From 9b8383758df02b4b60a7bbf5ab3c80fc74f7acf8 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Mon, 11 Mar 2024 16:20:47 +0100 Subject: [PATCH] Steering Group meeting notes -- old updates from 2023 (#365) * use utf-8 as encoding * add 2023 SG meeting notes * remove non-utf-8 chars * remove duplicate table? * remaining weird chars * missed one --- _posts/2023-08-17-Steering-Group-minutes.md | 2 +- _posts/2023-09-28-Steering-Group-minutes.md | 275 +++++++++++++++++++ _posts/2023-10-19-Steering-Group-minutes.md | 282 ++++++++++++++++++++ _posts/2023-11-09-Steering-Group-minutes.md | 217 +++++++++++++++ _posts/2023-11-30-Steering-Group-minutes.md | 205 ++++++++++++++ tools/convert_to_md.py | 2 +- 6 files changed, 981 insertions(+), 2 deletions(-) create mode 100644 _posts/2023-09-28-Steering-Group-minutes.md create mode 100644 _posts/2023-10-19-Steering-Group-minutes.md create mode 100644 _posts/2023-11-09-Steering-Group-minutes.md create mode 100644 _posts/2023-11-30-Steering-Group-minutes.md diff --git a/_posts/2023-08-17-Steering-Group-minutes.md b/_posts/2023-08-17-Steering-Group-minutes.md index ab2b0551..fd6a2140 100644 --- a/_posts/2023-08-17-Steering-Group-minutes.md +++ b/_posts/2023-08-17-Steering-Group-minutes.md @@ -132,7 +132,7 @@ Date: Thursday, August 17th, 2023

  • - Attempt to centralize list of converters, tools, BEPs… + Attempt to centralize list of converters, tools, BEPs, ... https://github.com/bids-standard/awesome-bids diff --git a/_posts/2023-09-28-Steering-Group-minutes.md b/_posts/2023-09-28-Steering-Group-minutes.md new file mode 100644 index 00000000..1eac4348 --- /dev/null +++ b/_posts/2023-09-28-Steering-Group-minutes.md @@ -0,0 +1,275 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/09/28 + +Date: Thursday, Sept 28th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + Topic + + + + Relevant Links + +
    + Continued Discussion from last meeting on Spatial Derivatives? + + + + https://github.com/bids-standard/bids-specification/issues/1602 + + +
    + The Neuro - Irv and Helga Cooper Foundation Open Science Prize +submission + + Done. Thank Ariel for making it happen! +
    + Any Follow up from Renzo Huber at Aperture? + + + KIM will follow up on this. + +
    +

    + OHBM Call for Content opened Sept 22nd. +

    +

    + Things to consider: +

    +
      +
    • +

      + Townhall meeting space request +

      +
      • +
    • +

      + BIDS symposium or other presentations +

      +
      • +
    +     		+

    + + + https://humanbrainmapping.org/i4a/pages/index.cfm?pageid=4229#:~:text=These%20are%20included%20in%20the,%2435%20USD%20again%20in%202024 + + + . +

    +
      +
    • +

      + Cyril to submit a round-table for town-hall meeting +

      +
      • +
    • +

      + Franco and Ariel will be submitting a symposium, more content +(a.o., Russ to present along the lines of recent paper) +

