Task Ref. 2026-14

Clinical Data Management for Myotonic Dystrophy Type 1 (DM1) - Three-Month Research Action Plan for IGTP. - Gary J. Espitia S.

All the documentation is presented within a fully reproducible environment - all the tools you need (R, RStudio, Python, tidyverse, Pandoc, LaTeX, etc.) are defined in a single Nix flake.

This report presents a three-month action plan to design, build, and validate a minimum viable platform for prospective data collection in Myotonic Dystrophy Type 1 (DM1). The platform is conceived as mobile-first, respects a clear role-based governance model, and is aligned with the General Data Protection Regulation (GDPR) and the European Health Data Space (EHDS). For clinical interoperability it adopts Fast Healthcare Interoperability Resources (FHIR), while the research analytics layer relies on the Observational Medical Outcomes Partnership Common Data Model (OMOP CDM). Every component in the stack is Free and Open-Source Software (FOSS) and follows a local-first philosophy, so that no proprietary dependency constrains future evolution.

Setup (step by step)

1. Install the Nix package manager

Linux (Ubuntu, Fedora, Debian, etc.)

sh <(curl -L https://nixos.org/nix/install) --daemon

Close and re-open your terminal when done.

macOS

sh <(curl -L https://nixos.org/nix/install)

Note: RStudio is Linux-only via Nix. Install it separately with brew install --cask rstudio or from https://posit.co/download/rstudio-desktop/.

Windows (via WSL2)

1. Open PowerShell as Administrator: wsl --install
2. Restart, then open the Ubuntu app.
3. Inside Ubuntu: sh <(curl -L https://nixos.org/nix/install) --daemon

2. Enable Flakes (one-time)

mkdir -p ~/.config/nix
echo "experimental-features = nix-command flakes" >> ~/.config/nix/nix.conf

3. Clone and enter the nix environment

git clone https://github.com/stradichenko/task-ref-2026-14.git
cd task-ref-2026-14
nix develop

Documents

How to render

Inside the Nix environment:

pandoc report.md -o report.pdf --pdf-engine=xelatex
pandoc annex.md -o annex.pdf --pdf-engine=xelatex

Artefact	Location
Report source	report.md
Annex source	annex.md
Rendered PDFs	report.pdf, annex.pdf (generated locally)

The report and annex reference images from architecture/, data_flow/, gantt/, raci/, rbac/, risk_matrix/, and small_exploratory_analysis/.

---

Exploratory Analysis

Interactive R Markdown report progressing from demographic summaries to Kaplan-Meier survival analysis, using synthetic CDISC data.

View	Link
GitHub Pages (recommended)	https://stradichenko.github.io/task-ref-2026-14/exploratory_analysis.html
Source Rmd	small_exploratory_analysis/exploratory_analysis.Rmd

Rscript -e 'rmarkdown::render("small_exploratory_analysis/exploratory_analysis.Rmd", output_dir = "docs")'

---

Architecture Diagram

Available as PNG (for the PDF report/annex) and .drawio (editable in app.diagrams.net or the VS Code Draw.io extension).

Platform Architecture Map. Zoned view of all system components-Client, API & Identity, Operational Data, Processing & ETL, Research & Analytics, and External & Interoperability-with Identity & Access Management and Observability as cross-cutting concerns. Data-flow sequence numbers indicate the order of interactions.