Commit b1df826f authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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update image paths

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......@@ -74,16 +74,16 @@ Open Community
- Encourage the community to share pre-prints of their papers.
![OS-Survey 2019 slide 3](../img/open-science-survey-results/Slide3.png)
![OS-Survey 2019 slide 3](../../img/open-science-survey-results/Slide3.png)
- Appreciate the value of open science practices in career development
![OS-Survey 2019 slide 4](../img/open-science-survey-results/Slide4.png)
![OS-Survey 2019 slide 4](../../img/open-science-survey-results/Slide4.png)
- 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.
![OS-Survey 2019 slide 5](../img/open-science-survey-results/Slide5.png)
![OS-Survey 2019 slide 5](../../img/open-science-survey-results/Slide5.png)
## Reduce barriers to engaging in open research practices
......@@ -91,12 +91,12 @@ 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), [acquisition protocols](OpenProtocols.md) and [analysis tools](OpenTools.md)
![OS-Survey 2019 slide 6](../img/open-science-survey-results/Slide6.png)
![OS-Survey 2019 slide 6](../../img/open-science-survey-results/Slide6.png)
![OS-Survey 2019 slide 7](../img/open-science-survey-results/Slide7.png)
![OS-Survey 2019 slide 7](../../img/open-science-survey-results/Slide7.png)
## 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.
![OS-Survey 2019 slide 8](../img/open-science-survey-results/Slide8.png)
![OS-Survey 2019 slide 8](../../img/open-science-survey-results/Slide8.png)
......@@ -11,7 +11,7 @@ nav_order: 4
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 }
![people](img/img-people.png)
![people](../img/img-people.png)
---
......
......@@ -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.
![responsible-bystander-pdf](../img/img-responsiblebystanderposterpdf.png)
![responsible-bystander-pdf](../../img/img-responsiblebystanderposterpdf.png)
......@@ -21,7 +21,7 @@ Find out who we are and where we sit in the wider WIN context.
* [Community Coordinator](#community-coordinator---cassandra-gould-van-praag-sheher)
* [WIN Open Neuroimaging Working Group](#win-open-neuroimaging-working-group)
![community-schematic](../img/img-community-schematic-h400-gold.png)
![community-schematic](../../img/img-community-schematic-h400-gold.png)
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!
......
......@@ -17,7 +17,7 @@ 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.
![mountain-of-engagement](../img/img-m-o-e.png)
![mountain-of-engagement](../../img/img-m-o-e.png)
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.
......
......@@ -14,7 +14,7 @@ Connect with us via any of the means below as per your preference and interests
---
## Open WIN Slack ![slack](img/icon-slack.png)
## Open WIN Slack ![slack](../img/icon-slack.png)
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.md), the [Open WIN community](community.md), and relevant external and internal [events](events.md).
......@@ -33,14 +33,14 @@ 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 ![mail-list](img/icon-maillist.png)
## Open WIN Mailing List ![mail-list](../img/icon-maillist.png)
Anyone interested in the Open WIN Community or these resources can join the [WIN Open Neuroimaging mailing list](https://mail.fmrib.ox.ac.uk/mailman/listinfo/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. We will also email round-ups of the discussion happening on the [Slack](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/contact.html#open-win-slack-)
## Email the Open WIN Community Coordinator Directly ![mailto](img/icon-at.png)
## Email the Open WIN Community Coordinator Directly ![mailto](../img/icon-at.png)
You are very welcome to [email Cassandra Gould van Praag](mailto:cassandra.gouldvanpraag@psych.ox.ac.uk) directly to discuss any issue relating to open research at WIN, the community, or this repository.
## Comment on the GitHub repository ![github](img/icon-github.png)
## Comment on the GitHub repository ![github](../img/icon-github.png)
If you want to report a problem or suggest an enhancement for this repository, we'd love for you to [open an issue](https://github.com/cassgvp/WIN-Open-Neuroimaging-Community/issues) on out GitHub page.
......@@ -28,7 +28,7 @@ The aims for the hack day were to:
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.
![hack day 1 attendance](../img/img-hackday-1-pies.png){:height="100%" width="100%"}
![hack day 1 attendance](../../img/img-hackday-1-pies.png){:height="100%" width="100%"}
## What did we achieve?
......
......@@ -18,7 +18,7 @@ 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.
![open-research-calendar](../img/img-orc.png)
![open-research-calendar](../../img/img-orc.png)
<div class="span3">
......
......@@ -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 structure](img/img-open-leadership.png)
![Mozilla Open Leadership structure](../img/img-open-leadership.png)
# 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.
![Open canvas section descriptions](img/mozilla-framework/open-canvas-instruc.png)
![Open canvas section descriptions](../img/mozilla-framework/open-canvas-instruc.png)
<!-- <img src="/img/mozilla-framework/open-canvas-instructpng" alt="Open canvas section descriptions" width="100%" height="50%"> -->
![Open canvas for WIN Open Ambassadors Program](img/mozilla-framework/open-canvas-ambas.png)
![Open canvas for WIN Open Ambassadors Program](../img/mozilla-framework/open-canvas-ambas.png)
<!-- <img src="/img/mozilla-framework/open-canvas-ambasspng" alt="Open canvas for WIN Open Ambassadors Program" width="100%" height="50%"> -->
......
