Versions Compared


  • This line was added.
  • This line was removed.
  • Formatting was changed.


  1. Do you want to integrate label printers?
  2. Do you want to integrate OpenSpecimen with any other database like clinical database, pathology systems or patient registry?

First steps

You need to know the following to start setting up the biobank in OpenSpecimen

  1. User detailsDetails of the users who will use OpenSpecimen
  2. Sites from where specimens will be collected or stored
  3. Storage container details structure and dimensions (E.g. Freezer, Rack, Box etc)
  4. Collection Protocol details (e.g. consents, events, type/quanity of specimens per event, aliqouts, derivatives, etc)


  1. Go to Advanced Query and check out the standard reports
  2. Are there additional reports do you want to generate?


What you need to know before the setup:


  1. Site name
  2. Site coordinator name


  1. Name, Email, address, phone number
  2. Roles and privileges, which site/repository are they associated with?


  1. What is container hierarchy, for example Freezer-Shelf-Rack-Box

  2. What are the dimensions? For example:
    1. Freezer - 5*1 ( which means it can hold 5 racks horizontally)
    2. Rack - 1*11 (which means it can hold 11 boxes vertically)
    3. Boxes - 9*9, 10*10
  3. Should there be restrictions set up for boxes like the boxes are assigned to specific specimen type like blood box, DNA box? This will help OpenSpecimen to auto assign containers accurately to the samples being collected.


  1. Planned protocol are like clinical trials - you will know in advance what will be collected under each patient visit and how it will be processed into aliquots and derivatives. For example:

    1. Visit one:  3 Blood tubes collected and processed into Serum, Plasma and Buffy which is further processed into aliquots
    2. Visit Two: Surgery where tumor and normal tissue collected from lung
    3. Follow up: Same as first visit
  2. Unplanned or Generic Biobanking protocol - Nothing is defined in protocol but defined when data entry is done
    OpenSpecimen allows you to do data entry for both types of protocols. In planned protocol, you are allowed to define all the details which will help you in data entry.

  3. Do you plan to capture consents for participants registered? You can set up consent tiers like below at protocol level to capture responses:
    1. Consent to store samples for future research purposes
    2. Consent to distribute samples for researchers within and outside the university
    3. Consent to process specimens into DNA for research
      OpenSpecimen allows you to capture consent responses to individual tiers like above or you can upload signed consent forms as pdf.


  1. Parent samples - patientID_sampleType_sampleNumber
  2. Child samples - ParentID_childNumber


  1. What will be format of the label?
  2. Will the format differ based on type of sample and for which protocol it was collected for?



Refer to the Questionnaire while collecting the details from the repository users.