diff --git a/docs/ACKNOWLEDGEMENTS.md b/docs/ACKNOWLEDGEMENTS.md
index 3254c30aba937cd8736cf0540bda8e97ce8a2aeb..46745d2c2abe9cd3a18f97e46817438d769af2b8 100644
--- a/docs/ACKNOWLEDGEMENTS.md
+++ b/docs/ACKNOWLEDGEMENTS.md
@@ -36,5 +36,5 @@ We promote the use of the [Tenzing webapp](https://rollercoaster.shinyapps.io/te
Figures have been created from images in the [Noun Project](https://thenounproject.com) repository, contributed by [Alice Design](https://thenounproject.com/rose-alice-design/), [Andrejs Kirma](https://thenounproject.com/andrejs/), [DinosoftLab](https://thenounproject.com/dinosoftlab/), [Luis Prado](https://thenounproject.com/Luis/), [Sergey Demushkin](https://thenounproject.com/mockturtle/), [Thuy Nguyen](https://thenounproject.com/milkghost/), [vectlab](https://thenounproject.com/vectlabmail/), and [Victor Llavata Bartual](https://thenounproject.com/victor.llavata/).
-The pages are regularly updated by the [Open Science Ambassadors](../community/ambassadors/). The last major update was made on June 2024 by [Anna Guttesen](https://orcid.org/0000-0003-0284-1578), [Lara Nikel](https://www.ndcn.ox.ac.uk/team/lara-nikel), [Lilian Weber](https://orcid.org/0000-0001-9727-9623), [Ying-Qiu (Akina) Zheng](https://orcid.org/0000-0003-1236-0700), [Juju Fars](https://orcid.org/0000-0001-7771-5029), [Bernd Taschler](https://orcid.org/0000-0001-6574-4789), [Yingshi Feng](https://orcid.org/0000-0001-9065-4945).
-We thank them for all the work they have put to make this possible.
\ No newline at end of file
+The pages are regularly updated by the [Open Science Ambassadors]({% link docs/community/ambassadors.md %}). The last major update was made on June 2024 by [Anna Guttesen](https://orcid.org/0000-0003-0284-1578), [Lara Nikel](https://www.ndcn.ox.ac.uk/team/lara-nikel), [Lilian Weber](https://orcid.org/0000-0001-9727-9623), [Ying-Qiu (Akina) Zheng](https://orcid.org/0000-0003-1236-0700), [Juju Fars](https://orcid.org/0000-0001-7771-5029), [Bernd Taschler](https://orcid.org/0000-0001-6574-4789), [Yingshi Feng](https://orcid.org/0000-0001-9065-4945).
+We thank them for all the work they have put to make this possible.
diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md
index 1df794efea3fc2c0eb42def6c4b6cb947d643c22..9423a61c7f0250d8f81a2fb90a037bc8a5031d32 100644
--- a/docs/CONTRIBUTING.md
+++ b/docs/CONTRIBUTING.md
@@ -18,7 +18,7 @@ This repository is designed to be used by members of the Wellcome Centre for Int
---
-We want to ensure that every user and contributor feels welcome and included in the WIN Open Neuroimaging community. We ask all contributors and community members to follow the [code of conduct](../community/CODE_OF_CONDUCT) in all community interactions.
+We want to ensure that every user and contributor feels welcome and included in the WIN Open Neuroimaging community. We ask all contributors and community members to follow the [code of conduct]({% link docs/community/CODE_OF_CONDUCT.md %}) in all community interactions.
**We hope that this guideline document will make it as easy as possible for you to get involved.**
@@ -30,11 +30,11 @@ If you are a WIN member you can join us on the slack channel of the WIN Communit
## 2. Check what we're working on
-We invite you to review our [roadmap](../community/roadmap) and see how we are progressing against our community milestones.
+We invite you to review our [roadmap]({% link docs/community/roadmap.md %}) and see how we are progressing against our community milestones.
## Or, 3. Jump straight in!
If you are confident using git, markdown, and GitLab pages, you are very welcome to [submit an issue to our GitLab repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues), and submit a merge request.
### New to GitLab?
-If you'd like to try out GitLab at your own pace, take a look at the [training materials available here](../gitlab).
+If you'd like to try out GitLab at your own pace, take a look at the [training materials available here]({ link docs/gitlab.md %}).
diff --git a/docs/ELN.md b/docs/ELN.md
index b282e72f3c144f73274d770761b367ef3e25b4bf..3d2a2737303cc4ed79fbd7f141600da22989f4bb 100644
--- a/docs/ELN.md
+++ b/docs/ELN.md
@@ -14,7 +14,7 @@ sub heading
---
-
+
Laboratory notebooks document the process of experimentation and discovery, and may be maintained as a legal document admissible as evidence in court of law (https://en.wikipedia.org/wiki/Electronic_lab_notebook). As such, there is a drive to promote the use of electronic laboratory notebooks (ELNs) over paper lab notebooks to improve fidelity, access and interoperability of this valuable information. Standards have been developed by the International Organization for Standardization (ISO) and the International Electrotechnical Commission (IEC) to describe minimum requirements in controlling access and editing of entries into an ELN; ELNs providers can apply to be accredited under a given ISO/IEC specification, giving users confidence that the information they enter into them is managed appropriately.
diff --git a/docs/ambassadors/application.md b/docs/ambassadors/application.md
index 98ecf9f3ccce48c4d6fce72b1a964540c584ea42..efe1390d142530ba343629f234e9013ca0eece18 100644
--- a/docs/ambassadors/application.md
+++ b/docs/ambassadors/application.md
@@ -27,7 +27,7 @@ Below we describe the application process, including how your application will b
Please take note of the [timeline](#timeline). If you apply to the programme, please keep the date of the first meeting free in your schedule.
-Please review the notes on [eligibility](../logistics#who-can-be-an-ambassador) and [time commitment](../expectations#time-commitment) before applying.
+Please review the notes on [eligibility]({% link docs/ambassadors/logistics.md %}) and [time commitment]({% link docs/ambassadors/expectations.md %}) before applying.
When you apply you will be asked to confirm that you have discussed your application with your supervisor or line manager and that they are supportive of your participation in the Ambassadors programme.
@@ -54,7 +54,7 @@ The above linked application form asks 3 questions to assess your interest and i
Please note that no prior experience with open science related projects or activities is required!
-You will then be asked to let us know about any logistical constraints you might have with participation according to our [proposed schedule](../programme#schedule).
+You will then be asked to let us know about any logistical constraints you might have with participation according to our [proposed schedule]({% link docs/ambassadors/programme.md %}).
We would like our Ambassadors to represent the full diversity of our community. We therefore ask applicants if they consider themselves to be a member of one or more historically excluded groups. We will also ask for your career stage, to ensure we get diverse representation.
diff --git a/docs/ambassadors/expectations.md b/docs/ambassadors/expectations.md
index 1caffaa41c9ced99f33fb67c38331bb57ab03597..634934c79900a63b42a4df8ffb98d6abc2a44f19 100644
--- a/docs/ambassadors/expectations.md
+++ b/docs/ambassadors/expectations.md
@@ -31,9 +31,9 @@ We would like WIN Open Ambassadors to undertake the following activities:
- Contribute to WIN Open Science policy.
## Time commitment
-- Participate in Ambassadors meetings as per the [published schedule](../programme#schedule).
+- Participate in Ambassadors meetings as per the [published schedule]({% link docs/ambassadors/programme.md %}).
- Engage in training, advocacy, and contributing to the Open WIN infrastructure for 3-4 hours per month, in addition to regular meetings (mostly on MS Teams).
-In return for their time and commitment, various [rewards and incentives](../benefits) will be offered to the Open WIN Ambassadors. We will continually reflect on and refine our expectations and commitments as we learn from our experience.
+In return for their time and commitment, various [rewards and incentives]({% link docs/ambassadors/benefits.md %}) will be offered to the Open WIN Ambassadors. We will continually reflect on and refine our expectations and commitments as we learn from our experience.
We will work to support Ambassadors in all these activities, with communication channels, training, presentation materials and defined routes of development. This support will develop as the project grows, and you will have an open invitation to suggest any additional ways we could support you in growing our community.
diff --git a/docs/ambassadors/goals.md b/docs/ambassadors/goals.md
index 4e41c9d1bd8f8a046fe947b70ccd1ac9f840edff..d136e31414c71809505ceee0d084be63b8368045 100644
--- a/docs/ambassadors/goals.md
+++ b/docs/ambassadors/goals.md
@@ -36,7 +36,7 @@ The Open WIN Ambassadors programme is an essential component in achieving the vi
### 1. Growing our user base
-Our overarching goal is to increase the number of users of our [sharing infrastructure](../../tools), so more people can share all stages of their research output, and receive appropriate credit for doing so. This will help us achieve the Open Neuroimaging Project goal of increasing the openness of our research, to facilitate discovery and accelerate the translation of methods and results to the clinic.
+Our overarching goal is to increase the number of users of our [sharing infrastructure]({% link docs/tools.md %}), so more people can share all stages of their research output, and receive appropriate credit for doing so. This will help us achieve the Open Neuroimaging Project goal of increasing the openness of our research, to facilitate discovery and accelerate the translation of methods and results to the clinic.
One of the most effective ways of growing our user base is to capitalise on the skills, reach and influence of a select group of "power users", who can advocate for local change and represent the interests of their colleagues. These power users (our Ambassadors) will have the best understanding of what others needs to see, feel, and experience in their journey in order to successfully adopt an effective open science practice.
@@ -187,16 +187,16 @@ Open Community
- Encourage the community to share pre-prints of their papers.
-
+
- Appreciate the value of open science practices in career development
-
+
- Appreciate the value of open sharing of code.
- Encourage the community to realise the value of sharing data within the current limits of our [open data policy](OpenData.md), and equip them with the tools and knowledge to do so.
-
+
## Reduce barriers to engaging in open research practices
@@ -204,12 +204,12 @@ Open Community
- Clarify and communicate legal and ethical obligations fo data sharing.
- Promote and train the community to use the newly developed WIN Open Infrastructure for sharing [data](OpenData.md), [experimental paradigms](OpenParadigms.md), [MR protocols](OpenProtocols.md) and [analysis tools](OpenTools.md)
-
+
-
+
## Create and share documentation
- Empower the community to learn together as we explore these topics, and share their knowledge on this repository <mark>update when moved</mark> in the form of written documentation.
- Hold in-person and online training workshops and "hacks" where we can learn together and create documentation.
- -->
+ -->
diff --git a/docs/ambassadors/logistics.md b/docs/ambassadors/logistics.md
index 30b155d9a4cf14d42f7c691a63f1161b0f77f668..148b9e8dfa06b59356e75bf51a2286c81046a2fe 100644
--- a/docs/ambassadors/logistics.md
+++ b/docs/ambassadors/logistics.md
@@ -39,7 +39,7 @@ While working on creating documentation, we envisage teams of two people or more
Ambassadors will be encouraged to work openly and publish their work-in-progress via GitLab. Training will be given to ensure all Ambassadors are comfortable and confident with this process.
-Ambassadors will be encouraged to join 30-60 minute update and co-working calls, where we will work together on documentation and projects. Calls will take place on MS Teams and we will use [hackmd.io](http://hackmd.io/) to write collaborative notes during the call, using markdown so they can be saved directly to a git repository. We may use [padlet](https://padlet.com) for creative exercises. Take a look at the [programme schedule](../programme) to see how our calls will be structured.
+Ambassadors will be encouraged to join 30-60 minute update and co-working calls, where we will work together on documentation and projects. Calls will take place on MS Teams and we will use [hackmd.io](http://hackmd.io/) to write collaborative notes during the call, using markdown so they can be saved directly to a git repository. We may use [padlet](https://padlet.com) for creative exercises. Take a look at the [programme schedule]({% link docs/ambassadors/programme.md %}) to see how our calls will be structured.
# How long will Ambassadors be in-post for?
@@ -49,7 +49,7 @@ The programme will run for roughly one calendar year. All recruited Ambassadors
Anyone! Student, postdoc, core staff, professional services, PI...!
-You do not need to have any knowledge or experience of open science. All we ask is that you are interested in contributing your time and energy to support the development of others. But this is not an entirely altruistic affair! By participating in this programme we expect you will directly [benefit](../benefits) in ways which are valuable to your career development and skills as a researcher. It should also be a fun and rewarding experience!