      +
      • +
    +

    + + DUE DATE Nov 17, 2023 + +

    +
    + Update on NSF POSE conference in Q1 2024 + + + + https://new.nsf.gov/funding/opportunities/pathways-enable-open-source-ecosystems-pose + + +
    + BIDS maintainers meeting in Seattle, April 10th - 12th, 2024 + +
    + Camille's email BIDS-Prov BEP028 + + + + https://github.com/bids-standard/bids-specification/pull/487 + + + has been closed +
    + +
    + + + +[[https://utexas.zoom.us/my/kimray]{.underline}](https://utexas.zoom.us/my/kimray) + +**Present:** Cyril Pernet, Ariel Rokem, Chris Markiewicz, Robert +Oostenveld, Guiomar Niso, Yaroslav Halchenko + +**Guest:** + + +Meeting Notes: + +**Kim's Maternity leave through the end of the year** + +Remaining 2023 agendas are listed in the steering group + +Sign up sheet is +[[here]{.underline}](https://docs.google.com/spreadsheets/d/1Ys52kgOebRxGPYSvowTcmaZhph8rZ0_kflFQ6jtRUU4/edit#gid=0) +for assuming Kim's role in meeting management: Guiomar, Robert and Ariel +take turns at the next three meetings. We won't meet on 21 Dec. + +**Meeting schedule:** + +- December 21st. NO MEETING - Kim will remove agenda and calendar. + +**Open science Prize:** + +- Application is complete! + +- Ariel will update the letters of support in the BIDS drive along + with the other application materials + +**OHBM content call:** + +- We should submit a round table request for the BIDS townhall + meeting - Cyril will submit this + +- Or should this be part of the Symposium for BIDS? + +**Aperture:** + +- Kim will follow up on any updates from the Aperture committee + +**NSF POSE Q1 2024:** + +- Ariel's proposal has been funded, there will be an open source + software meeting that will happen as a result of this funding. More + information to come + +**BIDS Maintainers Meeting** + +- April 10-12, 2023 - maintainers has indicated that this is an ideal + timeframe for them + +- NSF will only fund within US travel under this mechanism - non-US + maintainers will need to find funding to travel US and then the NSF + grant can pay for their travel within the US. + +```{=html} + +``` +- **NSF can support travel to the meeting** + +```{=html} + +``` +- Are there non-US projects funding BIDS? + + - Cyril - + +- Can BIDS connectivity project (Franco Pestilli?) support Peer's + travel? + +- Will non-maintainers also attend? + + - Maintainers may identify additional attendees + + - BEP leads that are ready to be merged may be ideal additional + attendees + +- Ariel will attend a maintainers meeting next week to help plan + further. + +**BIDS-Prov BEP028** (Camille's email Prov) + +- Is their BEP ready to be merged? What are the next steps? + +- This BEP will likely not be merged directly into the BIDS validator; + the validator could call to this BEP similar to how it is done for + PET data. + +- Maintainers will work with Camille to determine how to implement the + BIDS-Prov BEP + +**BIDS Spatial Derivatives** + +- Proposal seems to be converging, there needs to be a vote on how to + move forward + +- Meant to curb the explosion of Suffixes in file naming + +- Next steps: PR to BIDS extensions site for guidance that gets + up/down voted? + + - End discussion period, Allow two weeks for a voting period + +**Next Meeting Guest?** + +- Any BIDS leads? + +- Robert will invite the leads of the NIBS BEP (non invasive brain + stimulation, + [[BEP037]{.underline}](https://bids.neuroimaging.io/bep037)) to ask + whether they want to attend the next or next-next BIDS meeting. + +**More generally: BIDS advisory group (i.e., BEP leads) engagement** + +- Start meetings with BEP leads and SG + +- BIDS Townhall format? Additional meeting with lead for discussing diff --git a/_posts/2023-10-19-Steering-Group-minutes.md b/_posts/2023-10-19-Steering-Group-minutes.md new file mode 100644 index 00000000..8a1cdac5 --- /dev/null +++ b/_posts/2023-10-19-Steering-Group-minutes.md @@ -0,0 +1,282 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/10/19 + +Date: Thursday, October 19th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + Topic + + + + Relevant Links + +
    + Giacomo Bertazolli lead of BEP037 will join + + + + http://bids.neuroimaging.io/bep037 + + + , + + + https://mattermost.brainhack.org/brainhack/channels/nibs-bids + + +
    +

    + TOSI Prize: +

    +

    + - Who'll be going? +

    +

    + - Any presentation needed? +

    +

    + - Where to transfer the funding? +

    +

    + ... +

    +     		+
    + BIDS maintainers meeting in Seattle, April 11th - 12th, 2024 + +
    +

