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  1. LIMS
  2. LIMS-3183

Processing bulk Dairy Samples 1. Configuration


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


      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


      De-activate non Dairy setup items

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


      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


      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


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



      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

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            • Assignee:
              lemoene lemoene
              lemoene lemoene
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