sappelhoff
commented
5 years ago This is a great idea, thank you for the initiative @KirstieJane!
Closed KirstieJane closed 5 years ago
sappelhoff
commented
5 years ago This is a great idea, thank you for the initiative @KirstieJane!
KirstieJane
commented
5 years ago Submitted! Thank you @malinINCF for wrangling us! ✨
sappelhoff
commented
5 years ago fingers crossed :-)
franklin-feingold
commented
5 years ago @KirstieJane I can also assist with the mentoring and task development. Thank you for submitting to this!
KirstieJane
commented
5 years ago Thanks @franklin-feingold! If you want to be named on the application, you can fill in the mentor form (in the next 2 hours 😬😬) and let @malinincf know!
franklin-feingold
commented
5 years ago Hopefully I will be able to submit! Is there an option to be co-listed? I think your extensive experience will raise the chances of landing this!
malinINCF
commented
5 years ago Hi Franklin, assuming Kirstie is ok with it, I can list you as a co-mentor. You will need to complete the mentor registration form first, but that is rather quickly done.
On Tue, Apr 23, 2019 at 7:47 PM Franklin Feingold notifications@github.com wrote:
Hopefully I will be able to submit! Is there an option to be co-listed? I think your extensive experience will raise the chances of landing this!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bids-standard/bids-specification/issues/210#issuecomment-485906003, or mute the thread https://github.com/notifications/unsubscribe-auth/AJQZ5LU7WKISTBYPYNRWZR3PR5DURANCNFSM4HHWO3TQ .
-- Malin Sandström, PhD Community Engagement Officer malin.sandstrom@incf.org
International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org
KirstieJane
commented
5 years ago Yes - definitely great to be co-mentors. So sorry for doing this all last minute!! Thanks @franklin-feingold & @malinincf!
KirstieJane
commented
5 years ago This is the form @franklin-feingold: https://forms.gle/a1x26WQGzURLerv66
franklin-feingold
commented
5 years ago No worries! I have submitted the mentor registration form! I am glad we were able to get an application in!
malinINCF
commented
5 years ago And I've added Franklin as "secondary mentor" for BIDS in the Projects Ideas list!
Good work everyone, now keep your fingers crossed. We will know on April 30!
On Tue, Apr 23, 2019 at 8:48 PM Franklin Feingold notifications@github.com wrote:
No worries! I have submitted the mentor registration form! I am glad we were able to get an application in!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bids-standard/bids-specification/issues/210#issuecomment-485928455, or mute the thread https://github.com/notifications/unsubscribe-auth/AJQZ5LTPCYVFOWVIGNJN2CLPR5KZRANCNFSM4HHWO3TQ .
-- Malin Sandström, PhD Community Engagement Officer malin.sandstrom@incf.org
International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org
franklin-feingold
commented
5 years ago Thank you @malinINCF!
malinINCF
commented
5 years ago And I've added Franklin as "secondary mentor" for BIDS in the Projects Ideas list!
Good work everyone, now keep your fingers crossed. We will know on April 30!
On Tue, Apr 23, 2019 at 8:55 PM Malin Sandström malin.sandstrom@incf.org wrote:
And I've added Franklin as "secondary mentor" for BIDS in the Projects Ideas list!
Good work everyone, now keep your fingers crossed. We will know on April 30!
On Tue, Apr 23, 2019 at 8:48 PM Franklin Feingold < notifications@github.com> wrote:
No worries! I have submitted the mentor registration form! I am glad we were able to get an application in!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bids-standard/bids-specification/issues/210#issuecomment-485928455, or mute the thread https://github.com/notifications/unsubscribe-auth/AJQZ5LTPCYVFOWVIGNJN2CLPR5KZRANCNFSM4HHWO3TQ .
-- Malin Sandström, PhD Community Engagement Officer malin.sandstrom@incf.org
International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org
-- Malin Sandström, PhD Community Engagement Officer malin.sandstrom@incf.org
International Neuroinformatics Coordinating Facility Karolinska Institutet Nobels väg 15 A SE-171 77 Stockholm Sweden http://www.incf.org
sappelhoff
commented
5 years ago given this tweet, the initial application was successful, congrats! :-)
now let's hope someone applies for the project that @KirstieJane proposed
KirstieJane
commented
5 years ago 💯💯💯 Woooo!
franklin-feingold
commented
5 years ago Yay! :tada: :tada:
Hi everyone, INCF are applying to the first test run of the Google Season of Docs. I think we should put in an application to have some technical writing support for BIDS. I can be the named mentor, unless anyone else wants to jump in!
The deadline is today - sorry for dropping the ball over the holidays 😬 - so I'll write up a suggestion and you can comment on this issue while that's happening 😄. It will appear in the empty spaces below. The mentor form to submit is at https://forms.gle/a1x26WQGzURLerv66.
There's also a project idea submission that we'll have to send to Malin. I've copied and pasted those details below too.
[x] Email address: <Kirstie's email?>
[x] Open source project name: Brain imaging data structure
[x] Link to the open source project: https://github.com/bids-standard/bids-specification
[x] Mentor's full name: Kirstie Whitaker (can be someone else!)
