GeoEpi Lab Book

Practical guidance for organizing collaborative geographical epidemiology.

The GeoEpi Lab Book helps scientists and collaborators organize work that combines geography, epidemiology, ecology, biology, data, and computation. It is a practical living guide for improving scientific quality, reproducibility, continuity, and efficiency.

The basic model

A GeoEpi project is a network of linked analytical subprojects, data assets, computational work, and scientific products—not a single repository or directory.

flowchart TD
    H[GeoEpi Hub] --> P1[Project A]
    H --> P2[Project B]
    P1 --> R1[Subproject repository]
    P1 --> R2[Subproject repository]
    P2 --> R3[Subproject repository]
    R1 --> C[Atlas / Ceres]
    R2 --> C
    R3 --> C
    R1 --> S[Synthesis and products]
    R2 --> S
    R3 --> S
    S --> M[Manuscript]
    S --> D[Dashboard or report]
    S --> O[Released data or product]

• The GeoEpi Hub holds project context and coordination.
• A subproject repository holds the scientific implementation and analytical provenance for one coherent workstream.
• Atlas and Ceres hold approved large or controlled data and computational work.
• Products include manuscripts, reports, dashboards, released data, and other accepted outputs.

Run-level details—parameters, environments, random seeds, job IDs, logs, manifests, and outputs—stay with the subproject and its computational storage. They do not belong in the Hub.

Start with the question you have

• Start Here gives the shortest path for a new or inherited project.
• How GeoEpi organizes work explains Hub, project, subproject, repository, and run.
• Data management separates the project DMP, controlled-data inventory, and analytical provenance.
• Computing and repositories explains what belongs on GitHub versus Atlas or Ceres.
• Tools and collaboration describes the group’s common working tools.
• Templates provides a small set of reusable starting points.