+You do not need to have any knowledge or experience of open science. All we ask is that you are interested in contributing your time and energy to support the development of others. But this is not an entirely altruistic affair! By participating in this programme we expect you will directly [benefit]({% link docs/ambassadors/benefits.md %}) in ways which are valuable to your career development and skills as a researcher. It should also be a fun and rewarding experience!
# How can I become an Ambassador?
@@ -57,4 +57,4 @@ A competitive application for the 2025 cohort will be launched in November 2024.
# What is expected of Ambassadors
-Take a look at the [expectations](../expectations) of Ambassadors to learn more about the time commitments of participation.
+Take a look at the [expectations]({% link docs/ambassadors/expectations.md %}) of Ambassadors to learn more about the time commitments of participation.
diff --git a/docs/ambassadors/meet_ambassadors.md b/docs/ambassadors/meet_ambassadors.md
index 63d2bbf363ce4adcbd06e7880b7766393aca1739..7c583f8d661ceca412c9b842018c397390ec91dd 100644
--- a/docs/ambassadors/meet_ambassadors.md
+++ b/docs/ambassadors/meet_ambassadors.md
@@ -19,20 +19,9 @@ Find out about the current Open WIN Ambassadors
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/1025477303?badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture; clipboard-write" style="position:absolute;top:0;left:0;width:100%;height:100%;" title="What does it mean to be an Open WIN Ambassador?, October 2024"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
-<!--
-
-
-<iframe width="560" height="315" src="https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/blob/33d22c4573b91146a28704164aac85371b49f73a/img/OPEN_WIN_AMBS_PROMO_2024.mp4" frameborder="0" allowfullscreen></iframe>
----
-
-<video width="320" height="240" controls>
- <source src="../../img/OPEN_WIN_AMBS_PROMO_2024.mp4" type="video/mp4">
-</video>
--->
-
## The 2024 Ambassadors
-
+
{: .fs-3 .fw-300 }
### Anna Guttesen
@@ -59,7 +48,7 @@ Ying-Qiu (Akina) is a postdoctoral researcher in the Nuffield Department of Clin
## The 2022-2023 Ambassadors
-
+
{: .fs-3 .fw-300 }
### Peter Doohan
@@ -96,7 +85,7 @@ Mohamed is a Senior Physics Support Scientist (Clinical and Pre-clinical) in the
## The 2021-2022 Ambassadors
-
+
Open WIN Ambassadors 2021-2022 (left-right): Dejan Draschkow; Yingshi Feng; Verena Sarrazin; Bernd Taschler.
{: .fs-3 .fw-300 }
diff --git a/docs/ambassadors/programme.md b/docs/ambassadors/programme.md
index 4ae38b3aa730aa61097af5532834378badb4bd48..61b7e3f06bbc7a7a6deeb8dbc6c9c445937d8cca 100644
--- a/docs/ambassadors/programme.md
+++ b/docs/ambassadors/programme.md
@@ -58,12 +58,12 @@ You may choose to contribute outside of this time, or arrange co-working times w
<!--
## Shadowing
-In response to feedback from the 2021-2022 Ambassadors, we have incorporated various opportunities for you to shadow the work of our Community Engagement Coordinator, so you can learn about the operational aspects of doing open science and supporting the wider community. You will be invited to attend the termly [Open WIN Steering Group](../../community/community-who/#open-win-steering-group) meetings, join one-to-one support meetings with researchers seeking to incorporate open science practices in their work, and join a team inbox.
+In response to feedback from the 2021-2022 Ambassadors, we have incorporated various opportunities for you to shadow the work of our Community Engagement Coordinator, so you can learn about the operational aspects of doing open science and supporting the wider community. You will be invited to attend the termly [Open WIN Steering Group]({% link docs/community/community-who.md %}) meetings, join one-to-one support meetings with researchers seeking to incorporate open science practices in their work, and join a team inbox.
-->
## Launch and close meetings
-In January 2025 you will join the Ambassadors of previous years for a formal introduction to the Open WIN ambassadors programme (delivered by the [Open WIN Steering Group](../../community/community-who#open-win-steering-group), hear the results of our [programme evaluation](../goals/#evaluation-of-the-programme-and-your-experience) and share your expectations and goals for the year ahead. These activities will be held at a College in January 2025, in an informal environment where we can celebrate each others success and contributions, hear from external speakers and have dinner together.
+In January 2025 you will join the Ambassadors of previous years for a formal introduction to the Open WIN ambassadors programme (delivered by the [Open WIN Steering Group]({% link docs/community/community-who.md %}), hear the results of our [programme evaluation]({% link docs/ambassadors/goals.md %}) and share your expectations and goals for the year ahead. These activities will be held at a College in January 2025, in an informal environment where we can celebrate each others success and contributions, hear from external speakers and have dinner together.
## Schedule
diff --git a/docs/analysis.md b/docs/analysis.md
index 677321182128ab0d78fdae49d1f83f1565e1dd63..fd9438dfeb357e64153f6e131f24002c2a5e23dc 100644
--- a/docs/analysis.md
+++ b/docs/analysis.md
@@ -15,7 +15,7 @@ How to share reproducible FSL analysis pipelines
---
-
+
## Purpose
@@ -47,21 +47,19 @@ Coming soon
<br>
-<!-- [](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/analysis/#for-win-members) [](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/analysis/#for-external-researchers) -->
-
-[](#for-win-members) [](#for-external-researchers)
+[](#for-win-members) [](#for-external-researchers)
## For WIN members
### Benefits
-#### Version control 
-WIN members will be encouraged to develop their analysis pipelines into standalone scripts and store these on the [WIN GitLab instance](https://git.fmrib.ox.ac.uk). We will support our members in using git to version control their code, and employ best practice in ensuring their pipelines are robust and accurate. Find out more about [using GitLab](../gitlab)
+#### Version control 
+WIN members will be encouraged to develop their analysis pipelines into standalone scripts and store these on the [WIN GitLab instance](https://git.fmrib.ox.ac.uk). We will support our members in using git to version control their code, and employ best practice in ensuring their pipelines are robust and accurate. Find out more about [using GitLab]({% link docs/gitlab.md %})
-#### Citable research output 
-Versions of analysis code can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading them from GitLab. Once a DOI has been created, your analysis code becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository](../gitlab/4-2-you-doi).
+#### Citable research output 
+Versions of analysis code can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading them from GitLab. Once a DOI has been created, your analysis code becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository]({% link docs/gitlab/4-2-you-doi.md %}).
-#### Reproducible methods detail 
+#### Reproducible methods detail 
Alongside your analysis code, WIN members will be supported in implementing a "[wrapper](https://techterms.com/definition/wrapper)" script which can:
-1. access data stored on the WIN [Open Data](../data) servers;
+1. access data stored on the WIN [Open Data]({% link docs/data.md %}) servers;
2. access your GitLab code repository;
3. pull a stable version of the FSL analysis package in a [Singularity container](https://en.wikipedia.org/wiki/Singularity_(software));
4. Run the accessed data using the supplied code and the given version of FSL via the container on a high performance cluster.
@@ -76,13 +74,13 @@ External users will be able to access the shared code and singularity containers
Coming soon
{: .label .label-yellow }
-Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our [documentation hacks](../community/events/doc-hack-1)
+Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our [documentation hacks]({% link docs/community/events/doc-hack-1.md %})
#### Repository template
-You are free to include whatever material you wish in your repository. We have created this [guide on what to include](../gitlab/repo-include) to list some of the pages and sections which may be beneficial for readers. See also our guide on [how to license](../gitlab/repo-license) your material.
+You are free to include whatever material you wish in your repository. We have created this [guide on what to include]({% link docs/gitlab/repo-include.md %}) to list some of the pages and sections which may be beneficial for readers. See also our guide on [how to license]({% link docs/repo-license.md %}) your material.
#### Creating a doi
-We recommend using zenodo to create a doi for your material. See see the [creating a doi](../gitlab/repo-doi) page for instructions.
+We recommend using zenodo to create a doi for your material. See see the [creating a doi]({% link docs/gitlab/repo-doi.md %}) page for instructions.
## Working group members (alphabetically)
We are grateful to the following WIN members for their contributions to developing the Open Analysis tools
diff --git a/docs/community.md b/docs/community.md
index 262a92ff786b98cd0d48427c97bc7ed2ee3ed2ba..dd063cac4ee3925d4511e0bfb4bf40730be3927c 100644
--- a/docs/community.md
+++ b/docs/community.md
@@ -11,7 +11,7 @@ nav_order: 10
Find out about the Open WIN Community, what we're doing, and how you can be a part of this effort.
{: .fs-6 .fw-300 }
-
+
---
diff --git a/docs/community/CODE_OF_CONDUCT.md b/docs/community/CODE_OF_CONDUCT.md
index d4cacc58e73e5b405227c94c94fc59cb805c6b9e..dd4c60c2b31d4f81c6e7e401809f541c93a86371 100644
--- a/docs/community/CODE_OF_CONDUCT.md
+++ b/docs/community/CODE_OF_CONDUCT.md
@@ -38,4 +38,4 @@ We will begin events with a reminder of the Harassment Policy and expected behav
## Being a responsible bystander
In this community we value efforts to promote a positive work environment, free from intimidation and all forms of violence. We are therefore pleased to support the University in enacting the Harassment Policy by acting as responsible bystanders, and doing what we can to promote a safe and conducive work environment. We encourage all community members to be responsible bystanders.
-
+
diff --git a/docs/community/ambassadors.md b/docs/community/ambassadors.md
index bf5153be3ca4b250eee6e4233690581f6d2f8e9e..188ef813d69837b7d717ef6c17427ad472f399fe 100644
--- a/docs/community/ambassadors.md
+++ b/docs/community/ambassadors.md
@@ -14,6 +14,6 @@ nav_order: 5
The Open WIN Ambassadors are a team of individuals who are significant contributors to the Open WIN Community.
-
+
**See the sections below or navigate on the sidebar to find out more about the Open WIN Ambassadors.**
diff --git a/docs/community/community-goals.md b/docs/community/community-goals.md
index b88c10e1e1d8bdc1d2093dd81de18154eb885877..7f00058691b27935b0b6184119cc30202ec4f531 100644
--- a/docs/community/community-goals.md
+++ b/docs/community/community-goals.md
@@ -26,7 +26,7 @@ As these stages near completion, we are entering the second phase of work to bui
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. Create documentation and training materials to help others use the [Open WIN Tools](../../tools);
+3. Create documentation and training materials to help others use the [Open WIN Tools]({% link docs/tools.md %});
4. Build a community of researchers with the expertise and confidence to promote open research practices and the Open WIN Tools in our own labs and to wider audiences.
@@ -36,4 +36,4 @@ We intend to implement these solutions through regular co-working "hacks". These
## Ambassador program
Alongside the hacks, we will develop the WIN Open Ambassadors programme for launch in 2021, 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 significant contributors to the community, and recognised for the value of their contribution. They will be invited to shape the governance of the community, and be consulted on policies, incentives, guiding principles and reward systems which will be devised to promote uptake of open research practices at WIN.
-Take a look at our drafted outline for the [Ambassadors program](../../ambassadors). We would love to hear your thoughts on how it should be put together!
+Take a look at our drafted outline for the [Ambassadors program]({% link docs/community/ambassadors.md %}). We would love to hear your thoughts on how it should be put together!
diff --git a/docs/community/community-who.md b/docs/community/community-who.md
index 70d74acdb84c5f189c996bd9228368c87fd2888f..0b39866a19fb5a1400dd0846e133f8071c20fd53 100644
--- a/docs/community/community-who.md
+++ b/docs/community/community-who.md
@@ -21,13 +21,13 @@ Find out who we are and where we sit in the wider WIN context.
* [Community Coordinator](#community-coordinator---cassandra-gould-van-praag-sheher)
* [Open WIN Steering Group](#open-win-steering-group)
-
+
We are a community built from around 250 members of the University of Oxford [Wellcome Centre for Integrative Neuroimaging (WIN)](https://www.win.ox.ac.uk). We welcome students, researchers, [core staff](https://www.win.ox.ac.uk/about/core-staff), faculty, and anyone in between!
We were formed to facilitate the dissemination of knowledge and experience from the developers of the Open WIN Tools into the hands of the WIN Members who will make use of them. We are interested in the development of open research practices in our discipline, and informing the policy and incentives around the implementation of open research at WIN.
-Anyone can join and contribute to this community, with any level of commitment. You are free to dip in-and-out when you have capacity to engage, and you will always be welcomed into the discussion. We welcome peripheral contributions such as minor edits to documentation, all the way through to leadership of the community. Find out more about this in our [Mountain of Engagement](../mountain-of-engagement) community model.
