Open WIN Community issueshttps://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues2023-02-23T14:14:01+00:00https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/48[documentation] guide on CRediT2023-02-23T14:14:01+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] guide on CRediT## I'm submitting a ...
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
Here some draft notes on using CRediT for acknowledging author contributions.
The below needs to be re-written for a general audi...## I'm submitting a ...
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
Here some draft notes on using CRediT for acknowledging author contributions.
The below needs to be re-written for a general audience and published somewhere.
## Draft CRediT guide
The [CRediT framework](https://casrai.org/credit/) is a useful tool for acknowledging different types of author contributions. This may be particularly relevant if you are publishing non-traditional research outputs, such as data and code.
Using CRediT, you can identify *anyone* who has contributed to the work which went into the object you are publishing, and assign them to any of the roles listed (people can have multiple roles). You can then use [tenzing](https://martonbalazskovacs.shinyapps.io/tenzing/) to create an authorship statement which you add to zenodo. Example of a CRediT statement on [this zenodo entry](https://zenodo.org/record/5826183#.Yo5THC2ZPs0).
As a general rule I’m always super-inclusive on authorship. I don’t think it harms the output to show that the work/efforts of many people made it possible.https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/44[website] import h2mri2023-04-27T23:05:17+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[website] import h2mri## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
In 2018-2020, Cass wrote a guide on open science MRI data collection and analysis bes...## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
In 2018-2020, Cass wrote a guide on open science MRI data collection and analysis best practices for [PERL](https://www.google.com/search?client=safari&rls=en&q=oxford+perl&ie=UTF-8&oe=UTF-8). There is some content which could be usefully incorporated into the Community Pages.
## Action to take
Import relevant sections of [https://git.fmrib.ox.ac.uk/cassag/h2mri](https://git.fmrib.ox.ac.uk/cassag/h2mri).
To be considered:
- [x] What "chapters" to include?
- [ ] Where should they go? Analysis? Separate pages on RDM?
- [ ] move the code from git.fmrib...cassag/h2mri to a community repository (perhaps open-science/analysis?
- [ ] flag the known issues with the code! 1) singularity container should not be in there repo (people should pull it using a stated path to the container repo); 2) conda packages should not be in the repo, people should pull them!https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/6Readability - action findings of accessibility report2023-02-27T10:15:43+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukReadability - action findings of accessibility reportJuju FarsJuju Farshttps://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/1Add documentation on open access publishing2024-02-18T13:45:55+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukAdd documentation on open access publishingYing-Qiu ZhengYing-Qiu Zhenghttps://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/64[new feature] integrating data sharing decision tree2024-03-06T11:00:12+00:00Bernd Taschler[new feature] integrating data sharing decision tree## Issue
Existing material on data sharing (particularly around WIN's Xnat server) is not integrated yet with the community pages
## Where
- [data sharing repo](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tre...## Issue
Existing material on data sharing (particularly around WIN's Xnat server) is not integrated yet with the community pages
## Where
- [data sharing repo](https://git.fmrib.ox.ac.uk/open-science/community/data-sharing-decision-tree)
## What
- [ ] decide on where to put this on the community pages
- [ ] check that existing material is up to date
- [ ] integrate with community pageshttps://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/62Add info on DPIA2023-03-30T11:23:38+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukAdd info on DPIA## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report (eg. 404)
- [ ] documentation (eg. typos, broken links)
- [x] feature request (eg. add GitLab tutorial)
- [ ] question (eg. how does this work?...## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report (eg. 404)
- [ ] documentation (eg. typos, broken links)
- [x] feature request (eg. add GitLab tutorial)
- [ ] question (eg. how does this work?)
## Where is the issue?
[data pages](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/data/)
## What is the issue?
No guidance or links about DP(I)A.
## How do we solve the issue?
Give some guidance on what we know for certain (e.g. that data are not considered "biometric") and link to university pages.
Would be nice to include some big buttons on the data home page to make this and [data management plan](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/data/data-management-plans) pages more visibleCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukCassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukhttps://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/61Add info on sharing of data collected under "Technical Development" SOP2023-03-30T11:15:02+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukAdd info on sharing of data collected under "Technical Development" SOP## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report (eg. 404)
- [ ] documentation (eg. typos, broken links)
- [x] feature request (eg. add GitLab tutorial)
- [ ] question (eg. how does this work?...## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report (eg. 404)
- [ ] documentation (eg. typos, broken links)
- [x] feature request (eg. add GitLab tutorial)
- [ ] question (eg. how does this work?)
## Where is the issue?
The [can I share data: ethics](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/data/can-i/#ethics)
## What is the issue?
No details are available for data acquired under the [Technical Development SOP](https://sharepoint.nexus.ox.ac.uk/sites/NDCN/FMRIB/Shared%20Documents/SOP_Technical_Development_Scanning.pdf)
## How do we solve the issue?
Add the following (maybe a seperate drop down under ethics):
-----
From [SOP OHBA_009_V1 004-V4 (FMRIB)](https://sharepoint.nexus.ox.ac.uk/sites/NDCN/FMRIB/Shared%20Documents/SOP_Technical_Development_Scanning.pdf)
Data acquired under the Technical developmnent SOP may be published as long as:
1. No additional ethical approval was required (see section 4.1)
2. The data was not acquired to develope a sequence to be used in aother study which has or will have seperate ethical approval.
3. The data was not acquired for the purposes of training other researchers or scanner operators.
In all cases, this data may only be shared if it it "completely anonymised". Examples of completely anonymous data include:
- Restructed field of view (i.e. not a whole brain)
- B1 data
- B0 data
- Low resolution reference images (e.g. 6.4 mm isotropic) acquired to support B1 maps.
Please contact open@win.ox.ac.uk to discuss whether other data types can be considered completely anonymous.
------
## Anything else?
> Please give any additional detail which may be relevant or useful, for example detailed explanation, motivation, stacktraces, related issues, links for us to have context.
---
## Fix the issue yourself?
If you are able to, you are welcome to submit new content directly via a merge request. This will ensure you are attributed for your suggestion. See this guide on submitting a merge request via GitLab: https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/gitlab/3-2-collaborating-fork-their-repo/https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/57[documentation] Add information about deidentifiaction for patient cohorts2023-02-20T12:28:37+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] Add information about deidentifiaction for patient cohorts## Thank you for contributing to the Open WIN Community
## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report (eg. 404)
- [x] documentation (eg. typos, broken links)
- [ ] feature request (eg. add...## Thank you for contributing to the Open WIN Community
## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report (eg. 404)
- [x] documentation (eg. typos, broken links)
- [ ] feature request (eg. add GitLab tutorial)
- [ ] question (eg. how does this work?)
## Where is the issue?
> Please include links to the affected page(s) refering to specific lines or sentences.
https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/data/can-i/#deidentification
## What is the issue?
> Please describe the problem you have encountered or the feature/content you would like to extend.
Doesn't include a description of deidentification considerations for patient cohorts, e.g. it may not be possible to make data anonymous if rare cohorts are sampled.
## How do we solve the issue?
> Please describe how the problem could be fixed or what additional feature/content could be included.
Add some text to the deidentification list from line 168 on [docs/data/can-i.md](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/blob/master/docs/data/can-i.md?plain=1)
## Anything else?
> Please give any additional detail which may be relevant or useful, for example detailed explanation, motivation, stacktraces, related issues, links for us to have context.
---
## Fix the issue yourself?
If you are able to, you are welcome to submit new content directly via a merge request. This will ensure you are attributed for your suggestion. See this guide on submitting a merge request via GitLab: https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/gitlab/3-2-collaborating-fork-their-repo/https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/51[documentation] Add something to the protocols db instructions about sharing ...2022-07-07T13:17:29+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] Add something to the protocols db instructions about sharing custom sequences## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
> Please describe the problem you have encountered or the feature/content you would l...## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
> Please describe the problem you have encountered or the feature/content you would like to extend. Please include links to the affected page(s).
The protocols db instructions assume that we will be sharing standard sequences only. The guidance is incomplete for people who are creating modified/customised sequences as there is an additional layer of contracts required between Oxford, the recipient and Siemens.
## What is the expected/preferred behaviour?
> Please describe how the problem could be fixed or what additional feature/content could be included.
Add a line "if you are intending to openly share a custom sequence, please contact Stuart to arrange a Transfer Agreement and the appropriate approvals from Siemens."
## What is the motivation / use case for changing the behaviour?
> Why should we make this fix or include this content?
to make the documentation appropriate for Physics researchers.https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/47[documentation] Interactive web apps2022-10-19T13:12:41+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] Interactive web apps## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
Two different researchers have separately asked for support in creating an interacti...## I'm submitting a ...
