Introduction

Planning to use OpenSpecimen and wondering where to start? After OpenSpecimen is deployed, first step is for the administrators to set up the biobank data like users, containers and studies(protocols). This is one time set up initially after installation and every time a new container/protocol has to be created. This document covers the details about how to set up your biobank in OpenSpecimen.

Things to consider - before first steps

1. Do you want to integrate label printers?
2. Do you want to integrate OpenSpecimen with any other database?

First steps

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

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

Next steps

After completing the first steps, proceed to data entry steps to test your configurations. If you need to make changes, go a back and make the edits to the containers or protocols until the configuration is fine. You might encounter missing data fields at this step which will need to be created as "Custom forms".

Additional Information

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

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What you need to know before the setup:

1. Will there be single or multiple sites/repositories using OpenSpecimen? OpenSpecimen allows you to use single database for multiple repositories. You can create users of each site and separate out the data such that user of one site cannot operate/see data of another site.
   
   1. Site name
   2. Site coordinator name
2. Who will be the users of the system and what will be their roles? Need the details of:
   1. Name, Email, address, phone number
   2. Roles and privileges, which site/repository are they associated with?
3. How are your containers structured in your lab/repository? 

   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.

4. Is your biospecimen collection planned or unplanned? Based on this, collection protocol needs to be defined in OpenSpecimen:

   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.
5. How do you plan to label your specimens? You can define specimen label formats at protocol level so that system will auto generate it for you. For example
   1. Parent samples - patientID_sampleType_sampleNumber
   2. Child samples - ParentID_childNumber
6. Do you have a label printer which you plan to integrate with OpenSpecimen? This way, you will be able to print labels directly from the application. 
   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?
7. Are there other applications/software systems you want to integrate OpenSpecimen with like patient registry, clinical data systems, pathology systems? OpenSpecimen exposes REST APIs which helps you to easily integrate with other systems. This way you don't have to duplicate data that is already entered and can be pushed into OpenSpecimen database. 
8. Queries/Reports: What kind of queries you would like to do in your system to get data out for researcher requests of samples, biobank quarterly summary reports etc.
9. Do you give away your samples for researchers and you want to track in OpenSpecimen? You have to create distribution protocol for this based on different researchers/projects you give the samples OR you can create general distribution protocol.
10. Custom forms: OpenSpecimen allows you to capture additional annotations. Admins can create custom forms on their on. Identify such forms and fields to create the custom forms. 
    1. Are they participant, visit(Specimen Collection Group) or specimen level annotations?
    2. What are the fields, controls(drop down, text, date, checkbox etc.)?
    3. What are the values for the enumerated fields(drop down, radio button, checkbox)?