Documentation needs attention

[KeironO]

Is your feature request related to a problem? Please describe.

We need to start prioritising user documentation. Lots of new features and workflows have been added since 21.01.

Describe the solution you'd like

• Deployment: How to get the system set up. This can be limited to docker.
• Getting Started:
  • How to get a user set up after set up.
  • How to give feedback.
  • Overview Panel
  • Search.
  • Find out which version is being run.
• Sample Data Entry:
  • A graphical overview of Sample entry procedure.
  • Setting up required forms (PROTOCOLS).
  • Making a new Sample.
  • Viewing a Sample
• Donor Data Entry:
  • A graphical overview of Donor entry procedure.
  • Making a new Donor
  • Viewing a Donor
  • Associating a Donor to Sample
  • Setting up disease information

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.

Additional context
Add any other context or screenshots about the feature request here.

[KeironO]

https://github.com/AberystwythSystemsBiology/limbus/projects/9

[anthonyhorlock]

This is a basic idea of how I see the sections developing in the documentation. Some suggestions are also in the document of additional features that may or may not be useful.

I think separating out the functions into admin, use as a freezer log, Biobanking, batch functions etc. seems to make sense to me.

I am happy to arrange a TEAMS meeting to screen share my idea of how the workflow works, just in case I am missing something, or am doing something that you don't expect me to do. This might help to reduce unnecessary work your end:

(Edit from Keiron: Pasted document in here so people without MS Word can see 👍)

Documents for LIMBUS.docx

Using LIMBUS as a freezer log

• Similar to sample registration section, but only select info is needed (we can discuss that). - Perhaps a way of highlighting the areas of the database screenshots that are relevant.
• Assigning freezer log consent
• Selection of study/trial
• Entering trial-specific ID
• Creating the samples
• Deriving samples
• Aliquoting samples
• Storing samples in rack

LIMBUS Biobanking functions

Donor Registration

• Adding new donor
• Adding consent (can’t add new samples until this is done)
• Adding diagnosis info
• Adding samples to donor (sample creation basics already on site)

Donor index

• What info is shown
• How to filter
• How to search

Samples index

• What info is shown ✔️
• How to filter ✔️
• How to search ✔️

Sample shipments

• Through sample shipments or through sample cart
• Internal and external destinations
• Shipment index
• Updating shipment status
• Collected shipment update – tracking number etc
• Delivered shipment update – what actions receiving site needs to do when a sample is delivered
• Receiving site to review samples on receipt (probably quantity or identity check on most occasions)
• Adding received samples into cart
• Adding received samples/rack into a freezer shelf

Batch functions

• Adding samples & racks to the cart
• Batch shipments
• Batch review instructions
• Adding disposal instructions to reviews
• Batch destruction (highlight need for disposal instruction during sample review stage)

Document portal

• When would you need to add documents to the portal?
• Adding new documents ✔️
• Uploading files ✔️
• Associating documents to samples
• Do we need an option to assign documents to donors?

Consent form portal

• Creating new consent forms (importance of adding version to consent forms) ✔️
• Adding questions to consent forms ✔️
• Question types ✔️

Attribute portal

• When would you need to add attributes?
• Assigning attributes to samples
• Would you ever need to assign an attribute to a donor?

Diagnostic procedures

• Is there a need for this? When would you need to add it?
• Do we need to be proactive and add the option for a Biobank donor that might have been part of a study using medical devices? (Not currently carried out in the health board, but they do want to move into this area in the future)

Storage portal

• Adding buildings
• Adding rooms
• Adding freezers
• Adding shelves
• Creating racks
• Uploading barcodes into racks
• Assigning samples to the racks
• Re-positioning samples in racks

Admin functions

Adding New Users

• Assigning site & account type
• Assigning default password for user to change on receipt
• Updating user settings to additional sites/changing sites

Sample Audit (when complete)

• Filtering according to need
• Understanding content section of audit – new events vs. changes to existing samples/donors, as well as monitoring deletions

Adding/managing new sites

• Internal & external sites
• Adding addresses
• Can we add active/inactive option (perhaps a tick box that we can change) to external sites that would then only provide a list of external active sites when carrying out sample shipments.

Thank-you for all your work!

[KeironO]

Here's the rtd branch if you want to keep an eye out on the progress of this Issue: https://limbus.readthedocs.io/en/fix-general-documentation/