+Anyone can join and contribute to this community, with any level of commitment. You are free to dip in-and-out when you have capacity to engage, and you will always be welcomed into the discussion. We welcome peripheral contributions such as minor edits to documentation, all the way through to leadership of the community. Find out more about this in our [Mountain of Engagement]({% link docs/community/mountain-of-engagement.md %}) community model.
## Community members
@@ -52,8 +52,8 @@ GitHub: [@cassgvp](https://github.com/cassgvp)
This community feeds directly into the [WIN Open Neuroimaging Project](https://www.win.ox.ac.uk/open-neuroimaging/open-neuroimaging-project) and its working groups:
* Open Science (lead: [Tom Nichols](https://www.bdi.ox.ac.uk/Team/t-e-nichols))
-* [Open MR Protocols](../../tools/protocols) (lead: [Stuart Clare](https://www.win.ox.ac.uk/people/stuart-clare))
-* [Open Tasks](../../tools/tasks) (lead: [Laurence Hunt](https://www.win.ox.ac.uk/people/laurnece-hunt))
-* [Open Analysis](../../tools/analysis) (lead: [Mark Jenkinson](https://www.win.ox.ac.uk/people/mark-jenkinson))
-* [Open Data](../../tools/data) (lead: [Clare Mackay](https://www.win.ox.ac.uk/people/clare-mackay))
-* [Open WIN Ambassadors programme](../ambassadors) (lead: [Bernd Taschler](https://www.ndcn.ox.ac.uk/team/bernd-taschler))
+* [Open MR Protocols]({% link docs/protocols.md %}) (lead: [Stuart Clare](https://www.win.ox.ac.uk/people/stuart-clare))
+* [Open Tasks]({% link docs/tasks.md %}) (lead: [Laurence Hunt](https://www.win.ox.ac.uk/people/laurnece-hunt))
+* [Open Analysis]({% link docs/analysis.md %}) (lead: [Mark Jenkinson](https://www.win.ox.ac.uk/people/mark-jenkinson))
+* [Open Data]({% link docs/data.md %}) (lead: [Clare Mackay](https://www.win.ox.ac.uk/people/clare-mackay))
+* [Open WIN Ambassadors programme]({% link docs/community/ambassadors.md %}) (lead: [Bernd Taschler](https://www.ndcn.ox.ac.uk/team/bernd-taschler))
diff --git a/docs/community/events/doc-hack-1.md b/docs/community/events/doc-hack-1.md
index ef446416885b03a4ec161d1ccfa116eb999dea50..77a25cf910faf4dbe9dd02443e9d10ad245fa1e7 100644
--- a/docs/community/events/doc-hack-1.md
+++ b/docs/community/events/doc-hack-1.md
@@ -21,15 +21,15 @@ Find out what happened on our first hack day!
The aims for the hack day were to:
1. Introduce interested individuals to the community, and communicate how you may benefit from participation, what kind of activities you may be able to take part in, how you will be recognised for your contribution, and what behaviours or commitment may be expected of you.
-2. Provide training on how to use the Open WIN infrastructure for sharing [MR Protocols](../../../protocols), [experimental task](../../../tasks), [data](../../../data) and [analysis code](../../../analysis)
-3. Provide training on [GitLab](../../../gitlab) and how it will be used to update this repository.
+2. Provide training on how to use the Open WIN infrastructure for sharing [MR Protocols]({% link docs/protocols.md %}), [experimental task]({% link docs/tasks.md %}), [data]({% link docs/data.md %}}) and [analysis code]({% link docs/analysis.md %})
+3. Provide training on [GitLab]({% link docs/gitlab.md %}) and how it will be used to update this repository.
4. Begin crafting and contributing documentation to share our training with others.
## How did it go?!
The day was structured around “lightning pitches†from the infrastructure developers to advertise where they would benefit from community engagement, followed by training in how to use GitHub to make contributions (submitting a pull request to [an external repository](https://cassgvp.github.io/git-for-collaborative-documentation)), and then three hours of dedicated time to work with the tools developers to make contributions and build ideas for future interactions. Summary attendance and engagement figures from the hack day are provided in below.
-{:height="100%" width="100%"}
+{:height="100%" width="100%"}
## What did we achieve?
diff --git a/docs/community/events/doc-hack-template.md b/docs/community/events/doc-hack-template.md
index 91656cf3f15cfa31d0d14537b22753cb2502ec1e..3a564538b3737e6185bc515f472a77845c3edd7e 100644
--- a/docs/community/events/doc-hack-template.md
+++ b/docs/community/events/doc-hack-template.md
@@ -26,7 +26,7 @@ The event will be hosted via [Wonder](https://www.wonder.me) at [tinyurl.com/Ope
The aim for the hack day is to:
1. Introduce interested individuals to the community, and communicate how you may benefit from participation, what kind of activities you may be able to take part in, how you will be recognised for your contribution, and what behaviours or commitment may be expected of you.
-2. Provide training on how to use the [Open WIN Tools](../tools.md).
+2. Provide training on how to use the [Open WIN Tools]({% link docs/tools.md %}).
3. Provide training on GitHub/GitLab and how it will be used to update this repository.
4. Begin crafting and contributing documentation to share our training with others.
diff --git a/docs/community/events/external.md b/docs/community/events/external.md
index 3fae1c50524419644286d4ae8eafeec612327ebc..2ec8c7bbb47a3c5c7bc1da5821d83bbefc3c9277 100644
--- a/docs/community/events/external.md
+++ b/docs/community/events/external.md
@@ -19,7 +19,7 @@ Below is a live copy of the [Open Research Calendar](https://openresearchcalenda
Visit [@OpenResearchCal](https://twitter.com/OpenResearchCal) on twitter to find out how to add your events.
-
+
<div class="span3">
diff --git a/docs/community/mountain-of-engagement.md b/docs/community/mountain-of-engagement.md
index 209207c1d31a1a4d90f5de52440b6fe84a43175e..f0814996a8080241ce2765f061edd9aec5c8c167 100644
--- a/docs/community/mountain-of-engagement.md
+++ b/docs/community/mountain-of-engagement.md
@@ -17,8 +17,8 @@ How we will work with community members to build growth and sustainability
We want this community to grow in reach and ambition. We also want individual members to have to opportunity to direct their own growth and feel ownership of their community. This sense of ownership will build in sustainability, where each individual takes on partial and momentary responsibility for some aspect.
-
+
To achieve individual and community growth, we are following the "Mountain of Engagement" model. This is a tool for conceptualising how people will interact with your community, and building an understanding of how different people might grow from their first interaction to taking on some form of responsibility. Not all community members will progress to leadership, but it is useful to think about what actions or events may lead people to progress.
-We have used the Mountain of Engagement model to consider how our imaginary [personas](../personas-and-pathways) might interact with the Open WIN community. This exercise has provided useful insight into how we can support progression for a variety of people.
+We have used the Mountain of Engagement model to consider how our imaginary [personas]({% link docs/community/personas-and-pathways.md %}) might interact with the Open WIN community. This exercise has provided useful insight into how we can support progression for a variety of people.
diff --git a/docs/community/personas-and-pathways.md b/docs/community/personas-and-pathways.md
index dd8cfa5e233878727546ea348041301e62cb203f..8ebc5f976bce101d564dc032e96eecc9e563f7fd 100644
--- a/docs/community/personas-and-pathways.md
+++ b/docs/community/personas-and-pathways.md
@@ -16,7 +16,7 @@ Who will our Community Members be, how will they find us and how will we support
This exercise helped us to think about who might be interested in joining our community, how we can connect with them, and the journey they might go on. It is designed to help us reach different audiences and be welcoming to diverse contributors.
-**Follow the sections linked in the side bar to walk through the exercise and understand how we arrived at our [persona descriptions and described their pathways](../personas-and-pathways-descriptions) to engagement with this community.**
+**Follow the sections linked in the side bar to walk through the exercise and understand how we arrived at our [persona descriptions and described their pathways]({% link docs/community/personas-and-pathways-descriptions.md %}) to engagement with this community.**
Our intention is to update this document as we gain a clearer idea of who we are engaging with or missing from the community. Please contact us if any of the ideas presented here do not resonate with you, or if they hit the right note! 🎶
diff --git a/docs/community/roadmap.md b/docs/community/roadmap.md
index 50f4719702e3b9ff5402f0bba2be93eadc89e2c8..78c23b378d4d7cdfd57da2ec30501193c6a705ad 100644
--- a/docs/community/roadmap.md
+++ b/docs/community/roadmap.md
@@ -45,15 +45,15 @@ Complete 🥳
#### Tasks completed
- [x] [Project vision](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/open-leadership/#vision-statement)
-- [x] [Lean canvas: One page business plan describing how you will execute your vision](open-leadership.md)
-- [x] [Project landing page or README](../../index.md)
-- [x] [Roadmap for identifying milestones in the project](roadmap.md)
-- [x] [Personas and pathways: Understanding who you contributors are](personas.md)
-- [x] [Mountain of engagement](mountain-of-engagement.md)
-- [x] [Participation guidelines](CODE_OF_CONDUCT.md)
-- [x] [Contributor guidelines](../../CONTRIBUTING.md)
-- [x] [License and citation guidelines](../../LICENSE.md)
-- [x] [Publish repository openly](../../index.md)
+- [x] [Lean canvas: One page business plan describing how you will execute your vision]({% link docs/open-leadership.md %})
+- [x] [Project landing page or README]({% link index.md %})
+- [x] [Roadmap for identifying milestones in the project]({% link docs/community/roadmap.md %})
+- [x] [Personas and pathways: Understanding who you contributors are]({% link docs/community/personas-and-pathways.md %})
+- [x] [Mountain of engagement]({% link docs/community/mountain-of-engagement.md %})
+- [x] [Participation guidelines]({% link docs/community/CODE_OF_CONDUCT.md %})
+- [x] [Contributor guidelines]({% link docs/CONTRIBUTING.md %})
+- [x] [License and citation guidelines]({% link docs/LICENSE.md %})
+- [x] [Publish repository openly]({% link index.md %})
#### Due date
End of August 2020
@@ -105,7 +105,7 @@ Complete
#### Tasks completed
- [x] Action feedback from external presentation
- [x] Prepare talk (30 minutes)
-- [x] [Define and document routes for interested WIN members to engage](../../contact.md)
+- [x] [Define and document routes for interested WIN members to engage]({% link docs/contact.md %})
- [x] [Set up and communicate slack](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/#open-win-slack-)
- [x] Advertise date for hack-day
@@ -133,14 +133,14 @@ Launch 1st October 2020; Close 30th October 2020 (TBC); Analyse and report 7th N
### Milestone 6: First community hack day
#### Description
-Hold first [co-working documentation hack day](../events/doc-hack-1.md). Involve soft launch researchers and other interested parties in designing programming and evaluation.
+Hold first [co-working documentation hack day](% link docs/community/events/doc-hack-1.md %}). Involve soft launch researchers and other interested parties in designing programming and evaluation.
#### Status
Complete
#### Tasks completed
- [x] Complete Mozilla events exercise and review [CSCCE resources](https://www.cscce.org/resources/organizing-community-events/)
-- [x] [Draft program](../events/doc-hack-1.md)
+- [x] [Draft program]({% link docs/community/events/doc-hack-1.md %})
- [x] Invite speakers and check availability
- [x] Set date
- [x] Technology choices
diff --git a/docs/contact.md b/docs/contact.md
index 15551738b77fc68cb3ed93ffe25d171a6fb4adc3..52f150f5016152c54015bdc32511d059c546943b 100644
--- a/docs/contact.md
+++ b/docs/contact.md
@@ -16,7 +16,7 @@ Connect with us via any of the means below as per your preference and interests
## WIN members and external researchers
-### Email the Open WIN Community Coordinator directly 
+### Email the Open WIN Community Coordinator directly 
You are very welcome to [email open@win.ox.ac.uk](mailto:open@win.ox.ac.uk) directly to discuss any issue relating to open research at WIN, the community, or this repository.
@@ -24,9 +24,9 @@ You are very welcome to [email open@win.ox.ac.uk](mailto:open@win.ox.ac.uk) dire
## WIN members only
-### Open WIN Slack 
+### Open WIN Slack 
-Anyone affiliated with a WIN member Department is invited to [join our Slack workspace](https://join.slack.com/t/openwin/signup). We have channels dedicated to each of the [sharing tools](../tools), the [Open WIN community](../community), and relevant external and internal [events](../events).
