diff --git a/.nojekyll b/.nojekyll index 8959d4d..c010f9a 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -abbaed0d \ No newline at end of file +41c61c36 \ No newline at end of file diff --git a/about.html b/about.html index c7d5935..36e7544 100644 --- a/about.html +++ b/about.html @@ -106,7 +106,7 @@
  • - +
    • @@ -428,24 +428,24 @@

    2 Our implementation

    We store all features in a Microsoft SQL database, and for now have focused on the design of the feature generation pipeline. We have not (yet) implemented separate approaches for realtime time serving (for predictions) and batch serving (for training). As our data volumes and user base grow, we will review this decision.

    We chose MSSQL to ensure access to the database for the widest possible community within the NHS.

    -

    The feature pipeline is managed by the Data Forge repository.

    +

    The feature pipeline is managed by the Data Forge repository.

    The key components of this include:

    A pipeline configuration
    -This defines which features are built, and specifies specific configuration. See pipeline.json +This defines which features are built, and specifies specific configuration. See pipeline.json
    A pipeline trigger
    -This defines the schedule at which features are updated. See trigger.json. +This defines the schedule at which features are updated. See trigger.json.
    A per feature entry point
    -See bloodpressure.py that generates a feature for both the latest, and the average blood pressure (where the 24 hour aggregation window is defined in pipeline.json). The are regenerated hourly as per the trigger.json configuration. +See bloodpressure.py that generates a feature for both the latest, and the average blood pressure (where the 24 hour aggregation window is defined in pipeline.json). The are regenerated hourly as per the trigger.json configuration.
    A per feature ‘job’
    -See bloodpressure/job.py that fetches the source data, splits the text representation 120/70 into integers for systolic and diastolic pressures, +See bloodpressure/job.py that fetches the source data, splits the text representation 120/70 into integers for systolic and diastolic pressures,

    Each feature is keyed on an identifier for the hospital visit, and the horizon_datetime is the timestamp derived from the trigger against which all these features are anchored.

    @@ -1033,7 +1033,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/anatomy/gitea.html b/anatomy/gitea.html index 95ecfc9..cf4610a 100644 --- a/anatomy/gitea.html +++ b/anatomy/gitea.html @@ -107,7 +107,7 @@

  • - +
    • @@ -1010,7 +1010,7 @@

    What’s the difference between Azure, a landing zone, a TRE,

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/faq/contributing.html b/faq/contributing.html index 598ad9f..825ee84 100644 --- a/faq/contributing.html +++ b/faq/contributing.html @@ -141,7 +141,7 @@

  • - +
    • @@ -460,7 +460,7 @@

    How do I contribute to the documentation

  • Notebooks and vignettes can just be saved in ./docs/notebooks/. Please ensure the first cell in the notebook contains the YAML metadata for the author, title, and categories.
  • Quick notes in the style FAQ answers, or ‘today I learned’ notes can be saved into ./docs/faq/
-

Both will be automatically indexed when the site is deployed. The documentation is deployed using Quarto, and the documentation is built from the ./docs/ directory. Please fork or clone .

+

Both will be automatically indexed when the site is deployed. The documentation is deployed using Quarto, and the documentation is built from the ./docs/ directory. Please fork or clone .

You will need to have

  • installed basic python and jupyter extensions necessary including those for jupyter
    • @@ -1054,7 +1054,7 @@

    How do I contribute to the documentation

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/faq/cosmosdb.html b/faq/cosmosdb.html index 919e6be..2e30337 100644 --- a/faq/cosmosdb.html +++ b/faq/cosmosdb.html @@ -106,7 +106,7 @@
  • - +
    • @@ -1016,7 +1016,7 @@

    Please summarise the approach to Information Security?

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/faq/jupyter.html b/faq/jupyter.html index 5c3b2fc..30c464d 100644 --- a/faq/jupyter.html +++ b/faq/jupyter.html @@ -140,7 +140,7 @@
  • - +
    • @@ -1061,7 +1061,7 @@

    Running a Jupyter notebook from this documentation within a vi

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/faq/what-is-algorithm-stewardship.html b/faq/what-is-algorithm-stewardship.html index 8bd54ea..788be92 100644 --- a/faq/what-is-algorithm-stewardship.html +++ b/faq/what-is-algorithm-stewardship.html @@ -106,7 +106,7 @@

