Commit a6711087 authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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update README

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<a href=""><img src="" alt="Gem version"></a> <a href=""><img src="" alt="Build status"></a>
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<h1 align="center">Just the Docs</h1>
<p align="center">A modern, highly customizable, and responsive Jekyll theme for documentation with built-in search.<br>Easily hosted on GitHub Pages with few dependencies.</p>
<p align="center"><strong><a href="">See it in action!</a></strong></p>
<!-- Note from mkdocs: "If both an and a are in the same directorfy, mkdocs will render the index file" and the README will still be rendered on github ( Adding frontmatter to README breaks it." -->
Thank you for visiting the WIN Open Neuroimaging Community project repository.
# Cass just-the-docs theme
**This is the GitHub README**
This page is a hub to give you some information about the Community and our Open Science Ambassadors. Jump straight to one of the sections below, or scroll down to find out more.
## Installation
* [What are we doing? (And why?)](#what-are-we-doing)
* [Who are we?](#who-are-we)
* [What do we need?](#what-do-we-need)
* [How can you get involved?](#get-involved)
* [Get in touch](#contact-us)
* [Find out more](#find-out-more)
<!-- * [Understand the jargon](#glossary) -->
Add this line to your Jekyll site's Gemfile:
## What are we doing?
gem "just-the-docs"
We are a community built from around 250 members of the University of Oxford Wellcome Centre for Integrative Neuroimaging (WIN). Our community exists to support open and inclusive researchers, to develop the tools, policies, governance and structures we would like in place to support us in practicing open science.
And add this line to your Jekyll site's `_config.yml`:
We area committed to supporting transparent and reproducible research practices within WIN, to improve the efficiency and accuracy of our research, and contribute to an equitable, diverse and inclusive research environment.
theme: just-the-docs
### The problem
And then execute:
Funders and the Management Board of WIN have identified the value of open science and invested in computational infrastructure to support researchers in sharing their data, data acquisition methodology, experimental tools and analysis code, in an open, transparent and reproducible manner.
$ bundle
As these stages near completion, we are entering the second phase of work to build awareness, provide training and increase uptake in the use of this infrastructure. The problem is that there are no centralised resources, communication structures or identified community strategies in place to support researchers in using this new infrastructure.
Or install it yourself as:
### The solution
$ gem install just-the-docs
The WIN Open Neuroimaging Community will address the above problems by working together to: (1) Develop tools, policies and governance recommendations to promote open research practices; (2) Identify our own barriers to working open and devising strategies to remove these barriers for ourselves and others; (3) Build a community of researchers with the expertise and confidence to promote open research practices in our own labs and to wider audiences.
Alternatively, you can run it inside Docker while developing your site
We intend to implement these solutions through regular co-working "hacks". These hacks will be full day events where we will discuss, write and build together. A high value outcome of these hacks will be a sense of community among the researchers who attend. All material created during the hack will be openly shared on this repository. We will also generate materials and guidance about how we have created the hacks, so these events are themselves reproducible.
$ docker-compose up
Alongside the hacks, we will develop the WIN Open Ambassadors program, where motivated individuals will be supported in sharing knowledge and sign posting their peers around open research practices and how they are implemented at WIN. The Ambassadors will be recognised for the value of their contribution, and invited to shape the policies, incentives, guiding principles and reward systems which will be devised to promote uptake of open research practices at WIN.
## Usage
### Why here?
[View the documentation]( for usage information.
We are building our resources and documenting our growth using this version controlled git repository, rendered into an accessible "book" format. Using git makes it easy to review and accept contributions and flexibly update with a full history of activity. It also provides a starting point for researchers who are unfamiliar with git to practice contributing to a repository and gain confidence using the git process. This is an essential skill in open and reproducible research, an excellent skill to have on your CV, and one which will be vital to using some parts of the WIN Open Infrastructure. We are therefore pleased to offer all our contributors training and support in git throughout their engagement with the project. You will find training and linked resources for using git in our [contributing guide](
## Contributing
## Who are we?
Bug reports and pull requests are welcome on GitHub at This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant]( code of conduct.
### Open Neuroimaging Community Co-Ordinator - Cassandra Gould van Praag (she/her)
### Submitting code changes:
Cass is a postdoctoral researcher with 10 years of neuroimaging (fMRI) research. She was Co-Chair of the [Open Science Room 2020](, and has been both a participant and speaker at the [Berlin-Oxford Open Science Summer School](, an invited speaker at [Open MR Benelux]( and is a Fellow of [Reproducible Research Oxford]( Cass is an active contributor to a number of open community tools, including [Open Research Calendar](, the [COBIDAS Checklist]( and [The Turing Way](
- Open a [Pull Request](
- Ensure all CI tests pass
- Await code review
- Bump the version number in `just-the-docs.gemspec` and `package.json` according to [semantic versioning](
GitHub: @cassgvp
Twitter: @cassgvp
### Design and development principles of this theme:
### WIN Open Neuroimaging Working Group
1. As few dependencies as possible
2. No build script needed
3. First class mobile experience
4. Make the content shine
This community feeds directly into the [WIN Open Neuroimaging Project]( and its working groups listed below along with their leads.
## Development
* Open Data (Clare Mackay)
* Open Tools (Mark Jenkinson)
* Open Protocols (Stuart Clare)
* Open Paradigms (Laurence Hunt)
To set up your environment to develop this theme, run `bundle install`.
You can find out more about the WIN Open Neuroimaging Project by joining this [mailing list](
Your theme is set up just like a normal Jekyll site! To test your theme, run `bundle exec jekyll serve` and open your browser at `http://localhost:4000`. This starts a Jekyll server using your theme. Add pages, documents, data, etc. like normal to test your theme's contents. As you make modifications to your theme and to your content, your site will regenerate and you should see the changes in the browser after a refresh, just like normal.
### Ambassadors
Your name and image here!
When the theme is released, only the files in `_layouts`, `_includes`, and `_sass` tracked with Git will be released.
<mark>Ambassadors probably get an additional bio, like with picture and links. Think about how it is going to grow and be managable code to maintain. Might like to reuse bits from [OSR speakers pages](
## License
### Contributors
Your name and image here!
The theme is available as open source under the terms of the [MIT License](
<mark>Using the ['all contributors']( tool and design.
## What do we need?
**You**! We need people to join the community! If you would like to learn more about open research, become an [Ambassador]( or join one of our hacks, please join the WIN Open Neuroimaging Project [mailing list](, and stay tuned for further announcements. We will be putting out a call in the near future, with an official invitation to the community, more information about what will be involved and what is in it for you!
Please note that it's very important to us that we maintain a positive and supportive environment for everyone who wants to participate. When you join us we ask that you follow our [code of conduct](/docs/ in all interactions both on and offline.
## Contact us
<mark>To be completed</mark>
If you want to report a problem or suggest an enhancement we'd love for you to ... [open an issue](../../issues) at the project this GitHub repository because then we can get right on it. But you can also contact ...
You can also hang out, ask questions and share stories in the slack ...
<!-- ## Find out more
You might be interested in:
* Roadmap -->
And of course, you'll want to know our:
* [Contributors' guidelines](
## Thank you
<mark>To be completed</mark>
Thank you so much ...
<!-- ## Glossary -->
<!-- # Welcome
This repository contains materials for the cultivation of the University of Oxford Wellcome Centre for Integrative Neuroimaging (WIN) Open Neuroimaging Community.
This README is based on the [STEMM Role Models]( example highlighted as good practice in the OLS call on community repository essential materials ([week 4](./Week
I -->
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