> Put an x in the appropriate square brackets
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
Two different researchers have separately asked for support in creating an interactive web app. Would should publish some information about how to create these on the community pages!
## What is the expected/preferred behaviour?
This issues is to collect that information which I've shared with these researchers. It should next be re-written into something generic and published somewhere. Not sure what topic it would sit under the current structure! Open Data?
## Other information: Central University Support
[Laurence Brown](https://blogs.it.ox.ac.uk/acit-rs-team/team/laurence-brown/) has a lot of experience on this an is willing to give advice/support.
## Other information: Researcher requirements of an interactive web app)
### 1. Interactive table
#### Requirement
> We'd quite like to share a table online as a tool people can interact with and get information from, copy data out of etc (like in an google/xls spreadsheet where you can sort by different columns etc) - it would be not the usual written-up publication format but rather a shared data table summarizing parameters from many previous studies that we have put together.
#### Advice
> You could do this with either a [Jupiter notebook and binder](https://mybinder.org), a [shiny app](https://shiny.rstudio.com) if you’re using R, or a [heroku app](https://www.heroku.com) (free to host as a single app).
>I’ve found [this example](https://the-internet.herokuapp.com/tables) of a data table hosted using heroku, where clicking on the column header sorts the rows (I’m sure you could do more sophisticated things too). [This r-shiny example](https://shiny.rstudio.com/gallery/basic-datatable.html) looks very cool too, and perhaps more what you’re looking for?
> These are the more 'high-tech’ code heavy options, but if you’re not feeling confident going down this route it would still be entirely valid to share it as a nicely commented csv on OSF ([as I have done here](https://osf.io/ery2q/)). Less upfront work for you (and you still get a citable output), but more limited in the end user experience.
### 2. Data simulator
#### Requirement
> We'd like to put up a ‘live’ version of one part of the code in our manuscript – this particular paper would lend itself well to a sort of online simulator that people could run in a browser and play around with, like one of our other colleagues has done here: [http://shapegen.herokuapp.com/](http://shapegen.herokuapp.com/)
#### Advice
> You could do this using a [Jupiter notebook and binder](https://mybinder.org), or a [shiny app](https://shiny.rstudio.com) if you’re using R or a [heroku app](https://www.heroku.com).
> My instinct is the binder option will be less overhead to get it working but potentially less “slick", whereas the heroku app can be prettier (another example here) although may be more work to get started?
#### Response - Researchers
> We prefer the slicker version, like the Heroku app we sent you. Mostly because we think the easier the tool is to use, the more it will be used.
> The only thing is that in our experience, the (free) hosting by Heroku is quite slow, which doesn't help with the user experience. Are you aware of any (paid) services that the university promotes to use?
#### Response - Laurence Brown
> My experience is mostly with Python’s Panel library (https://panel.holoviz.org/index.html), which will let you create small dashboards and apps, including from a Jupyter notebook (A very brief example here in notebook 2D https://github.com/LozRiviera/LAB_Intro_Jupyter)
> There are a number of hosting options, including Heroku, but I succeeded with AWS on their free tier for a while.
https://panel.holoviz.org/user_guide/Server_Deployment.html
> We also have free university hosting of R-Shiny apps (https://idn.it.ox.ac.uk/idn-shiny-service) (I have a small amount of Shiny experience) This has a bit more resource behind it.
> I agree web apps on free resources can be slow. Binder is always a good option, but is on free/donated resources, so again they often have to be frugal. Sometimes this is due to the hosting instance, but it can sometimes be improved by limiting data or options to reduce certain behaviours in the browser.
> There may also be options with Matlab (if that was the original code) and via PowerBI, which the University currently licence.https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/41[documentation] Protocols db administrators guide2022-03-31T10:41:40+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] Protocols db administrators guide## I'm submitting a ...
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
There is no published administrators guide for the protocols db.
## What is the expected/preferred behaviour?
Detail administrator...## I'm submitting a ...
- [ ] bug/error report
- [x] feature request
## What is the current behaviour?
There is no published administrators guide for the protocols db.
## What is the expected/preferred behaviour?
Detail administrators actions and responsibilities.
To include:
- [ ] Who can be made an administrator (inc. process)
- [ ] What to look for when reviewing open access requests
- [ ] How to contact and communicate accept/deny request. Remembering that the researcher can't edit the entry while it is under review
- [ ] Any other administrator things (e.g. superuser list?)
## What is the motivation / use case for changing the behaviour?
- Sustainability of platform usage
- Will also be useful for the publication supporting the release of the protocols db.