  • - +
    • @@ -1002,7 +1002,7 @@

    Walkthrough notes

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/administrator/administrator.html b/personas/administrator/administrator.html index 4f709e8..6fc1f84 100644 --- a/personas/administrator/administrator.html +++ b/personas/administrator/administrator.html @@ -108,7 +108,7 @@
  • - +
    • @@ -993,7 +993,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/administrator/configuration.html b/personas/administrator/configuration.html index 5950a36..edae76c 100644 --- a/personas/administrator/configuration.html +++ b/personas/administrator/configuration.html @@ -108,7 +108,7 @@
  • - +
    • @@ -1029,7 +1029,7 @@

    <

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/datascientist/datascientist.html b/personas/datascientist/datascientist.html index 7ebd6d3..6d7a1e7 100644 --- a/personas/datascientist/datascientist.html +++ b/personas/datascientist/datascientist.html @@ -108,7 +108,7 @@

  • - +
    • @@ -994,7 +994,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/datascientist/onboarding.html b/personas/datascientist/onboarding.html index 29e9caf..906ccbe 100644 --- a/personas/datascientist/onboarding.html +++ b/personas/datascientist/onboarding.html @@ -110,7 +110,7 @@
  • - +
    • @@ -1121,7 +1121,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/developer/building-an-app.html b/personas/developer/building-an-app.html index 29ea70a..16f2971 100644 --- a/personas/developer/building-an-app.html +++ b/personas/developer/building-an-app.html @@ -108,7 +108,7 @@

  • - +
    • @@ -1055,7 +1055,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/developer/developer.html b/personas/developer/developer.html index 4136d59..f63e70b 100644 --- a/personas/developer/developer.html +++ b/personas/developer/developer.html @@ -108,7 +108,7 @@

  • - +
    • @@ -1018,7 +1018,7 @@

    Personas

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/personas/steward/steward.html b/personas/steward/steward.html index b38f6a9..5d66569 100644 --- a/personas/steward/steward.html +++ b/personas/steward/steward.html @@ -108,7 +108,7 @@
  • - +
    • @@ -993,7 +993,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/10_prerequisites.html b/quickstart/10_prerequisites.html index 03ef883..cfed151 100644 --- a/quickstart/10_prerequisites.html +++ b/quickstart/10_prerequisites.html @@ -107,7 +107,7 @@
  • - +
    • @@ -1031,7 +1031,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_ads.html b/quickstart/20_setup_ads.html index 3db13bd..fefb462 100644 --- a/quickstart/20_setup_ads.html +++ b/quickstart/20_setup_ads.html @@ -108,7 +108,7 @@

  • - +
    • @@ -1021,7 +1021,7 @@

    Azure Data Studio

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_conda.html b/quickstart/20_setup_conda.html index beac123..5331b17 100644 --- a/quickstart/20_setup_conda.html +++ b/quickstart/20_setup_conda.html @@ -142,7 +142,7 @@
  • - +
    • @@ -1068,7 +1068,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_flowehr_locally.html b/quickstart/20_setup_flowehr_locally.html index dd87075..4377fd9 100644 --- a/quickstart/20_setup_flowehr_locally.html +++ b/quickstart/20_setup_flowehr_locally.html @@ -142,7 +142,7 @@

  • - +
    • @@ -452,14 +452,14 @@

    Set-up & deployment

    1 Get the repositories

    Repositories:

      -

    1. Model-Seedling - starting point for a new Data Science project

      2. -

    2. Dash-Seedling - used for creating Dash web apps

      3. +

    3. Model-Seedling - starting point for a new Data Science project

      4. +

    4. Dash-Seedling - used for creating Dash web apps

    5. AzureTRE-Deployment - FlowEHR Azure TRE deployment, linking the AzureTRE with flowEHR and custom data sources

      6. -

    6. Azure-Bootstrap - Utility for bootstrapping common Azure resources needed to store Terraform state, containers and configure build agents, used in CI.

      7. -

    7. FlowEHR-Data-Pot - fork or clone this repo. Example data pipeline.

      8. -

    8. FlowEHR - this a template repo so you create your own repo from the template and customise it to your institution.

      9. -

    9. Powershell-Scripts - allows VM Customisations of windows VMs

      10. -

    10. Data source deployments - can use Satellite for synthetic EMAP star schema

      11. +

    11. Azure-Bootstrap - Utility for bootstrapping common Azure resources needed to store Terraform state, containers and configure build agents, used in CI.

      12. +

    12. FlowEHR-Data-Pot - fork or clone this repo. Example data pipeline.

      13. +

    13. FlowEHR - this a template repo so you create your own repo from the template and customise it to your institution.

      14. +

    14. Powershell-Scripts - allows VM Customisations of windows VMs

      15. +

    15. Data source deployments - can use Satellite for synthetic EMAP star schema

    @@ -1169,7 +1169,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_gitea.html b/quickstart/20_setup_gitea.html index 94786f5..cb24ec9 100644 --- a/quickstart/20_setup_gitea.html +++ b/quickstart/20_setup_gitea.html @@ -142,7 +142,7 @@

  • - +
    • @@ -1054,7 +1054,7 @@

    Gitea set-up

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_overview.html b/quickstart/20_setup_overview.html index 7dab087..1677f1e 100644 --- a/quickstart/20_setup_overview.html +++ b/quickstart/20_setup_overview.html @@ -110,7 +110,7 @@
  • - +
    • @@ -1079,7 +1079,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_vm.html b/quickstart/20_setup_vm.html index b7874b3..8d402e9 100644 --- a/quickstart/20_setup_vm.html +++ b/quickstart/20_setup_vm.html @@ -108,7 +108,7 @@

  • - +
    • @@ -1009,7 +1009,7 @@

    Virtual Machine set-up

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/20_setup_vscode.html b/quickstart/20_setup_vscode.html index c0f42e6..312cc1a 100644 --- a/quickstart/20_setup_vscode.html +++ b/quickstart/20_setup_vscode.html @@ -108,7 +108,7 @@
  • - +
    • @@ -1014,7 +1014,7 @@

    Setting up VS Code

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/30_connecting.html b/quickstart/30_connecting.html index c40698a..dd693a5 100644 --- a/quickstart/30_connecting.html +++ b/quickstart/30_connecting.html @@ -108,7 +108,7 @@
  • - +
    • @@ -433,7 +433,7 @@

    4 Accessing Synthetic Data

      -
    1. We have built a tool (Satellite) that streams structually correct but semantically meaningless data for the purposes of development.
      2. +
    2. We have built a tool (Satellite) that streams structually correct but semantically meaningless data for the purposes of development.
    3. We have collaborated with colleagues at the Alan Turing Institute, and have used their SQLSynthGen tool to create a replica of data.
    @@ -1035,7 +1035,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/30_connecting_feature_store.html b/quickstart/30_connecting_feature_store.html index d960029..a0f92bd 100644 --- a/quickstart/30_connecting_feature_store.html +++ b/quickstart/30_connecting_feature_store.html @@ -140,7 +140,7 @@

  • - +
    • @@ -1136,7 +1136,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/40_features.html b/quickstart/40_features.html index d7288ff..ebc1ee3 100644 --- a/quickstart/40_features.html +++ b/quickstart/40_features.html @@ -109,7 +109,7 @@

  • - +
    • @@ -1024,7 +1024,7 @@

    Feature building

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/50_modelling.html b/quickstart/50_modelling.html index 4e9e924..f9829f5 100644 --- a/quickstart/50_modelling.html +++ b/quickstart/50_modelling.html @@ -108,7 +108,7 @@
  • - +
    • @@ -992,7 +992,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/60_deployment.html b/quickstart/60_deployment.html index eb4be46..550d3b5 100644 --- a/quickstart/60_deployment.html +++ b/quickstart/60_deployment.html @@ -142,7 +142,7 @@
  • - +
    • @@ -450,8 +450,8 @@

    Author & deploy a FlowEHR App

    Let’s deploy your first FlowEHR App!

    1 Pick a 🌱 Seedling

    -

    The first step is to pick a seedling. A seedling is a pre-built FlowEHR App template that you can use as a starting point for your own app. You can find a list of seedlings in the UCLH Foundry GitHub Org. Which you use largely depends on which frameworks you want, whether you’re building a dashboard, web API, model etc.

    -

    If you have no strong preference at this point, the Dash Seedling is a good place to start for building a simple dashboard.

    +

    The first step is to pick a seedling. A seedling is a pre-built FlowEHR App template that you can use as a starting point for your own app. You can find a list of seedlings in the UCLH Foundry GitHub Org. Which you use largely depends on which frameworks you want, whether you’re building a dashboard, web API, model etc.

    +

    If you have no strong preference at this point, the Dash Seedling is a good place to start for building a simple dashboard.

    2 Add app to FlowEHR config

    @@ -1148,7 +1148,7 @@

    Built for the NHS | 2022-2023

    -
    +
     
    diff --git a/quickstart/70_stewardship.html b/quickstart/70_stewardship.html index 54f1f37..6472f0b 100644 --- a/quickstart/70_stewardship.html +++ b/quickstart/70_stewardship.html @@ -110,7 +110,7 @@

  • - +
    • @@ -427,7 +427,7 @@

    Stewardship

    -

    Models should not be deployed without a monitoring strategy. To this end, we provide a template that addresses data drift and model drift. These steps are in addition to the data testing that is built into the feature engineering pipeline.