+Anyone affiliated with a WIN member Department is invited to [join our Slack workspace](https://join.slack.com/t/openwin/signup). We have channels dedicated to each of the [sharing tools]({% link docs/tools.md %}), the [Open WIN community]({% link docs/community.md %}), and relevant external and internal [events]({% link docs/community/events.md %}).
**Slack is where the conversation will be most active and we will share resources with each other. If you're new to the Community, this should be your first contact point!**
@@ -43,11 +43,11 @@ The above [slack invite link](https://join.slack.com/t/openwin/signup) will acce
- [psych.ox.ac.uk](https://www.psych.ox.ac.uk)
- [win.ox.ac.uk](https://www.win.ox.ac.uk)
-### Open WIN mailing list 
+### Open WIN mailing list 
Anyone interested in the Open WIN Community or these resources can join the [WIN Open Neuroimaging mailing list](https://web.maillist.ox.ac.uk/ox/info/win-open-imaging). *The list is open only to University of Oxford staff and students (requires an SSO login)*. This mailing list is used for open distribution of information.
### Comment on the GitLab repository
-<!--  -->
+ <!---->
-If you want to report a problem or suggest an enhancement for this repository, we'd love for you to [open an issue](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues) on our GitLab page (requires a [WIN GitLab account](../gitlab/2-1-starting-gitlab-account).
+If you want to report a problem or suggest an enhancement for this repository, we'd love for you to [open an issue](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues) on our GitLab page (requires a [WIN GitLab account]({% link docs/gitlab/2-1-starting-gitlab-account.md %}).
diff --git a/docs/converting-to-bids.md b/docs/converting-to-bids.md
index f244c0489228e827d2ebca21074eb7bdcb423d69..cacaf2b146dcc8ab110b2b43413c929740051335 100644
--- a/docs/converting-to-bids.md
+++ b/docs/converting-to-bids.md
@@ -14,7 +14,7 @@ sub heading
---
-
+
The Brain Imaging Data Structure (BIDS) is a highly specified file naming format which is growing in use across neuroimaging communities. By converting our data into BIDS format, we are benefitting from many years of experience in determining the best way to structure our data to make it easily readable for both humans and machines. Applying the BIDS format also reduces friction in sharing our data with other neuroimagers, and applying code developed on other projects. We therefore improve the transparency and reproducibility of our research by converging on this community standard.
diff --git a/docs/data.md b/docs/data.md
index 45f826e3dc8eb8a6faafe129bfcb1784ca80b1fc..28f1f355637c640a792d1f8ebbf3e18af57dd367 100644
--- a/docs/data.md
+++ b/docs/data.md
@@ -14,9 +14,9 @@ Click on the images below to learn more about the practicalities of sharing your
---
-[](../data/why) [](../data/can-i)
+[]({% link docs/data/why.md %}) []({% link docs/data/can-i.md %})
<br><br>
-[](../data/how) [](../data/when)
+[]({% link docs/data/how.md %}) []({%link docs/data/when.md %})
@@ -34,7 +34,7 @@ The Data Usage Agreement and de-identification process is being developed with t
#### Quality control
WIN members will also be encouraged to run and share the results of predefined quality control algorithms, so anyone accessing the data can have a ready measure of image quality.
-[](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-win-members) [](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-external-researchers) -->
+[](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-win-members) [](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-external-researchers) -->
<!-- Coming soon
{: .label .label-yellow }
@@ -46,15 +46,15 @@ WIN members will also be encouraged to run and share the results of predefined q
<!-- ### Benefits
-#### Version control 
+#### Version control 
Coming soon
{: .label .label-yellow }
-#### Citable research output 
+#### Citable research output 
Coming soon
{: .label .label-yellow }
-#### Reproducible methods detail 
+#### Reproducible methods detail 
Coming soon
{: .label .label-yellow }
-->
diff --git a/docs/data/can-i.md b/docs/data/can-i.md
index 5f4788ff0cc832aee656ba0322a5afd3d874d7cf..d914ff22a19c71e4000ab817d08002abbe661210 100644
--- a/docs/data/can-i.md
+++ b/docs/data/can-i.md
@@ -16,17 +16,17 @@ Things to consider when planning to share your data
---
-<!--  -->
+ <!-- -->
<!-- -->
-[](#governance)
-[](#ethics)
-[](#deidentification)
-[](#metadata)
-[](#appropriate-reuse)
+[](#governance)
+[](#ethics)
+[](#deidentification)
+[](#metadata)
+[](#appropriate-reuse)
Click on any of the images above to jump to each section.
@@ -40,9 +40,9 @@ Click on any of the images above to jump to each section.
## Governance
-<!--  -->
-<!-- <html><body><i class="fas fa-exclamation-triangle"></i></body></html> -->
-<!-- <html><body><i class="fas fa-check-circle"></i></body></html> -->
+ <!-- -->
+ <!--<html><body><i class="fas fa-exclamation-triangle"></i></body></html> -->
+ <!--<html><body><i class="fas fa-check-circle"></i></body></html> -->
<details>
<summary><html><body><i class="fas fa-exclamation-triangle"></i></body></html> <b>Is sharing restricted under Intellectual Properties rights?</b></summary><br>
@@ -109,7 +109,7 @@ Click on any of the images above to jump to each section.
## Deidentification
-<!--  -->
+ <!-- -->
<!-- <html><body><i class="fas fa-exclamation-triangle"></i></body></html> -->
<!-- <html><body><i class="fas fa-check-circle"></i></body></html> -->
@@ -168,7 +168,7 @@ Click on any of the images above to jump to each section.
## Metadata
-<!--  -->
+ <!-- -->
<details>
<summary><html><body><i class="fas fa-check-circle"></i></body></html> <b>Is your data FAIR?</b></summary><br>
@@ -224,7 +224,7 @@ Click on any of the images above to jump to each section.
## Appropriate reuse
-<!--  -->
+<!--  -->
<!-- <html><body><i class="fas fa-exclamation-triangle"></i></body></html> -->
<!-- <html><body><i class="fas fa-check-circle"></i></body></html> -->
diff --git a/docs/data/data-management-plans.md b/docs/data/data-management-plans.md
index e7f1090c3eff82e336e773fdab11c86c059ca7c9..3d8b5fd78cfe65d5b35fd7a2c5cb400ccf3bea2d 100644
--- a/docs/data/data-management-plans.md
+++ b/docs/data/data-management-plans.md
@@ -36,12 +36,12 @@ There are a number of central University resources available to support you in d
- [Data protection policy (Compliance)](https://compliance.admin.ox.ac.uk/data-protection-policy)
- [Information Security Policy and Implementation Guidance (InfoSec)](https://www.infosec.ox.ac.uk/guidance-policy)
- [Oxford Open Access](https://openaccess.ox.ac.uk)
-- [Licensing and IP guidance via Oxford University Innovation (OUI)](https://innovation.ox.ac.uk/university-members/commercialising-technology/ip-patents-licenses/). See also the short [Open WIN Community guide to licensing code](../../gitlab/repo-license)
+- [Licensing and IP guidance via Oxford University Innovation (OUI)](https://innovation.ox.ac.uk/university-members/commercialising-technology/ip-patents-licenses/). See also the short [Open WIN Community guide to licensing code]({% link docs/repo-license.md %})
- [Research contracts support](https://researchsupport.admin.ox.ac.uk/contracts)
## WIN specific examples
-Below we have collected some example responses in the formats required by [Wellcome](#wellcome-data-management-plan---discovery-platform-2022), [BBSRC](#bbsrc-data-management-plan---7t-upgrade-2021) and [MRC](#mrc-data-management-plan---mica-2018). Further examples are very welcome! If you have some material you'd like to share, please take a look at our [contributing guide](../../CONTRIBUTING).
+Below we have collected some example responses in the formats required by [Wellcome](#wellcome-data-management-plan---discovery-platform-2022), [BBSRC](#bbsrc-data-management-plan---7t-upgrade-2021) and [MRC](#mrc-data-management-plan---mica-2018). Further examples are very welcome! If you have some material you'd like to share, please take a look at our [contributing guide]({% link docs/CONTRIBUTING.md %}).
**The details in the plans below were correct at the time of writing, however some aspects of how WIN manages your data may have changed. Please refer to the following WIN policies to ensure you have the most up to dat information about our data handling:**
diff --git a/docs/data/docker.md b/docs/data/docker.md
index 83d56343dc55f10fdf320f55dd60a79fa56b30c2..9cf33822ce499bd4c30c1c9de5c627b36bfbdc2b 100644
--- a/docs/data/docker.md
+++ b/docs/data/docker.md
@@ -43,7 +43,7 @@ You will first need to enable a container for a project (provided you have suffi
### BIDS Containers (DICOM to NIFTI + BIDS, BIDS MRIQC)
-For examples on how to use BIDS related containers see the [BIDS](../bids) page.
+For examples on how to use BIDS related containers see the [BIDS]({% link docs/data/bids.md %}) page.
### FSL Containers
diff --git a/docs/data/how.md b/docs/data/how.md
index 03d6e6dd12f77e3775e2b45610910812b016f5fc..6b0cea0e259214b06dc5196009f471a3de18dd79 100644
--- a/docs/data/how.md
+++ b/docs/data/how.md
@@ -18,9 +18,9 @@ Places you can share your data from
How you share your data (or where you share it from) will depend on the format of the data, the degree which you have been able to deidentify it, and your requirements for managed access or attribution.
Before sharing your data on any of these platforms, we suggest you:
-1. Confirm your requirements for [governance](../can-i#governance), [ethics](../can-i#ethics) and [reuse](../can-i#appropriate-reuse).
-2. [Deidentify](../can-i#deidentification) your data
-3. Curate your [metadata](../can-i#metadata)
+1. Confirm your requirements for [governance]({% link docs/data/can-i.md %}), [ethics]({% link docs/data/can-i.md %}) and [reuse](%{link docs/data/can-i-reuse.md %}).
+2. [Deidentify]({% link docs/data/can-i.md %}) your data
+3. Curate your [metadata]({% link docs/data/can-i.md %})
After these stages have been considered, one or a combination of the below [repositories](#repositories) may be appropriate for sharing your data.
@@ -39,7 +39,7 @@ Tabular or text data (for example behavioural results or derived region of inter
When using OSF we recommend creating an account using your ORCID, ensuring your ORCID is linked to your SSO (see [Already have an ORCID? link it to Oxford](https://libguides.bodleian.ox.ac.uk/ORCID/orcid/register)). Once your SSO and ORCID are linked (allow this to process overnight), you can add Oxford affiliation to your OSF projects via the `Settings` tab as shown below. Note currently your affiliation needs to be added to each project individually (there is no bulk add option).
-
+
Take a look at this recording from the WIN Graduate program to learn more about OSF.
