CDISC 360i defines a vision and roadmap to enable standards-driven automation across the clinical research data life cycle - from study design to analysis. The purpose of these notebooks is to demonstrate the 360i Technical Roadmap by showcasing a strategy for research data pipeline automation using end-to-end, machine-readable standards metadata.
These notebooks automate study design using concepts and a standardized model to build a digital protocol. Aligned Case Report Forms (CRFs) and SDTM resources will be automatically generated as downstream artifacts using metadata from the digital protocol.
This environment exists as two Docker containers; one hosting a PostgreSQL relational database and the other, the Jupyter notebook environment.
- Navigate to https://github.com/git-guides/install-git to install the latest git distribution for your platform.
- Navigate to https://www.docker.com/ to Download Docker Desktop. This will include all binaries that are required to run Docker containers on your chosen platform.
- Start Docker Desktop on your platfrom.
- Clone this repository to the desired directory.
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Change into the root of the cloned directory.
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Populate the file .env.template for the variables in the file.
Note1: The OSB_BEARER_TOKEN value is only required if running the OSB-specific API calls included in the Notebook
Note2: The CDISC_API_KEY value is required to run the generation of the LB domain
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Execute
source initial-startup.sh -
Open a browser to http://localhost:8888
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Navigate to the notebooks directory and open the CDISC_360i_Jupyter_Protocol_to_Submission.ipynb notebook.
All CDISC utilities as well as the resources will be created in the notebooks directory in the clinical-notebook container.
All tables will be created in the PostgreSQL database in the clinical-database container.
Other GitHub projects used in the notebooks
| Project | GitHub Repository |
|---|---|
| Study Definition Workbench | https://github.com/data4knowledge/study_definitions_workbench |
| Open Study Builder | https://gitlab.com/Novo-Nordisk/nn-public/openstudybuilder/OpenStudyBuilder-Solution |
| Study USDM documents | https://github.com/cdisc-org/360i/tree/main/data/protocol/LZZT/usdm |
| USDM validation utility | https://github.com/pendingintent/cdisc-json-validation |
| CDISC CORE Rules Engine | https://github.com/cdisc-org/cdisc-rules-engine |
| CRF creation | https://github.com/lexjansen/cdisc360i-pocs |
| Trial Design Dataset creation | https://github.com/pendingintent/cdisc-usdm-utils |
| Define-XML template creation | https://github.com/dostiep/360i |
| Define-XML creation | https://github.com/swhume/template2define |
| Raw subject data | https://github.com/alidootson/UpdatedCDISCPilotData/tree/main/UpdatedCDISCPilotData/CDASH |