[x] Mentor's display name: @KirstieJane (can be someone else!)
[x] What previous experience have you had creating documentation or collaborating with technical writers? If you have worked with technical writers before, or have developed documentation, mention this in your answer. Describe the documentation that you produced and the ways in which you worked with the technical writer. For example, describe any review processes that you used, or how the technical writer's skills were useful to your project. Explain how this previous experience may help you to work with a technical writer in Season of Docs.
The BIDS Starter Kit was a Google Summer of Code project in 2018. I mentored Patrick Park as he worked to make the Brain Imaging Data Structure a little more accessible (https://summerofcode.withgoogle.com/archive/2018/projects/5052346392379392). Although we originally proposed the project as developing interactive tutorials, we realised that what the community really needed was additional - and accessible - documentation. This has developed into a detailed README file (https://github.com/bids-standard/bids-starter-kit/blob/master/README.md), a clear set of contributing guidelines (https://github.com/bids-standard/bids-starter-kit/blob/master/CONTRIBUTING.md) and extensive wiki support (https://github.com/bids-standard/bids-starter-kit/wiki). For contributions to the main repository we (Patrick, myself and the four co-mentors from that summer project) reviewed each other's work in pull requests, for contributions to the wiki we used GitHub issues to track where changes had happened and give feedback.
Patrick did an excellent job as GSOC student, but it was clear where the expertise of a technical writer would have benefitted us both. From asking the right questions, knowing their audience and having the skills to capture implicit knowledge, I am confident that the BIDS project (not just the starter kit) will greatly benefit from their expertise.
[x] What previous experience have you had mentoring individuals? If you have taken part in Google Summer of Code or a similar program, mention this in your answer. Describe your achievements in that program. Explain how this experience may influence the way you work in Season of Docs.
I mentored a GSOC Student (Patrick Park, https://summerofcode.withgoogle.com/archive/2018/projects/5052346392379392/) in 2018 and have been selected as a mentor for two more projects in 2019 (assuming we are successful at being allocated the slots): https://neurostars.org/t/gsoc-project-idea-13-improving-unit-testing-and-test-coverage-for-the-te-dependence-analysis-tedana-toolbox/3372 and https://neurostars.org/t/gsoc-project-idea-14-producing-publication-ready-brain-network-analysis-results-and-visualisations-from-the-command-line/3373.
I have extensive experience mentoring PhD and MSc students in person and in distributed networks across multiple timezones. I have core collaborators in Canada, the USA, and across five instiutions in the UK. I am confident working and mentoring using GitHub for project management, Slack and Gitter for distributed conversations, and my weekly lab meetings have members "Zoom" in from around the world.
The BIDS community itself is spread around the world, which I hope will be a benefit to the GSOD technical writer. They will not be the only person connecting remotely. Rather, they will be joining a large and distributed group of people passionate about contributing to open science tools, practices and systems.
[x] I agree to this Participant Agreement
Each project idea must include at least the following information:
[x] Project name: Building BIDS Apps
[x] Description:
A longer description of the documentation work required. Describe your initial idea in detail. Offer opportunities for any interested technical writers to expand or refine the idea.
Neuroimaging experiments result in complicated data that can be arranged in many different ways. Even two researchers working in the same lab can opt to arrange their data in a different way. Lack of consensus leads to misunderstandings and time wasted on rearranging data or rewriting scripts expecting certain structure. The Brain Imaging Data Structure (BIDS) proposes a standard naming system so that researchers around the world can easily share and re-use datasets for new and exciting neuroscience research.
BIDS formatted datasets can be processed by BIDS Apps: docker containers that capture a neuroimaging pipeline. Each BIDS App has the same core set of command line arguments, making them easy to run and integrate into automated platforms. BIDS Apps are constructed in a way that does not depend on any software outside of the image other than the container engine.
BIDS Apps are one of the "carrots" to incentivise data sharing in BIDS format. Tools like fMRIPrep (https://github.com/poldracklab/fmriprep) or MRIQC (https://github.com/poldracklab/mriqc) make it much faster and easier to reliably and reproducibly analyse large neuroimaging datasets. If analyses were accompanied by a BIDS App we would see a much greater rate of innovation in human brain imaging.
While the BIDS specification can handle quite a lot of different use cases, the documentation to build your own BIDS App is quite sparse. The GSOD technical writer will work with the BIDS community (a cohort of more than 80 researchers around the world) to enhance the current tutorials and to provide accessible guidance for researchers wanting to share their particular analyses for BIDS datasets.
The GSOD writer will have many opportunities to refine this idea depending on their interests. It may be best to support very small BIDS Apps that can be used as a starting point for a large number of research teams, or to focus on one or two BIDS Apps that are particularly useful to the neuroimaging community. For example, expanding the tools available for EEG (https://doi.org/10.31234/osf.io/63a4y) or MEG (https://doi.org/10.1038/sdata.2018.110) datasets.
[x] Related material: