Could be better
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: None
    • Labels:

      Description

      Using a first configuration for Bika LIMS being implemented at http://greenhilllabs.co.za/ analysing Raw Milk for Mastitis

      Use Case

      Veterinarian samples dairy herd on farm, composite udder samples, and requests analyses on them using the Batch Sample import spreadsheets
      Samples are analysed for:

      • Somatic Cell Count (Greenhill DU.SSC) on the Somascope LIMS-3112
      • Bacteriological Identification on MALDI Biotyper LIMS-3096
        Results are manually captured as interfaces Biotyper and Somascope are not currently available. Some results are retracted for retesting. When done, results are verified in the lab, and then by a vet and published by email

      Preparation

      De-activate non Dairy setup items

      To make testing easier, Sample Types, Analysis Services, Profiles, CRM’s etc..

      Configuration

      Auto Receive


      In the end you'd want lab clients to remotely register their Samples, which will then start-off in state 'Due' and when they arrive at lab, be checked in and promoted to 'Received'.
      Especially for the beginning now, i am setting Bika up as if all samples are registered at reception in the lab, and they start as Received, saving time. Clients can still register new Samples remotely

      Double verification

      • 1st Lab manager Verification/Retraction
      • 2nd Verification/Retraction by Vet

      The Verifiying Vet is a lab appointed consultant veterinarian that has to give final approval for results to be published. His/her user is configured as labclerk with added verifier authentication and cannot capture results. This role will be formalised in upcoming customisations

      Globally,

      x-checked on individual ASs

      Client Vet Contact

      Not the same as the lab's Verifiying Vet but the client's own vet that is monitoring the herd, He/she is created as a Contact at the client and included for copies of results for the Client's other Contacts

      Analysis Services

      Apologies irritating new bug here, listing ASs twice, once categorised and a second time not. To be sorted. Also encountered omn Profiles and Specifications described lower down

      Bacterial IDentification

      Greenhill MU.MID

      3 IDs with lookup lists (Bika Results options) populated from the BDAL sheets + ‘No reliable identification’.

      These are called Milk Bacteriology ID 1, ID 2 and ID 3 at the moment. Please modify if you have better titles for them

      3 BioTyper Scores, 1 for each ID, as Hidden - only seen in the lab and not on the COA

      SCC. Somatic Cell Count

      Numeric. I put an specification together, Test Spec Raw Milk, that will raise an amber alert for any values above 500 (from email, the vets’ warning) and red for results above 1000

      Analysis Profiles

      I created a new Profile, DU MID and SCC, to include all 6 DU.MID ASs, and SCC

      Reference Samples

      Since reference Samples frequently expire, some quicker than others, we create a Definition, or specification, for it first. This Reference Definition can then be used every time a new Reference SAmple is opened or made up from stock

      https://bikatest.greenhilllabs.co.za/bika_setup/bika_referencedefinitions/referencedefinition-4

      The actual Reference Sample is obtained from a Supplier, in this example we use Bika Lab Systems


      https://bikatest.greenhilllabs.co.za/bika_setup/bika_suppliers

      https://bikatest.greenhilllabs.co.za/bika_setup/bika_suppliers/supplier-6

      Create the Sample by selecting the corresponding Reference Definition, and complete most importantly its expiry date

      The Reference Sample inherits its specification from th Reference Definition used to create it

      Worksheet Templates

      Created 2 worksheet Templates, for DU.MID and SCC respectively. The latter includes the Counter Control Reference Sample

      Until the interfaces for the Somascope and BioTyper has been sorted out, these will be completed manually, and I limited them to 50 Samples each to make them manageable

      Import spreadsheet

      I updated the GreenHill Master Sample Import Template v1.0 with the new Profile and all GreenHills Clients and other config items, and removed everybody’s editing authorisation to protect its integrity.

      Please please make own copy when needed

      Continued in Processing bulk Dairy Samples 2. Batch Sample Import

      1. capture-for-jira-screenshot-20200614-192941-156.png
        152 kB
      2. capture-for-jira-screenshot-20200614-193029-018.png
        173 kB
      3. capture-for-jira-screenshot-20200614-193141-272.png
        159 kB
      4. capture-for-jira-screenshot-20200614-194116-568.png
        162 kB
      5. capture-for-jira-screenshot-20200614-194837-947.png
        266 kB
      6. capture-for-jira-screenshot-20200614-195443-955.png
        156 kB
      7. capture-for-jira-screenshot-20200614-200020-472.png
        260 kB
      8. capture-for-jira-screenshot-20200614-200815-089.png
        194 kB
      9. capture-for-jira-screenshot-20200614-201615-012.png
        128 kB
      10. capture-for-jira-screenshot-20200614-205627-708.png
        107 kB
      11. capture-for-jira-screenshot-20200614-205704-425.png
        96 kB
      12. capture-for-jira-screenshot-20200616-083718-976.png
        207 kB
      13. capture-for-jira-screenshot-20200616-084549-972.png
        226 kB
      14. capture-for-jira-screenshot-20200616-084618-720.png
        172 kB
      15. capture-for-jira-screenshot-20200616-084653-650.png
        160 kB
      16. capture-for-jira-screenshot-20200616-084749-337.png
        138 kB
      17. capture-for-jira-screenshot-20200616-084858-886.png
        143 kB
      18. capture-for-jira-screenshot-20200616-084926-233.png
        122 kB
      19. capture-for-jira-screenshot-20200617-115418-408.png
        200 kB
      20. capture-for-jira-screenshot-20200617-115449-301.png
        347 kB
      21. capture-for-jira-screenshot-20200617-115742-811.png
        408 kB
      22. capture-for-jira-screenshot-20200617-115837-105.png
        212 kB
      23. capture-for-jira-screenshot-20200617-115917-827.png
        169 kB
      24. capture-for-jira-screenshot-20200617-120030-844.png
        167 kB

        Issue Links

          Activity

          There are no comments yet on this issue.

            People

            • Assignee:
              lemoene lemoene
              Reporter:
              lemoene lemoene
            • Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

              Dates

              • Created:
                Updated:
                Resolved: