Commit 54b11451 authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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fix links

parent f41c38f2
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## For WIN members
### Benefits
#### 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. Find out more about [using GitLab](../../gitlab)
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)
#### 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. Find out how to [create a doi for your repository](../../gitlab/4-2-you-doi).
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).
#### 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:
......@@ -61,13 +61,13 @@ 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](../../events/doc-hack-1)
Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our [documentation hacks](../community/events/doc-hack-1)
#### 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](../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.
#### 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](../gitlab/repo-doi) page for instructions.
## Working group members (alphabetically)
We are grateful to the following WIN members for their contributions to developing the Open Analysis tools
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......@@ -21,8 +21,8 @@ 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 Tools](../tools.md).
3. Provide training on GitHub/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](../../../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.
4. Begin crafting and contributing documentation to share our training with others.
## How did it go?!
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......@@ -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.md) page.
For examples on how to use BIDS related containers see the [BIDS](../bids) page.
### FSL Containers
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......@@ -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](./data/bids.md) page.
For the current overview of how BIDS works in XNAT, see the [BIDS](../bids) 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](data/python.md) 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](../python) for more info on pyxnat, xnatpy and dax.
#### Docker in XNAT
To see how Docker works in XNAT, see the [Docker](data/docker.md) page.
To see how Docker works in XNAT, see the [Docker](../docker) page.
#### Case Studies
The [OPDC project](data/opdc.md) uploaded DICOM data from jalapeno using python and dcmtk.
The [OPDC project](../opdc) uploaded DICOM data from jalapeno using python and dcmtk.
TODO: More case studies!
......@@ -26,10 +26,10 @@ The Open Tasks working group aims to encourage and incentivise researchers desig
## For WIN members
### Benefits
#### 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. Find out more about [using GitLab](gitlab.md)
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)
#### 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. Find out how to [create a doi for your repository](gitlab/4-2-you-doi.md).
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).
#### 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.
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