diff --git a/docs/data/when.md b/docs/data/when.md
index 72458dbe736290acb8b5a023316808d67c4c616a..f0810a75adc2df578561c72f4a87401f99c84485 100644
--- a/docs/data/when.md
+++ b/docs/data/when.md
@@ -24,8 +24,8 @@ Sharing data can be hard if you have not built in the intention to share from th
| Stage | What to think about now
|:-:|:--|
-|  **Planning** | When your project is in the planning stage, you can think think carefully about the [ethical](../can-i#ethics), [governance](../can-i#governance) and [identifiability](../can-i#deidentification) issues which might limit your ability to share your data completely openly. Once you know the limits of what is theoretically possible, you can describe how you can achieve this practically in a data management plan. |
-|  **Data collection** | When collecting your data you should aim to work with non-proprietary file file formats where possible. You can also begin to [collate metadata and organise your data according to community standards](../can-i#metadata). |
-|  **Analysis** | While you are analysing your data, be mindful of the restrictions which might be necessary to ensure the shared data are maximally [deidentified](../can-i#deidentification). For example, it might be preferable to conduct your analysis using binned categorical data rather than continuous variables which make individual participants more identifiable. Consider writing your code in a way that allows for flexible and efficient re-analysis on any such factors. You should also keep an active [data dictionary](https://faircookbook.elixir-europe.org/content/recipes/interoperability/creating-data-dictionary.html), where you describe the variables you create, how they are named in your code or data, and how they are derived. |
-|  **Writing up** | While writing up your project, think about the reason you are sharing your data. If you are sharing data so another researcher can validate your figures, focus on ensuring the data (and code) required for that purpose are accessible and well described. If you are sharing a larger or more complete data set, you may wish to focus on ensuring that the value in the reuse of that data is appropriately emphasised and 'advertised' in your project write-up. Where the time and resources allow, you may wish to or consider publishing a separate [data paper](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-article.html). |
-|  **Publishing** | You should aim to have all of your data available in your [intended repository](../how#repositories) *before you submit your project manuscript to a journal for publication*. Your repository may have specific metadata requirements (much like journal formatting guidelines) and in some cases the data may need to be reviewed before it is made public (for example [EBRAINS](https://ebrains.eu)), so sharing it may take some time. By having the data available in advance of submission, you can include a persistent digital object identifier (doi) or reviewer-only access link with your manuscript. Ensure that you have carefully considered [how contributors to your data will be recognised](../can-i#contributor-attribution).|
+|  **Planning** | When your project is in the planning stage, you can think think carefully about the [ethical](can-i#ethics), [governance]({% link docs/data/can-i.md %}) and [identifiability]({% link docs/data/can-i.md %}) issues which might limit your ability to share your data completely openly. Once you know the limits of what is theoretically possible, you can describe how you can achieve this practically in a data management plan. |
+|  **Data collection** | When collecting your data you should aim to work with non-proprietary file file formats where possible. You can also begin to [collate metadata and organise your data according to community standards]({% link docs/data/can-i.md %}). |
+|  **Analysis** | While you are analysing your data, be mindful of the restrictions which might be necessary to ensure the shared data are maximally [deidentified]({% link docs/data/can-i.md %}). For example, it might be preferable to conduct your analysis using binned categorical data rather than continuous variables which make individual participants more identifiable. Consider writing your code in a way that allows for flexible and efficient re-analysis on any such factors. You should also keep an active [data dictionary](https://faircookbook.elixir-europe.org/content/recipes/interoperability/creating-data-dictionary.html), where you describe the variables you create, how they are named in your code or data, and how they are derived. |
+|  **Writing up** | While writing up your project, think about the reason you are sharing your data. If you are sharing data so another researcher can validate your figures, focus on ensuring the data (and code) required for that purpose are accessible and well described. If you are sharing a larger or more complete data set, you may wish to focus on ensuring that the value in the reuse of that data is appropriately emphasised and 'advertised' in your project write-up. Where the time and resources allow, you may wish to or consider publishing a separate [data paper](https://the-turing-way.netlify.app/reproducible-research/rdm/rdm-article.html). |
+|  **Publishing** | You should aim to have all of your data available in your [intended repository]({% link docs/data/how.md %}) *before you submit your project manuscript to a journal for publication*. Your repository may have specific metadata requirements (much like journal formatting guidelines) and in some cases the data may need to be reviewed before it is made public (for example [EBRAINS](https://ebrains.eu)), so sharing it may take some time. By having the data available in advance of submission, you can include a persistent digital object identifier (doi) or reviewer-only access link with your manuscript. Ensure that you have carefully considered [how contributors to your data will be recognised]({% link docs/data/can-i.md %}).|
diff --git a/docs/data/xnat-tools.md b/docs/data/xnat-tools.md
index ed2e5627e8a37b9d916f48a9dd159e2ce83105d4..4da270cf06f65a75ff22256a076e0a6a4d7e9f8d 100644
--- a/docs/data/xnat-tools.md
+++ b/docs/data/xnat-tools.md
@@ -24,16 +24,16 @@ You can log into [WIN XNAT](https://xnat.win.ox.ac.uk) using your WIN IT account
The [XNAT](https://xnat.org) website has useful background information about the XNAT platform.
#### BIDS in XNAT
-For the current overview of how BIDS works in XNAT, see the [BIDS](../bids) page.
+For the current overview of how BIDS works in XNAT, see the [BIDS]({% link docs/data/bids.md %}) page.
#### Python libraries
-There are several python libraries](data/python.md) that can be used to write scripts against the XNAT API. See [python libraries](../python) for more info on pyxnat, xnatpy and dax.
+There are several python libraries](data/python.md) that can be used to write scripts against the XNAT API. See [python libraries]({% link docs/data/python.md %}) for more info on pyxnat, xnatpy and dax.
#### Docker in XNAT
-To see how Docker works in XNAT, see the [Docker](../docker) page.
+To see how Docker works in XNAT, see the [Docker]({% link docs/data/docker.md %}) page.
#### Case Studies
-The [OPDC project](../opdc) uploaded DICOM data from jalapeno using python and dcmtk.
+The [OPDC project]({% link docs/data/opdc.md %}) uploaded DICOM data from jalapeno using python and dcmtk.
TODO: More case studies!
diff --git a/docs/getting-started.md b/docs/getting-started.md
index 1f5b57995a1f7901c4d913317977bdd74c25d59b..8c2d25a67bd3de11820e6416c9b03c9693ea036d 100644
--- a/docs/getting-started.md
+++ b/docs/getting-started.md
@@ -13,7 +13,7 @@ Incorporating open science practices into your research project.
{: .fs-6 .fw-300 }
---
-
+
## The life cycle of a research project
@@ -44,4 +44,4 @@ At almost every stage of your research project, there are open science related p
## Remaining Questions?
- [How to get help?](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/community/)
-- open@win.ox.ac.uk
\ No newline at end of file
+- open@win.ox.ac.uk
diff --git a/docs/gitlab.md b/docs/gitlab.md
index 56cc047b6287a8fb86f2dff4403afccb09f991c8..752898bca2ba4fa8af2cfe7654f825c003155833 100644
--- a/docs/gitlab.md
+++ b/docs/gitlab.md
@@ -14,7 +14,7 @@ How to use the WIN GitLab instance for your code and documentation
---
-
+
## Overview
GIT is a service which allows version control of material and syncing between local (on your computer) and remote (on a server, accessible through a web browser) versions of material. These remote and local versions are useful for backup and collaboration, where different users can access the same remote content.
@@ -29,20 +29,20 @@ This 30 min presentation introduces GitLab and version control. It explains key
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/668637653?h=a710d4e187&badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="Introduction to version control with GitLab. Dr Cassandra Gould van Praag, WIN Reboot Camp, January 2022"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
### Benefits
-#### Version control 
+#### Version control 
GitLab manages your version control. This means that each change you make to the remote repository is tracked and can be reversed. This is helpful for undoing changes (you can revert to earlier points in time) and tracking who has made changes on a collaborative project.
-#### Citable research output 
-Your gitlab repository can be assigned a digital object identifier (doi). This means everything containing within your repository can be cited as a research output, be it code or documentation. Find out how to [create a doi for your repository](../gitlab/repo-doi).
+#### Citable research output 
+Your gitlab repository can be assigned a digital object identifier (doi). This means everything containing within your repository can be cited as a research output, be it code or documentation. Find out how to [create a doi for your repository]({% link docs/gitlab/repo-doi.md %}).
#### Managed and attributable collaboration
Git and GitLab are an excellent resource for inviting others to contribute to your material. Potential collaborators can be internal to WIN or external. Changes can be incorporated automatically if the collaborator is trusted and known to you (invited directly), or suggested via a "merge request" if the collaborator is not part of your invited group. This process also makes it very easy to follow who has made what contribution, so they can be appropriately attributed for their efforts.
#### GitLab pages
-GitLab pages allows you to build professional looking websites, like this one! It is relatively straightforward to build a simple website to share your work with the world, and the options for building in additional complexity are endless. Take a look at this [tutorial for building a GitLab pages site](../gitlab/4-4-create-gitlab-pages-site).
+GitLab pages allows you to build professional looking websites, like this one! It is relatively straightforward to build a simple website to share your work with the world, and the options for building in additional complexity are endless. Take a look at this [tutorial for building a GitLab pages site]({% link docs/gitlab/4-4-create-gitlab-pages-site.md %}).
## Getting started
-If you're new to GitLab, we suggest you take a look a the [tutorials](../gitlab/gitlab-tutorials) and find the appropriate jumping off point for your experience.
+If you're new to GitLab, we suggest you take a look a the [tutorials]({% link docs/gitlab/gitlab-tutorials.md %}) and find the appropriate jumping off point for your experience.
## More information from WIN IT
Take a look at the [WIN IT help pages](https://sharepoint.nexus.ox.ac.uk/sites/NDCN/FMRIB/IT/User%20Guides/Git.aspx) (internal only) for additional resources on using git.
diff --git a/docs/gitlab/1-2-tools-markdown.md b/docs/gitlab/1-2-tools-markdown.md
index 1cd9dd615b1dd06fb87e124d98aff6de435fb353..01495e721b396b9b14f75b2d3c1fdffc19edf81a 100644
--- a/docs/gitlab/1-2-tools-markdown.md
+++ b/docs/gitlab/1-2-tools-markdown.md
@@ -20,7 +20,7 @@ Markdown is a simple syntax for formatting text and adding graphics to documenta
Using markdown also supports you to use "heading" identifiers, rather than simply changing the font size. This is because it is so *easy* to use heading syntax and it is comparatively complex to change a font size! This makes for content which is more accessible to screen readers used by individuals with a visual impairment ✌🻠✌🼠✌🽠✌🾠✌ðŸ¿
-Markdown is used by GitHub to translate your text and formatting into webpage (GitHub Pages) content. You will be writing your documentation (maybe in [Atom](../1-3-tools-atom)) using markdown syntax, and it will automatically be rendered into something beautiful on your Pages site.
+Markdown is used by GitHub to translate your text and formatting into webpage (GitHub Pages) content. You will be writing your documentation (maybe in [Atom]({% link docs/gitlab/1-3-tools-atom.md %})) using markdown syntax, and it will automatically be rendered into something beautiful on your Pages site.
There are *many* markdown tutorials online which you can follow. I've listed the syntax I use most commonly below:
diff --git a/docs/gitlab/1-3-tools-atom.md b/docs/gitlab/1-3-tools-atom.md
index 0a3cd949991f49abd5d572c37e9d255fae2f83b3..df3fa9ef620b2a50f050f5e366a07714b6dafbb0 100644
--- a/docs/gitlab/1-3-tools-atom.md
+++ b/docs/gitlab/1-3-tools-atom.md
@@ -15,7 +15,7 @@ How to set up and use text editors for writing markdown
---
-
+
Sublime is my favourite text editor. Python, Bash, Markdown, C++, html... you name it. It can even handle Matlab!
@@ -44,12 +44,12 @@ Good text editors also provide a graphical point-and-click way of committing cha
If you want to use a good open science text editor (and you should!). You might want to try [Vim](https://www.vim.org/download.php). This powerful text editor is available on Windows, Linux and MacOS. Although git is not directly build in the software, you can find a lot of Git plugins that will satisfy you.
-
+
Same can be said about [Geany](https://geany.org/) which bear the same characteristics! And several git plugins for Geany exists as well!!!
-
+
You can also use Microsoft Visual Studio (BOOOOOOOOOOOOOH - sorry, I went through terrible nights trying to make a C#/C++ software work).
diff --git a/docs/gitlab/2-3-starting-local-repo.md b/docs/gitlab/2-3-starting-local-repo.md
index 5d9153af225f944e0083fe99cdce922c48ce76c0..d7066a2b7536a34ee118fef19b568088f9bd6382 100644
--- a/docs/gitlab/2-3-starting-local-repo.md
+++ b/docs/gitlab/2-3-starting-local-repo.md
@@ -20,9 +20,9 @@ Currently your "test-git-project" exists online and your computer is configured
In your terminal, move to the directory where you would like your local version of the repository to be stored. Enter the "Create a new repository" commands into your terminal, one line at a time.
-Note you will be asked for the SSH key password you generated when you [first accessed your gitlab account](../2-1-starting-gitlab-account).
+Note you will be asked for the SSH key password you generated when you [first accessed your gitlab account]({% link docs/gitlab/2-1-starting-gitlab-account.md %}).
-Below is a brief explanation of what each line is doing. You'll learn more about some of these commands in the [git basics tutorial](../2-4-starting-git-basics).
+Below is a brief explanation of what each line is doing. You'll learn more about some of these commands in the [git basics tutorial]({% link docs/gitlab/2-4-starting-git-basics.md %}).
After entering these commands, return to the [gitlab webpage](https://git.fmrib.ox.ac.uk) and refresh your project. You will now see that the instructions for creating a new project have gone and the commit message you just entered is shown on the top.
diff --git a/docs/gitlab/2-4-starting-git-basics.md b/docs/gitlab/2-4-starting-git-basics.md
index 5ab7eee300f7da86b21c8bc085fc6a0abc2dbddc..faf44bd929f6f07ab9945171e88883faddbc981b 100644
--- a/docs/gitlab/2-4-starting-git-basics.md
+++ b/docs/gitlab/2-4-starting-git-basics.md
@@ -27,7 +27,7 @@ In the spirit of inclusivity, I'm going to show you the git commands I know, and
## Watch and learn
-We're not yet going to actually practice doing these things right now. I'd just like you to become familiar with (memorize?!) them. You'll get a chance to use them when you have a go at [contributing to this repository](../3-3-collaborating-play-with-this-page), and again when you make your [GitLab pages](../4-4-create-gitlab-pages-site) or [GitHub pages](../4-3-you-make-your-pages-site) site.
