design.qmd

---
title: "Design"
description: "Expanded explanations and descriptions of the principles, practices, tools, methods, and decisions we have for work across DP-Next."
---

## Principles

Part of the aim for DP-Next, and the purpose of Work Package 1, is to
produce scientific results that follow open scientific and reproducible
practices. In addition to this aim, Work Package 1 also aims to help
produce better research in less time and resources. Aligning with these
overall aims and expanding on the [guiding
principles](strategy.qmd#guiding-principles) in the Strategy page, we
want to eventually follow these principles:

-   Incorporate explicit feedback loops in how we collaborate
-   Actively and continually seek out and identify ways we can improve
    how we work
-   Start with what we can do now and improve iteratively and
    incrementally
-   Make work visible (at least to the group), including tasks to do,
    project management
-   Incorporate regular upskilling activities, such as "pair-working"
-   Prefer written communication over verbal communication to ensure
    more people can participate
-   Use open source software as much as possible and is reasonable
-   Have meetings sparingly and only when extensive, concurrent
    discussions and brainstorming are needed

## Practices, tools, and methods

And to achieve these principles, we also eventually (not all at once)
want to work towards a point where we:

-   Use GitHub or just Git to manage and track all files
-   Use R or Python for doing data analysis
-   Use Quarto Markdown for writing documentation
-   Use Quarto with R or Python code to write reproducible scientific
    output
-   Use Quarto to create websites of our work
-   Use FAIR principles when managing data
-   Use Seedcase software to structure and manage data
-   Use Zenodo to upload protocols (before submitting to other outlets),
    analysis code, and preprints
-   Use GitHub Project boards to follow a
    [Kanban](https://en.wikipedia.org/wiki/Kanban_board)-style approach
    to project management
-   Use Discord for informal communication or for coordinating across
    groups
-   Use Discord for video meetings, including for upskilling activities
-   Use Teamup, a calendar tool, for scheduling meetings and events
    relevant to all groups
-   Use GitHub Projects and Issues to create, discuss, and manage tasks
    and issues

## Decisions

To be explicit about the reasons for our choices of tools, methods, and
approaches that apply to the DP-Next project, we have documented them in
the [Decisions](decisions/index.qmd) section. This website will not
document choices for things that are specific to a single work package,
for instance, the type of machine to measure a specific biological
marker. Instead, we will focus on the decisions that are relevant to the
entire project or to multiple work packages.

## Design patterns

To help simplify how we work, it's useful to follow commonly used
patterns in project development and collaboration. In our case, the
design patterns we will use are:

### One Git or GitHub repository per scientific output

The pattern of "one repo, one product" is a widely used pattern in many
types of projects. There are many tools, templates, and workflows that
are built around this pattern. For instance, it is easier to ensure a
scientific document is reproducible if it follows this pattern. So
administratively and collaboratively, it is easier to use a pattern like
this, since it is a standardized way of structuring work. For DP-Next,
this pattern includes the protocols as well as the scientific results.

Some servers don't allow internet or easy access to outside resources
like GitHub. But all servers have Git installed. In those cases, each
scientific output is one Git repository.