......@@ -13,7 +13,7 @@ How to use WIN infrastructure to share each stage of your research output
---
![tools](img/img-tools.png)
![tools](../img/img-tools.png)
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.
......
......@@ -15,7 +15,7 @@ How to share your magnetic resonance imaging acquisition sequences
---
![open-acquisition](../img/img-open-acq-flow.png)
![open-acquisition](../../img/img-open-acq-flow.png)
## Purpose
......@@ -30,16 +30,16 @@ Coming soon
<br>
[![For WIN members](../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/acquisition.html#for-win-members) [![For external researchers](../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/acquisition.html#for-external-researchers)
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/acquisition.html#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/acquisition.html#for-external-researchers)
## For WIN members
#### Version control ![version-control](../img/icon-version-control.png)
#### Version control ![version-control](../../img/icon-version-control.png)
The acquisition database is version controlled, so WIN members are invited to upload their protocols during pilotting to keep track of optimisation and final versions. Comments and notes can be added to each entry to 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.md) server
#### Citable research output ![doi](../img/icon-doi.png)
#### Citable research output ![doi](../../img/icon-doi.png)
Versions (with minor and major edits) can be assigned a digital object identified (DOI) using the [Oxford Research Archive (ORA) Data repository](https://deposit.ora.ox.ac.uk) using the stable link provided by the acquisition database. Once a DOI has been created, your acquisition protocol becomes a citable object which you can add to your list of research outputs.
#### Reproducible methods detail ![reproduce](../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
Depositing your acquisition 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). All sequence detail is 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.
## For external researchers
......
......@@ -16,7 +16,7 @@ How to share reproducible FSL analysis pipelines
---
![open-analysis](../img/img-open-anal-flow.png)
![open-analysis](../../img/img-open-anal-flow.png)
## Purpose
......@@ -35,16 +35,16 @@ Coming soon
<br>
[![For WIN members](../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/analysis.html#for-win-members) [![For external researchers](../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/analysis.html#for-external-researchers)
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/analysis.html#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/analysis.html#for-external-researchers)
## For WIN members
#### Version control ![version-control](../img/icon-version-control.png)
#### Version control ![version-control](../../img/icon-version-control.png)
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.
#### Citable research output ![doi](../img/icon-doi.png)
#### Citable research output ![doi](../../img/icon-doi.png)
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.
#### Reproducible methods detail ![reproduce](../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
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.md) servers;
2. access your GitLab code repository;
......
......@@ -14,7 +14,7 @@ How to share your data responsibly
---
![open-data](../img/img-open-data-flow.png)
![open-data](../../img/img-open-data-flow.png)
## Purpose
......@@ -36,7 +36,7 @@ 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.
[![For WIN members](../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/data.html#for-win-members) [![For external researchers](../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/data.html#for-external-researchers)
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/data.html#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/data.html#for-external-researchers)
Coming soon
{: .label .label-yellow }
......@@ -46,15 +46,15 @@ Coming soon
<br>
## For WIN members
#### Version control ![version-control](../img/icon-version-control.png)
#### Version control ![version-control](../../img/icon-version-control.png)
Coming soon
{: .label .label-yellow }
#### Citable research output ![doi](../img/icon-doi.png)
#### Citable research output ![doi](../../img/icon-doi.png)
Coming soon
{: .label .label-yellow }
#### Reproducible methods detail ![reproduce](../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
Coming soon
{: .label .label-yellow }
......
......@@ -15,23 +15,23 @@ How to share your experimental tasks
---
![open-tasks](../img/img-open-tasks-flow.png)
![open-tasks](../../img/img-open-tasks-flow.png)
## 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>
[![For WIN members](../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/tasks.html#for-win-members) [![For external researchers](../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/tasks.html#for-external-researchers)
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/tasks.html#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/Open-WIN-Community/docs/tools/tasks.html#for-external-researchers)
## For WIN members
#### Version control ![version-control](../img/icon-version-control.png)
#### Version control ![version-control](../../img/icon-version-control.png)
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.
#### Citable research output ![doi](../img/icon-doi.png)
#### Citable research output ![doi](../../img/icon-doi.png)
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.
#### Reproducible methods detail ![reproduce](../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
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.
......@@ -56,7 +56,7 @@ Yes! We think the [Pavlovia](https://pavlovia.org) system for task sharing is a
### How do I add my task to the WIN Open Tasks repository and/or to the OPEN_WIN Pavlovia repository?
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:
![Pavlovia example](../img/pavlovia_OPENWIN_walkthrough.png)
![Pavlovia example](../../img/pavlovia_OPENWIN_walkthrough.png)
### Who should I ask for further advice about sharing my tasks?
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......@@ -53,7 +53,7 @@ To comment on the issues you will need a GitHub login. If you haven’t got 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!
![github-issue-emoji](img/img-github-issue-emoji.png)
![github-issue-emoji](../img/img-github-issue-emoji.png)
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.
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