    +

    Models should not be deployed without a monitoring strategy. To this end, we provide a template that addresses data drift and model drift. These steps are in addition to the data testing that is built into the feature engineering pipeline.

    1 Key terms

      @@ -440,7 +440,7 @@

      2 Walk through

        -
      • Clone the ‘model seedling’ template
        • +
      • Clone the ‘model seedling’ template
      @@ -1038,7 +1038,7 @@

      Built for the NHS | 2022-2023

      -
      +
       
      diff --git a/quickstart/quickstart.html b/quickstart/quickstart.html index d34e83a..fc9cdac 100644 --- a/quickstart/quickstart.html +++ b/quickstart/quickstart.html @@ -106,7 +106,7 @@

    • - +
      • @@ -978,7 +978,7 @@

      Built for the NHS | 2022-2023

      -
      +
       
      diff --git a/sitemap.xml b/sitemap.xml index 67b1d82..3314e10 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -2,178 +2,178 @@ https://SAFEHR-data.github.io/Garden-Path/personas/administrator/administrator.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/personas/datascientist/datascientist.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/personas/steward/steward.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/personas/developer/building-an-app.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/index.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/anatomy/apps.html - 2024-08-28T10:01:31.896Z + 2024-08-28T13:06:22.057Z https://SAFEHR-data.github.io/Garden-Path/anatomy/tre.html - 2024-08-28T10:01:31.900Z + 2024-08-28T13:06:22.061Z https://SAFEHR-data.github.io/Garden-Path/anatomy/gitea.html - 2024-08-28T10:01:31.900Z + 2024-08-28T13:06:22.061Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_overview.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_vscode.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_vm.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/10_prerequisites.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_conda.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/60_deployment.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/quickstart.html - 2024-08-28T10:01:32.000Z + 2024-08-28T13:06:22.157Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_flowehr_locally.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/vignettes/dicom_access.html - 2024-08-28T10:01:32.000Z + 2024-08-28T13:06:22.161Z https://SAFEHR-data.github.io/Garden-Path/faq/jupyter.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/faq/information-security.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/faq/faq.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/faq/contributing.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/notes/walkthrough_v1.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/about.html - 2024-08-28T10:01:31.896Z + 2024-08-28T13:06:22.057Z https://SAFEHR-data.github.io/Garden-Path/faq/cosmosdb.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/faq/what-is-algorithm-stewardship.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/faq/emap.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/faq/azure-anatomy.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/vignettes/vignettes.html - 2024-08-28T10:01:32.000Z + 2024-08-28T13:06:22.161Z https://SAFEHR-data.github.io/Garden-Path/vignettes/data_lake_access.html - 2024-08-28T10:01:32.000Z + 2024-08-28T13:06:22.157Z https://SAFEHR-data.github.io/Garden-Path/quickstart/40_features.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/30_connecting.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_gitea.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/30_connecting_feature_store.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/20_setup_ads.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/50_modelling.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/quickstart/70_stewardship.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/anatomy/aml.html - 2024-08-28T10:01:31.896Z + 2024-08-28T13:06:22.057Z https://SAFEHR-data.github.io/Garden-Path/anatomy/feature_store.html - 2024-08-28T10:01:31.900Z + 2024-08-28T13:06:22.061Z https://SAFEHR-data.github.io/Garden-Path/anatomy/vm.html - 2024-08-28T10:01:31.900Z + 2024-08-28T13:06:22.061Z https://SAFEHR-data.github.io/Garden-Path/anatomy/monitoring.html - 2024-08-28T10:01:31.900Z + 2024-08-28T13:06:22.061Z https://SAFEHR-data.github.io/Garden-Path/personas/developer/developer.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/personas/personas.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/personas/datascientist/onboarding.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z https://SAFEHR-data.github.io/Garden-Path/personas/administrator/configuration.html - 2024-08-28T10:01:31.908Z + 2024-08-28T13:06:22.069Z diff --git a/vignettes/data_lake_access.html b/vignettes/data_lake_access.html index 65e68d9..8e34361 100644 --- a/vignettes/data_lake_access.html +++ b/vignettes/data_lake_access.html @@ -142,7 +142,7 @@
    • - +
      • @@ -1202,7 +1202,7 @@

      Built for the NHS | 2022-2023

      -
      +
       
      diff --git a/vignettes/dicom_access.html b/vignettes/dicom_access.html index 962f841..1859b87 100644 --- a/vignettes/dicom_access.html +++ b/vignettes/dicom_access.html @@ -142,7 +142,7 @@