+We're not yet going to actually practice doing these things right now. I'd just like you to become familiar with (memorize?!) them. You'll get a chance to use them when you have a go at [contributing to this repository]({% link docs/gitlab/3-3-collaborating-play-with-this-page.md %}), and again when you make your [GitLab pages]({% link docs/gitlab/4-4-create-gitlab-pages-site.md %}) or [GitHub pages]({% link docs/gitlab/4-3-you-make-your-pages-site.md %}) site.
## The three(ish) stages of adding to your repository online
@@ -67,8 +67,8 @@ Everything you have added will be uploaded ("pushed") to your repository.
At this point (especially if it is a big load of changes I'm uploading) I'll often skip excitedly over to my online repository and have a look at my commit and the file changes. It's almost as if I don't trust the magic!?! 😉
-
+
Give it a few minutes to let the changes take effect, then go back and refresh your Pages site. Boom! Updated content.
-
+
diff --git a/docs/gitlab/3-2-collaborating-fork-their-repo.md b/docs/gitlab/3-2-collaborating-fork-their-repo.md
index b36bede64d2d9e843099b72ea3c1b0038bc073c5..253dea8f2d516a689cce7aff8d5472bd211ce91a 100644
--- a/docs/gitlab/3-2-collaborating-fork-their-repo.md
+++ b/docs/gitlab/3-2-collaborating-fork-their-repo.md
@@ -31,7 +31,7 @@ Once you have found the documentation you want to contribute to, you need to loc
When you have found the GitHub repository, you need to "fork" it, to create a copy in your own GitHub account.
-
+
## 2. Clone your online copy to your local computer
@@ -41,7 +41,7 @@ Get the https address of the repository you want to clone via the "code" button,
`git clone [https-address]`
-
+
## 3. Create a branch
@@ -51,7 +51,7 @@ Create your branch by entering the command below, replacing `[your-branch-name]`
`git checkout -b [your-branch-name]`
-
+
## 4. Make and push your changes
@@ -63,17 +63,17 @@ First confirm you are working on the new branch with the command below:
Then open your text editor and make and save the changes.
-Finally, add, commit and save the changes as described in the earlier [git basics](../2-4-starting-git-basics)
+Finally, add, commit and save the changes as described in the earlier [git basics]({% link docs/gitlab/2-4-starting-git-basics.md %})
Notice the git gave me a helpful error which told me that it din't know where to push my changes - there was not "upstream branch" - and very kindly told me what commands I need to enter to set the upstream to be this branch on my copy of the repository. Thanks, Git.
-
+
## 5. Submit your pull request master
Once your changes have been pushed, GitHub online will tell you that your copy and your branch are "ahead of" (have more changes than) the original repository. You can compare the changes and submit your pull request if you are happy with them!
-
+
Note that depending on how long it has been between you forking the original repository and submitting your pull request, you may have become out of sync with the original if there has been more work done on it. Follow the instructions [here from "7. Sync your forked master branch"](https://www.freecodecamp.org/news/how-to-make-your-first-pull-request-on-github-3/) to get yourself back in sync before submitting your pull request.
@@ -81,7 +81,7 @@ Note that depending on how long it has been between you forking the original rep
If you're feeling excited by all this wonderful collaboration, jump back into the original repository you cloned from, and check that the pull request is there. You can even write something nice to the repository owners, if you're feeling friendly.
-
+
Your pull request will now be reviewed by the repository owners, and you will get an email if/when it has been accepted. Now you have left a comment, you will also be notified when there are additional comments added to your thread.
diff --git a/docs/gitlab/3-3-collaborating-play-with-this-page.md b/docs/gitlab/3-3-collaborating-play-with-this-page.md
index d218f63a7bdb0226f896201315911ee4bdae1e86..b13b137d8fdfe3e2c395975e9c8cbd0bda04eb95 100644
--- a/docs/gitlab/3-3-collaborating-play-with-this-page.md
+++ b/docs/gitlab/3-3-collaborating-play-with-this-page.md
@@ -30,7 +30,7 @@ Coming soon
Below is a list of numbers. For your first contribution to someone else's documentation, I would like you to write your name, your pronouns, today's date, and your GitHub profile link against one of these numbers. If you don't know your profile link, click your profile icon (top right side) and open 'Your Profile' in a new tab. You can use the URL of that page to build your GitHub profile link. Use the link format: `[Link text here](LINK URL HERE)`. If you want to get jazzy, you can do something more complicated, like add a picture or some formatting! I invite you to freestyle or keep it functional as you wish.
-Use the procedure described earlier to [fork, clone, branch, edit, push, and submit a pull request](../3-2-collaborating-fork-their-repo) to update the lines below.
+Use the procedure described earlier to [fork, clone, branch, edit, push, and submit a pull request]({% link docs/gitlab/3-2-collaborating-fork-their-repo.md %}) to update the lines below.
We're going to assume we're in a "class" setting right now, and I'm expecting your pull requests to come in. I'll accept them as soon as I can! If we're not in an active tutorial, I'll still aim to get to them as soon as I can, but please accept my apologies if it is not instantaneous. Often collaboration is asynchronous!
diff --git a/docs/gitlab/4-1-you-make-your-repo.md b/docs/gitlab/4-1-you-make-your-repo.md
index 5274dfc5b2a3d16dd29e9d10fdeda58c1d84f89f..7d56c1664ebf8c99856b560270ad1d556fa978f4 100644
--- a/docs/gitlab/4-1-you-make-your-repo.md
+++ b/docs/gitlab/4-1-you-make-your-repo.md
@@ -28,7 +28,7 @@ Next git it a name, description, and add a README file. I've chosen not to add a
Click "Create Repository" Ta-da! You have a repository! 🎉
-
+
## 2. Update your README.md
@@ -50,7 +50,7 @@ To get a quick outline of the README structure (and to differentiate it from the
To save your changes, describe what you did in the commit message, then press "commit"
-
+
## 3. Create a LICENSE.md
@@ -60,7 +60,7 @@ To get the license file in place, I'm going to use the "add file" function and a
To save your changes, describe what you did in the commit message, then press "commit"
-
+
## 4. Create a CONTRIBUTING.md
@@ -70,6 +70,6 @@ To get the contributing file in place, I'm going to use the "add file" function
To save your changes, describe what you did in the commit message, then press "commit"
-
+
-Have a look at our [what to include in a repository](../analysis/repo-include.md) guide for a more complete description of these files.
+Have a look at our [what to include in a repository]({% link docs/gitlab/repo-include.md %}) guide for a more complete description of these files.
diff --git a/docs/gitlab/4-3-you-make-your-pages-site.md b/docs/gitlab/4-3-you-make-your-pages-site.md
index 088ff984c43432c5b0345706817b15bb91cf049d..8424ebc267f8f89050da6e41fe02b75399bb407b 100644
--- a/docs/gitlab/4-3-you-make-your-pages-site.md
+++ b/docs/gitlab/4-3-you-make-your-pages-site.md
@@ -18,12 +18,12 @@ Use the magic of Jekyll to transform markdown pages into a website
> **Note**
>
-> This guide describes how to publish your repo with **GitHub** Pages. If you are planning to publish a GitLab project, see the [GitLab Pages Guide](../4-4-create-gitlab-pages-site) instead!
+> This guide describes how to publish your repo with **GitHub** Pages. If you are planning to publish a GitLab project, see the [GitLab Pages Guide]({% link docs/gitlab/4-4-create-gitlab-pages-site.md %}) instead!
## 1. Turn your repo into a GitHub Pages site!
-Now the magic! Turn the simple collection of files made in [the previous tutorial](../4-1-you-make-your-repo) into something which looks like a user friendly (and not GitHub scary!) website!
+Now the magic! Turn the simple collection of files made in [the previous tutorial]({% link docs/gitlab/4-1-you-make-your-repo.md %}) into something which looks like a user friendly (and not GitHub scary!) website!
Go into your site settings and scroll down to the "GitHub Pages section". Change the "Source" into your "master" branch and click "save".
@@ -33,7 +33,7 @@ Click "Select Theme" to return to your setting page. You will now see that the U
Woohoo! You have a website! 🎉
-
+
## 2. Change your theme
@@ -43,11 +43,11 @@ If you chose to use a theme other than one GitHub already supports, you can use
To change your theme, update the "_config" file which was created automatically by GitHub when you created your pages site. Edit this file in GitHub directly to include the "remote_theme" tag (as described on the [remote themes blog](https://github.blog/2017-11-29-use-any-theme-with-github-pages/)), and the name of the developer and theme you have chosen (the name of their repository).
-
+
While you're here, it's a good idea to add the URL of your pages site to the "About" description on your GitHub repository. This is useful to help people find your pages site if they land on your repository first. Remember, your GitHub repository and your Pages site both exist as separate entities (at separate URLs), with the content repeated on both but "rendered" differently at each URL.
-
+
@@ -67,7 +67,7 @@ git clone [https address for your repo]
Boom! You have a local copy of your code 💃.
-
+
Now dig into the "how to" guide of your chosen theme to learn what you can add to make your pages site 💯.
@@ -75,13 +75,13 @@ Pro-tip: Search the internet for examples where other people have used the same
In the below I've edited my repo in atom. I've added a few pages, and the front matter (text at the top) to define the order I want pages to appear in, and whether they should have sub-pages ("children").
-Once you've made a few changes, simply [add, commit and push](../2-4-git-basics) them to your repo!
+Once you've made a few changes, simply [add, commit and push]({% link docs/gitlab/2-4-starting-git-basics.md %}) them to your repo!
-
+
It takes a little while for your pushed changes to appear on your site (especially if they are more complex things than adding/removing words). Be patient â³. Wait for them to arrive and see what you have created!
-
+
## 4. Tweak your theme and content as you wish!
diff --git a/docs/gitlab/4-4-create-gitlab-pages-site.md b/docs/gitlab/4-4-create-gitlab-pages-site.md
index 25e6c2f0d3c6fe1664ee78c6acd1e5f84c5d95b9..a62e34bef415693dedf6826dc6555ae540058d3d 100644
--- a/docs/gitlab/4-4-create-gitlab-pages-site.md
+++ b/docs/gitlab/4-4-create-gitlab-pages-site.md
@@ -18,12 +18,12 @@ Use the magic of Jekyll to transform markdown pages into a website
> **Note**
>
-> This guide describes how to publish your project with **GitLab** Pages. If you are planning to publish a GitHub repo, see the [GitHub Pages Guide](../4-3-you-make-your-pages-site) instead!
+> This guide describes how to publish your project with **GitLab** Pages. If you are planning to publish a GitHub repo, see the [GitHub Pages Guide]({% link docs/gitlab/4-3-you-make-your-pages-site.md %}) instead!
## 1. Turn your repo into a GitLab Pages site!
-Now the magic! Turn the simple collection of files made in [the previous tutorial](../4-1-you-make-your-repo) into something which looks like a user friendly website!
+Now the magic! Turn the simple collection of files made in [the previous tutorial]({% link docs/gitlab/4-1-you-make-your-repo.md %}) into something which looks like a user friendly website!