## Other information
See issue [#43 on the tool repo](https://git.fmrib.ox.ac.uk/acquisition/win-protocols-db/-/issues/43)https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/22[website] Update CONTIBUTING.md for gitlab and where milestones are hosted.2021-09-08T11:18:14+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[website] Update CONTIBUTING.md for gitlab and where milestones are hosted.CONTIBUTING.md needs to be updated for move of repo to gitlab.
Also an opportunity to revisit milestones, roadmap, what we're working on etc.CONTIBUTING.md needs to be updated for move of repo to gitlab.
Also an opportunity to revisit milestones, roadmap, what we're working on etc.https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/21[task] Get blanket approval for open source licensing of software2021-09-06T21:32:05+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[task] Get blanket approval for open source licensing of software[University recommendations on open source licensing](https://researchsupport.admin.ox.ac.uk/reporting/openaccess#collapse393821) requires permission from HoD to apply open source license to software.
If we can shift responsibility from...[University recommendations on open source licensing](https://researchsupport.admin.ox.ac.uk/reporting/openaccess#collapse393821) requires permission from HoD to apply open source license to software.
If we can shift responsibility from HoD to Heidi for approval, then we can get a blanket approval statement around "we approve in principle open source licensing (suggest MIT), if you are reasonably confident that your resources have limited immediate commercial potential. If you are unsure of the commercial potential of your resources, please speak with OUI at one of their drop-ins" **Speak to Heidi about this, and OUI to shift responsibility to Heidi from HoD.
- [ ] Establish with Oxford University Innovation that Head of WIN can act as Head Of Department in granting permission for research software to be given an open source license.
- [ ] Request from Head of WIN that they grant a blanket approval of open source licensing, with the assumption that the PI has explored commercial applications. This negates the need for hypothetical requests for each new material.
- [ ] This about how to incorporate the above in practice. Where is the approval communicated? How is it applied? Do we need to host a signed letter?https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/19[documentation] How to access gitlab once left Oxford2024-02-18T13:47:00+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] How to access gitlab once left OxfordGuide for people to access their existing repositories once they have left Oxford, and create new repositories for work remaining.
Proposed process (to be confirmed):
1. Ask IT to create a guest (external) account
2. List the existing r...Guide for people to access their existing repositories once they have left Oxford, and create new repositories for work remaining.
Proposed process (to be confirmed):
1. Ask IT to create a guest (external) account
2. List the existing repositories which you would like to be added too
3. Provide the proposed name of any new repositories which you would like created
4. IT adds new guest account as owner/maintainer on repost listed in 2 and 3.
To do:
- [x] Confirm process with IT
- [ ] Add this to community pages https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/gitlab/Ying-Qiu ZhengYing-Qiu Zhenghttps://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/17[documentation] Creating a doi with zenodo2022-01-28T10:00:36+00:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.uk[documentation] Creating a doi with zenodoWrite section about how to create a doi for a gitlab repository using zenodo. Basic stages below.
First time creating a doi for this project:
- [x] 1. Have the repository exist on GitLab (and/or DigitalBrainBank)
- [x] 2. In [zenodo](h...Write section about how to create a doi for a gitlab repository using zenodo. Basic stages below.
First time creating a doi for this project:
- [x] 1. Have the repository exist on GitLab (and/or DigitalBrainBank)
- [x] 2. In [zenodo](https://zenodo.org), log in or create an account. Go to "[new upload](https://zenodo.org/deposit/new)" and add details about your material. Click the "resave doi" button to get the doi which will be issued by zenodo.
- [x] 3. Copy this doi into your README for your project on GitLab, or other documentation. Include this in a section entitled "How to cite this material".
- [x] 4. Make a “[release](https://stackoverflow.com/questions/29520905/how-to-create-releases-in-gitlab)” of the repository. Add a note to mark this as the initial release.
- [x] 5. Download the repository from GitLab (download icon on the repository home page) as a .zip or other compressed file type.
- [x] 6. Upload the compressed file collection to zenodo.
- [x] 7. Finalise the zenodo entry will all contributors including their ORDIC IDs. Include a link to the GitLab repository.
- [x] 8. Set an embargo period for the material if it is not yet publicly available on GitLab.https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues/9Quick guides for different use cases2021-10-21T11:12:12+01:00Cassandra Gould van Praagcassandra.gouldvanpraag@psych.ox.ac.ukQuick guides for different use cases