**Start from a WIN template**
diff --git a/docs/gitlab/gitlab-tutorials.md b/docs/gitlab/gitlab-tutorials.md
index 8ac888b59871e463e38abc310dff65f888df37ae..a9b31c74934bc8b47822aa1b4d7d0d1ffcec2c2b 100644
--- a/docs/gitlab/gitlab-tutorials.md
+++ b/docs/gitlab/gitlab-tutorials.md
@@ -21,30 +21,30 @@ Follow the below tutorials (left in the navigation panel) to set up and use GitL
**NOTE: These tutorials contain gifs of the processes being demonstrated on GitHub rather than GitLab. These are being included as they are still a useful demonstration. Please stay tuned for a GitLab based update.**
### 1. Tools for git and GitLab
-- [1.1 Using the command line](../1-1-tools-command-line)
-- [1.2 Writing in markdown](../1-2-tools-markdown)
-- [1.3 Text editors](../1-3-tools-atom)
+- [1.1 Using the command line]({% link docs/gitlab/1-1-tools-command-line.md %})
+- [1.2 Writing in markdown]({% link docs/gitlab/1-2-tools-markdown.md %})
+- [1.3 Text editors]({% link docs/gitlab/1-3-tools-atom.md %})
### 2. Getting started
-- [2.1 Your GitLab account](../2-1-starting-gitlab-account)
-- [2.2 Global git configuration](../2-2-starting-configure-git)
-- [2.3 Your local repository](../2-3-starting-local-repo)
-- [2.4 Basic git commands](../2-4-starting-git-basics)
+- [2.1 Your GitLab account]({% link docs/gitlab/2-1-starting-gitlab-account.md %})
+- [2.2 Global git configuration]({% link docs/gitlab/2-2-starting-configure-git.md %})
+- [2.3 Your local repository]({% link docs/gitlab/2-3-starting-local-repo.md %})
+- [2.4 Basic git commands]({% link docs/gitlab/2-4-starting-git-basics.md %})
### 3. Collaborating on GitLab
-- [3.1 Collaborating on GitLab](../3-1-collaborating-stranger-or-collaborator)
-- [3.2 Collaborating with a stranger](../3-2-collaborating-fork-their-repo)
-- [3.3 Play with this page](../3-3-collaborating-play-with-this-page)
+- [3.1 Collaborating on GitLab]({% link docs/gitlab/3-1-collaborating-stranger-or-collaborator.md %})
+- [3.2 Collaborating with a stranger]({% link docs/gitlab/3-2-collaborating-fork-their-repo.md %})
+- [3.3 Play with this page]({% link docs/gitlab/3-3-collaborating-play-with-this-page.md %})
### 4. Making and publishing your repository
-- [4.1 Make a repository](../4-1-you-make-your-repo)
-- [4.2 Create a doi](../4-2-you-doi)
-- [4.3 Create a GitHub Pages site](../4-3-you-make-your-pages-site)
-- [4.4 Create a GitLab Pages site](../4-4-create-gitlab-pages-site)
+- [4.1 Make a repository]({% link docs/gitlab/4-1-you-make-your-repo.md %})
+- [4.2 Create a doi]({% link docs/gitlab/4-2-you-doi.md %})
+- [4.3 Create a GitHub Pages site]({% link docs/gitlab/4-3-you-make-your-pages-site.md %})
+- [4.4 Create a GitLab Pages site]({% link docs/gitlab/4-4-create-gitlab-pages-site.md %})
### 5. Managing your project on GitLab
-- [5.1 GitLab issues](../5-1-projectmanagement-issues)
-- [5.2 GitLab milestones](../5-2-projectmanagement-milestones)
+- [5.1 GitLab issues]({% link docs/gitlab/5-1-projectmanagement-issues.md %})
+- [5.2 GitLab milestones]({% link docs/gitlab/5-2-projectmanagement-milestones.md %})
## Who should I ask for further advice about using GitLab
The Open WIN community are a great resource for support in using GitLab. [Join the community](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/) and try asking your question on slack!
diff --git a/docs/gitlab/repo-doi.md b/docs/gitlab/repo-doi.md
index c77297f9f7c1ea32af8a55dc40a3a215ff2e1d16..cd747b8c989b0329598a118d9f271009f3c5ed30 100644
--- a/docs/gitlab/repo-doi.md
+++ b/docs/gitlab/repo-doi.md
@@ -15,7 +15,7 @@ How to create a doi in zenodo for your GitLab project
---
-*Note this is a duplicate of [tutorial 4.2 Create a DOI](../4-2-you-doi)*
+*Note this is a duplicate of [tutorial 4.2 Create a DOI]({% link docs/gitlab/4-2-you-doi.md %})*
Zenodo is free to use tool for creating a digital object identifier (doi) for your shared resources. A doi is essential for enabling other researchers to cite and reuse your material, and for you to receive proper attribution. Your doi entry will include your [ORCID ID](https://info.orcid.org/benefits-for-researchers/), so it can be tracked against all your other research outputs.
diff --git a/docs/gitlab/repo-include.md b/docs/gitlab/repo-include.md
index bddbefafff7d4da99527c9729cfaa55c45a4fa58..5c3e41685eae7fadbc113da0e90322dacb3c6d91 100644
--- a/docs/gitlab/repo-include.md
+++ b/docs/gitlab/repo-include.md
@@ -33,14 +33,14 @@ Take a look at the Open WIN "[Data Sharing Decision Tree](https://git.fmrib.ox.a
4. **What do we need?**: Describe what contributions you would like to receive. Link to your CONTRIBUTING.md file for more information.
5. **Who are we?**: Identify who you are. Link to your lab pages.
6. **Contact us**: Give clear instructions for how people can get in touch.
-7. **Acknowledgements and citation**: Give clear guidance on how people should cite your material. This should include the [doi for the repository](../repo-doi) and any supporting papers.
+7. **Acknowledgements and citation**: Give clear guidance on how people should cite your material. This should include the [doi for the repository]({% link docs/gitlab/repo-doi.md %}) and any supporting papers.
### CONTRIBUTING.md
This file describes what contributions you would like to this material and how people should get in touch. Remember, an important benefit of sharing your resource is to invite collaborators. Make it easy for people to get involved.
### CITATION.cff
-This is a standardised file format which provides the exact metadata people will need to cite your repository (using the [doi you generate](../repo-doi)). It is easy to read by machines and humans, and is quickly becoming a sector standard - look out for a CITATION.cff in other software tools you use!
+This is a standardised file format which provides the exact metadata people will need to cite your repository (using the [doi you generate]({% link docs/gitlab/repo-doi.md %}). It is easy to read by machines and humans, and is quickly becoming a sector standard - look out for a CITATION.cff in other software tools you use!
You can generate a CITATION.cff for your project using [this online tool from Citation File Format](https://citation-file-format.github.io/cff-initializer-javascript/#/).
@@ -51,4 +51,4 @@ This file lists the terms of reuse of your material. GitLab will suggest some st
Any material you produce while employed by the University of Oxford should be [copyright to the University](https://innovation.ox.ac.uk/university-members/commercialising-technology/ip-patents-licenses/software-copyright/)
-See the [licensing guide](../repo-license) for a more complete discussion of which license you should consider applying to your code.
+See the [licensing guide]({% link docs/repo-license.md %}) for a more complete discussion of which license you should consider applying to your code.
diff --git a/docs/open-leadership.md b/docs/open-leadership.md
index 79812191847939a9f670b18e8be86232143733d2..86efbd15bcc6e4b479dda29f3f8bd9db83eab02c 100644
--- a/docs/open-leadership.md
+++ b/docs/open-leadership.md
@@ -16,7 +16,7 @@ Find out about the principles guiding this project
This project is being developed with the guiding principle of "Open Leadership". The Open Leadership framework was developed by Mozilla to support open source community projects. It describes a set of tools and practices which have been used in creating this repository along with exercises which have helped design effective paths to contribution. These principles were passed to the Open WIN Community Coordinator through participation in the [Open Life Science](https://openlifesci.org) program.
-
+
# Mozilla Open Leadership Framework
@@ -53,11 +53,11 @@ We are working open as this is an effective way to develop a user focused and in
The open canvas is designed to help define project goals, strategy and resource needs to create a minimum viable product (MVP). The images below describe the sections for the open canvas and the model we have drafted for the future [Open WIN Ambassadors](ambassadors.md) program.
-
+
<!-- <img src="/img/mozilla-framework/open-canvas-instructpng" alt="Open canvas section descriptions" width="100%" height="50%"> -->
-
+
<!-- <img src="/img/mozilla-framework/open-canvas-ambasspng" alt="Open canvas for WIN Open Ambassadors Program" width="100%" height="50%"> -->
@@ -65,37 +65,37 @@ The open canvas is designed to help define project goals, strategy and resource
A project README is your welcome mat. It should set the tone for the project, clearly describe the motivations and orient potential contributors.
-The README for the Open WIN Community is the [home page of this repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/blob/master/README.md?ref_type=heads) (../index.md).
+The README for the Open WIN Community is the [home page of this repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/blob/master/README.md?ref_type=heads) ({% link index.md %}).
### Project Roadmap
The roadmap outlines the plan for work ahead and should be shared openly with potential contributors. It summarises your vision and timeline for tasks. It is shared so people can see your progress along with the path you intend to travel. Openness here fosters trust and demonstrates an intention to involve your community in your activities.
-Take a look at our [roadmap for the community](community/roadmap.md).
+Take a look at our [roadmap for the community]({% link docs/community/roadmap.md %}).
### Personas and pathways
This exercise helps you think about the different people who will engage with the project, how they will find you, and how you will help to develop them into sustained contributors and future leaders of the project.
-Take a look at our [personas and pathways analysis for the community](community/personas-and-pathways.md).
+Take a look at our [personas and pathways analysis for the community]({% link docs/community/personas-and-pathways.md %}).
### Code of conduct
This sets out how we will interact with each other when working on this project, and how we will report and take appropriate actions against violations of this code of conduct
-Take a look at our [participation guidelines](community/CODE_OF_CONDUCT.md) and how we will support enacting University wide policies on harassment
+Take a look at our [participation guidelines]({% link docs/community/CODE_OF_CONDUCT.md %}) and how we will support enacting University wide policies on harassment
### Contributor guidelines
This describes how you can engage with the project, both as a one-time contributor or sustained participant.
-Take a look at our [contributing guidelines](CONTRIBUTING.md).
+Take a look at our [contributing guidelines]({% link docs/CONTRIBUTING.md %}).
### License and citing the repository
We would love for others to use, share and reference this repository and the materials contained within. We have applied a CC-BY 4.0 licence so you can share and adapt the materials here as long as attribution is given to this project.
-Take a look at our [license and citation guidelines](LICENSE.md).
+Take a look at our [license and citation guidelines]({% link docs/LICENSE.md %}).
### Publish your project openly
diff --git a/docs/protocols.md b/docs/protocols.md
index af4e0ab5cfe93c8e90aed32b4a8db63adc1d4eb4..08fcb062d35df51a309d9826b0ca6420379b1246 100644
--- a/docs/protocols.md
+++ b/docs/protocols.md
@@ -14,7 +14,7 @@ How to share your magnetic resonance imaging protocols
---
-
+
## Purpose
@@ -32,7 +32,7 @@ Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/p
Training guides are available for WIN members and external users. Access the guides below or via the left navigation menu.
-[](../protocols/protocols_guide_internal-how-1) [](../protocols/protocols_guide_external)
+[]({% link docs/protocols/protocols_guide_internal-how-1.md %}) []({% link docs/protocols/protocols_guide_external.md %})
<!-- ## Citation
diff --git a/docs/protocols/protocols_guide_external.md b/docs/protocols/protocols_guide_external.md
index 1a3f7d0ef4192b662fcc87ec95a67ce7ae4cfa20..c65aae10af715f20cc28efa7c7276ec2201ed903 100644
--- a/docs/protocols/protocols_guide_external.md
+++ b/docs/protocols/protocols_guide_external.md
@@ -22,7 +22,7 @@ A guide for external researchers on how to use the Open WIN MR protocols databas
## For external researchers
External researchers are able to search the database for MR protocols which research teams have chosen to make openly available. These may be deposited to support publications as supplementary methods material, or they may form the main body of research in sequence development.
-
+
### 1. Access the MR Protocols database
Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/protocols/)
diff --git a/docs/protocols/protocols_guide_internal-how-1.md b/docs/protocols/protocols_guide_internal-how-1.md
index 2e1ebee2fe259f1d388bd26a3b060b895f27f419..ebc699afe6d20a21ce21ab05f8ee4329d086576f 100644
--- a/docs/protocols/protocols_guide_internal-how-1.md
+++ b/docs/protocols/protocols_guide_internal-how-1.md
@@ -13,7 +13,7 @@ nav_order: 2
---
-<!--  -->
+<!--  -->
## Contents
@@ -50,7 +50,7 @@ You might want to add a statement such as "available for re-use, but I'm unable
Only WIN members (as determined by SSO authentication) are able to deposit protocols in the database.
-
+
To log in:
1. Go to [https://open.win.ox.ac.uk/protocols/](https://open.win.ox.ac.uk/protocols/)
@@ -63,7 +63,7 @@ To log in:
Protocols are saved to individual user profiles.
-
+
1. Once you are logged in, you will see the `Add Protocol` icon.
2. Click on `Add Protocol`, and you will be taken to the `Add new protocol` page.
@@ -81,7 +81,7 @@ You can enter details about your protocol which are relevant to the study as a w
NOTE: If you are publishing customised pulse sequences, please be sure to indicate your willingness and requirements for sharing them (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences) below).
-
+
### 3.1 Project, hardware and species
Some fields of this section are autmatically retrieved from your pdf and other ones have to be added by selecting the appropriate items from the dropdown menus like:
@@ -141,7 +141,7 @@ You can add details specific to individual sequences. These details may make the
Each of the sections below should be completed for each sequence.
-
+
### 5.1 Sequence name
This is identified from the pdf. You can update it or add any additional context where necessary.
@@ -181,4 +181,4 @@ Add any references which are relevant to this protocol for example the accompany
We recommend that you consider using the [CRediT](https://casrai.org/credit/) system for identifying individual author contributions. You may wish to order authors alphabetically.
-
+
diff --git a/docs/protocols/protocols_guide_internal-how-2.md b/docs/protocols/protocols_guide_internal-how-2.md
index 7ec823d6234e0ece6212fc86c50195365af1e0a8..6c93f2e9c24dad754bbd053a9e9eb6b8624afa79 100644
--- a/docs/protocols/protocols_guide_internal-how-2.md
+++ b/docs/protocols/protocols_guide_internal-how-2.md
@@ -13,7 +13,7 @@ nav_order: 3
---
-<!--  -->
+ <!-- -->
We suggest using the free tool Zenodo for creating a Digital Object Identifier (DOI) for your protocol. This will allow others to cite your protocol independently from other work in the study and add contributors who may not be named elsewhere.
diff --git a/docs/protocols/protocols_guide_internal-how-3.md b/docs/protocols/protocols_guide_internal-how-3.md
index edc0f37c06cedfe03acc775bd502d5385b797710..f4f8d6096ba0f437ed4bc2052123e47d8670dfcf 100644
--- a/docs/protocols/protocols_guide_internal-how-3.md
+++ b/docs/protocols/protocols_guide_internal-how-3.md
@@ -13,12 +13,12 @@ nav_order: 4
---
-<!--  -->
+<!---->
If you are using the protocols database to track changes made to your protocol while piloting, you can amend the entry and create a new version that can be reviewed at any point.
-
+
1. Go to `my protocols` and find the entry you would like to update.
2. Select if you are adding a new protocol pdf file (`Update with new protocol file`) or making changes to other parts of the entry (`Update keeping existing protocol file`)
diff --git a/docs/protocols/protocols_guide_internal-how-4.md b/docs/protocols/protocols_guide_internal-how-4.md
index 3cb704accda80d7a939fe602b160618554bb2e01..79ca39ff7931a89de7927832c2a094d1af461b12 100644
--- a/docs/protocols/protocols_guide_internal-how-4.md
+++ b/docs/protocols/protocols_guide_internal-how-4.md
@@ -13,7 +13,7 @@ nav_order: 5
---
-<!--  -->
+<!---->
You can track how many times your protocol has been viewed and downloaded from the `Engagement Statistics` panel. Views and downloads are separated into internal to Oxford (users have logged in with an SSO) or external. When reporting on the impact of your entry, remember to also include the Zenodo views and downloads statistics, if you have used Zenodo to create a DOI.
diff --git a/docs/protocols/protocols_guide_internal-why-use.md b/docs/protocols/protocols_guide_internal-why-use.md
index 0ac6ef920edb83984bdfcb6e039d124aee0d842d..4b7708dc82101405ad5cad50a85b796b69b0cb7b 100644
--- a/docs/protocols/protocols_guide_internal-why-use.md
+++ b/docs/protocols/protocols_guide_internal-why-use.md
@@ -15,20 +15,20 @@ Why you should consider using the WIN MR protocols database to record and share
---
-<!--  -->
+ <!-- -->
*The MR protocol database has been developed to share MR protocols internally across WIN as well as externally. The database provides access to standard protocols and to the latest experimental protocols uploaded by WIN members. The database facilitates sharing your MR sequence within and between research groups and helps you to keep track of updates using version control. Each deposited protocol contains all information necessary to reproduce that sequence on an appropriately licensed scanner, allowing yourself and others to have a permanent and full record of your data acquisition methodology.*
## Benefits
-### Version control 
-The MR Protocols database is version controlled, so WIN members are invited to upload their protocols during piloting to keep track of optimisation and final versions. Comments and notes can be added to each entry so you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data](../../data) server
+### Version control 
+The MR Protocols database is version controlled, so WIN members are invited to upload their protocols during piloting to keep track of optimisation and final versions. Comments and notes can be added to each entry so you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data]({% link docs/data.md %}) server.
-### Citable research output 
+### Citable research output 
Versions (with minor and major edits) can be assigned a digital object identifier (DOI) using the [Oxford Research Archive (ORA) Data repository](https://deposit.ora.ox.ac.uk) using the stable link provided by the MR Protocols database. Once a DOI has been created, your MR protocol becomes a citable object which you can add to your list of research outputs.
-### Reproducible methods detail 
+### Reproducible methods detail 
Depositing your MR protocol in the database is as simple as uploading the sequence pdf available from the scanner console, or alternatively you can upload the .exar file used by our [Siemens scanners](https://www.win.ox.ac.uk/about/facilities). Sequences' details are captured from either document and parsed into a unified machine readable and searchable format. You can upload a single sequence or all sequences used in a single imaging session (a protocol) together.
diff --git a/docs/protocols/protocols_guide_internal.md b/docs/protocols/protocols_guide_internal.md
index e8ca57cc913d81dc71f77e65a638c059a04de205..ac79f8a20cf3d508d4ce051d82e497d16f061fe3 100644
--- a/docs/protocols/protocols_guide_internal.md
+++ b/docs/protocols/protocols_guide_internal.md
@@ -14,4 +14,4 @@ nav_exclude: true
---
-
+
diff --git a/docs/tasks.md b/docs/tasks.md
index 0a22f3e764fa3565d0357328c3e0b209cecbdfd2..6c41db25ba51c5999d344463f35cbca057518aaf 100644
--- a/docs/tasks.md
+++ b/docs/tasks.md
@@ -14,16 +14,14 @@ How to share your experimental tasks
---
-
+
## Purpose
The Open Tasks working group aims to encourage and incentivise researchers designing experimental tasks for functional neuroimaging to share these tasks openly with other researchers. They have established online repository for these paradigms to be shared, alongside documentation and analysis scripts for behavioural results. This working group also aims to train new members of the centre in open-source coding languages for paradigm development, and sharing reproducible environments.
<br>
-<!-- [](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-win-members) [](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-external-researchers) -->
-
-[](../tasks/tasks_guide_internal-how-1) [](../tasks/tasks_guide_external)
+[]({% link docs/tasks/tasks_guide_internal-how-1.md %}) []({% link docs/tasks/tasks_guide_external.md %})
## Contributors
We are grateful to the following WIN members for their contributions to developing the Open Tasks
diff --git a/docs/tasks/tasks_guide_internal-how-1.md b/docs/tasks/tasks_guide_internal-how-1.md
index 84a2a802c326bf719ed7d21b77d04b18aca03d5a..e0349370085db83c7054424d9881067b36c1744a 100644
--- a/docs/tasks/tasks_guide_internal-how-1.md
+++ b/docs/tasks/tasks_guide_internal-how-1.md
@@ -13,7 +13,7 @@ nav_order: 2
---
-<!--  -->
+ <!---->
## Contents
@@ -42,7 +42,7 @@ We think the [Pavlovia](https://pavlovia.org) system for task sharing is a great
## How do I add my task to the Open WIN Tasks repository(s)?
Once you've been added as a member of the WIN Open Tasks reposistory and/or the OPEN_WIN Pavlovia repository (see above), you can add your repositories to these groups! In WIN GitLab, go to your repository, and then click on "Members", then "Invite Group", and choose "open-science" in your group to invite. In PsychoPy, go to [Pavlovia GitLab](https://gitlab.pavlovia.org/), and then click on "Settings", "Members", "Invite Group", and choose "OPEN_WIN" as the group. We recommend that you add the repository to the group with 'reporter' permissions. See below for an example of how to do this:
-
+
## Who can I get further advice?
diff --git a/docs/tasks/tasks_guide_internal-why-use.md b/docs/tasks/tasks_guide_internal-why-use.md
index 3cdb47b951bb63ff7c4a1d02a0f95d4689779b2b..064c4df3839c599e00ee5c5a7fb4134d73a2112d 100644
--- a/docs/tasks/tasks_guide_internal-why-use.md
+++ b/docs/tasks/tasks_guide_internal-why-use.md
@@ -15,14 +15,14 @@ Why you should consider using the WIN MR tasks repository.
---
-<!--  -->
+ 
## Benefits
-### Version control 
-The [WIN Open Tasks repository](https://git.fmrib.ox.ac.uk/open-science) is maintained in the WIN GitLab server. WIN members are invited to deposit their task code and materials when they are using a stable version, by cloning from their own GitLab or GitHub repository. This implies that WIN members will be using a git process when developing their task, and as such their development journey will be version controlled. Find out more about [using GitLab](../gitlab)
+### Version control 
+The [WIN Open Tasks repository](https://git.fmrib.ox.ac.uk/open-science) is maintained in the WIN GitLab server. WIN members are invited to deposit their task code and materials when they are using a stable version, by cloning from their own GitLab or GitHub repository. This implies that WIN members will be using a git process when developing their task, and as such their development journey will be version controlled. Find out more about [using GitLab]({% link docs/gitlab.md %})
-### Citable research output 
-Versions of task materials can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading individual task repositories from GitLab. Once a DOI has been created, your task material becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository](../gitlab/4-2-you-doi).
+### Citable research output 
+Versions of task materials can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading individual task repositories from GitLab. Once a DOI has been created, your task material becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository]({% link docs/gitlab/4-2-you-doi.md %}).
-### Reproducible methods detail 
+### Reproducible methods detail 
WIN members will be supported in developing the necessary and sufficient documentation and running environments to enable others to launch, maintain and adapting their tasks. This facilitates effective re-use and modification of tasks within a research group, and with external collaborators.
diff --git a/docs/tools.md b/docs/tools.md
index 72a22416cfe6f7f58a57da50ffd83adf513de1ce..baa6501d3b9ca83934a38b9cc6853bf81b96aafc 100644
--- a/docs/tools.md
+++ b/docs/tools.md
@@ -14,7 +14,7 @@ How to use WIN infrastructure to share each stage of your research output
---
-
+
WIN have created a number of tools to help you share your research output effectively and openly. In some cases these have been built using infrastructure. In most cases, however, it has been necessary to design custom databases and software solutions to suite our specific needs.
diff --git a/docs/using-this-repo.md b/docs/using-this-repo.md
index d0846b688d137a711cd905af3ec86874df29184b..a452e9a595c0ccd053d8247eba4385503b4c64bf 100644
--- a/docs/using-this-repo.md
+++ b/docs/using-this-repo.md
@@ -46,18 +46,18 @@ An "issue" is a term used by GitLab for a place to track ideas, enhancements, ta
Folks with a WIN IT account can leave feedback on this site by commenting on the [issues in our GitLab repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues). You are welcome to comment on any issue that feels relevant. If you are new to the community you might like to first have a go with the issues labelled "good first issue".
## Creating a GitLab account to comment
-To comment on the issues you will need a WIN GitLab login. If you haven’t got a WIN GitLab account, take a look at [this guide](../gitlab/2-1-starting-gitlab-account) for how to create one.
+To comment on the issues you will need a WIN GitLab login. If you haven’t got a WIN GitLab account, take a look at [this guide]({% link docs/gitlab/2-1-starting-gitlab-account.md %}) for how to create one.
## Do I have to write something?
No. If you don't feel like writing out something, you are very welcome to add a quick emoji to something someone else has written. Feedback on other people's feedback is also really helpful!
-
+
If you are able to write something, you are welcome to add just a few words, sentences, or paragraphs if you'd like. Whatever works for you is great.
## Will my comments be public?
Yes. We'd really like for all feedback to be public. This will ensure that everything is transparent and well recorded. The aim is to show that community members have had input on these pages, and we’ve listened to and incorporated your feedback.
-Please don’t be worried about being critical (if something’s not right, we need to know about it!), but please try to be respectful and courteous, as per the [community participation guidelines](../community/CODE_OF_CONDUCT).
+Please don’t be worried about being critical (if something’s not right, we need to know about it!), but please try to be respectful and courteous, as per the [community participation guidelines]({% link docs/community/CODE_OF_CONDUCT.md %}).