    + OHBM Call for Content opened Sept 22nd. +

    +

    + Things to consider: +

    +
      +
    • +

      + Townhall meeting space request +

      +
      • +
    • +

      + BIDS symposium or other presentations +

      +
      • +
    +     		+

    + + + https://humanbrainmapping.org/i4a/pages/index.cfm?pageid=4229#:~:text=These%20are%20included%20in%20the,%2435%20USD%20again%20in%202024 + + + . +

    +
      +
    • +

      + Cyril to submit a round-table for town-hall meeting +

      +
      • +
    • +

      + Franco and Ariel will be submitting a symposium, more content +(a.o., Russ to present along the lines of recent paper) +

      +
      • +
    +

    + + DUE DATE Nov 17, 2023 + +

    +
    + BIDS advisory group (i.e., BEP leads) engagement + +
      +
    • +
      • +
    +
    + Steering Group Election and Governance Amendments + + + + BIDS +governance amendment + + +
    + Quick one: add ppl to github organization BEO032 team or give +@yarikoptic more super-powers: + + + + bids-standard/.github/issues/6 + + +
    + + + +[[https://utexas.zoom.us/my/kimray]{.underline}](https://utexas.zoom.us/my/kimray) + +**Present:** Guiomar, Ariel, Robert, (Cyril, Yaroslav) + +**Guest:** Giacomo Bertazzoli, Marta Bortoletto, Vittorio Iacovella + + +BIDS Meeting Notes: + +Next year we should be in time for the [[Chan-Zuckerberg funding +scheme]{.underline}](https://chanzuckerberg.com/science/science-funding/). +It is aimed at software, but we have plenty of that. Now it just closed +2 days ago. + +Yarik offered to pick up the prize on 30 Nov. He probably will have to +give a ~~talk~~speach! + +Funds -- Ariel (or maybe split to Cyril to have part in America and part +in Europe) // other must be spent on salary support for each of the +applications (i.e. 25k divided by 5). Is this necessarily or could be +transferred to other things? Ariel mentioned that he does not need it, +Robert mentions that for him it would be valuable to maintain +involvement past his steering group term. Yarik could cover his steering +group involvement % but does not have to. Any BIDS maintainer needing +funds? I could check if I could "subcontract/consult" them out to those +through Dartmouth. + +Roundtable (Town Hall) proposal: +[[https://docs.google.com/document/d/1sYXI_uUmkMMZg4OqYRSOCRkb66IZ_qQJbvI-nP3Z024/edit]{.underline}](https://docs.google.com/document/d/1sYXI_uUmkMMZg4OqYRSOCRkb66IZ_qQJbvI-nP3Z024/edit) + +Symposium proposal: +[[https://docs.google.com/document/d/1Uy58ZP0P6D0VkeqDF4bx2unoxR7kokReugWVG94O8AM/edit#heading=h.97ozz5yj15hg]{.underline}](https://docs.google.com/document/d/1Uy58ZP0P6D0VkeqDF4bx2unoxR7kokReugWVG94O8AM/edit#heading=h.97ozz5yj15hg) + +### Seattle meeting proposed attendee list (PLEASE ADD PEOPLE): + +People + +\-\-\-\-\-\-\-\-\-- + +Ross Blair + +Anthony Galassi + +Remi Gau + +Chris Markiewicz + +Stefan Appelhof + +Christine Rogers + +Nell Hardcastle + +\## Connectivity + +Peer Heerholz + +Dan Levitas + +Franco Pestilli + +\## PET + +Martin Norgaard + +Melanie Ganz + +\## Statsmodels + +Alejandro de la Vega, James Kent, Dylan Nielson + +\## Sundry + +Greg Kiar + +Satra Ghosh + +Russ Poldrack + +Yaroslav Halchenko (other steering people?) + +Guillaume Flandin (SPM) + +\## HED + +Arno Delorme + +Dora Hermes + +### BEP037 NIBS extension + +External guests: Marta Bortoletto, Giacomo Bertazzoli, Vittorio +Iacovella + +Some delay because Giacomo moved to the USA. + +Giacomo suggests to split it into sub-BEPS and first deal with TMS-EEG +and later with the others. That is well received by the steering group. +Attention to common fields across modalities. + +There are specific subgroups (in UK, ...) interested in contributing to +specific combinations of stimulation and other data. + +Budget in Italy, probably easiest to try to allocate it for Stefan or +Remi. First part of the budget needs to be spent by March and the next +batch in December. [ACTION POINT: Anthony to ask other +maintainers.]{.mark} + +Ariel comments that the relationship should not be only financial, but +also that the BEP team should be trained to take on the maintenance and +the next sub-BEPs more onto themselves. diff --git a/_posts/2023-11-09-Steering-Group-minutes.md b/_posts/2023-11-09-Steering-Group-minutes.md new file mode 100644 index 00000000..ca4e0d7d --- /dev/null +++ b/_posts/2023-11-09-Steering-Group-minutes.md @@ -0,0 +1,217 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/11/09 + +Date: Thursday, November 9th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + Topic + + + + Relevant Links + +
    + Consolidation: we have so many people that struggle converting with +the available converter tools and the starter kit documentation. Those +people are our stakeholders and could use better support. E.g. extending +the starter kit, office hours, ... + +
    +

    + Are we all clear with receiving our part of the prize money? And +are we clear with the split between the USA and EU? +

    +

    + Also: meeting with TOSI Leaders Council November 15th at 13:30 +EST +

    +     		+
    + OHBM town hall meeting + +

    + + + OHBM +Round table + + +

    +

    + + + BIDS_Symposium_OHBM_2024 + + +

    +
    + Election new steering group members + +
    + Dung Truong from UCSD suggested to be a co-lead on HED for the +advisory committee. + +
      +
    • +
      • +
    +
    + From last meeting: Some BEP037 budget in Italy, probably easiest to +try to allocate it for Stefan or Remi. First part of budget needs to be +spent by March and next batch in December. ACTION POINT: Anthony to ask +other maintainers. + +
    + BIDS paper Guio drafted history line: + + + BIDS +history timeline + + + +
    + + + +[[https://utexas.zoom.us/my/kimray]{.underline}](https://utexas.zoom.us/my/kimray) + +**Present:** + +**Guest:** no guest planned + + +BIDS Meeting Notes: + +Ariel will do the TOSI talk 13:30 Eastern US Time. Others from the +steering group are also invited to join, but nobody else seems to be +available. + +Yarik will give the prize acceptance talk at the Open Science symposium +on 30 Nov. Try to give a take home message to influential people in the +audience (for future funding etc). Look at the application pitch for +some figure. + +Ariel is confident that half of the money that UW receives can be +transferred to Copenhagen. Ariel will write something for Copenhagen as +subcontractor, and Cyril should send an invoice. Since the first +maintainers workshop to be organized is by Ariel, it is best to have the +money first go to UW, then Copenhagen. + +OHBM deadline was extended, the round table will consist of two +(5-minute?) talks and a discussion, but especially should be +free-format. Christine volunteered to be one of the speakers, which is +very welcome for a more diverse representation. + +[[OHBM Round +table]{.underline}](https://docs.google.com/document/d/1sYXI_uUmkMMZg4OqYRSOCRkb66IZ_qQJbvI-nP3Z024/edit) + +[[BIDS_Symposium_OHBM_2024]{.underline}](https://docs.google.com/document/d/1Uy58ZP0P6D0VkeqDF4bx2unoxR7kokReugWVG94O8AM/edit?pli=1#heading=h.vapm8s87pxc2) + +We should invite the Chinese and Korean chapters of OHBM to join (or +have a representative join) in the round table meeting. ACTIO POINT: +Cyril will contact them. + +New steering group members: quorum has been reached but results are not +yet available. Should become available tomorrow. + +Stefan and Remi seem to be interested to work on BEP037 as +subcontractors. ACTION point: Robert will check with Remi and Stefan. + +Consolidation: there is general agreement that it would be good to get +more content under a single web-presence (bids-standard.org). Cyril +could pay Anthony to work on this, as it is part of the goals of +OpenNeuroPet. It would also be possible to hire external communication +and UX expertise to support this. ACTIO point: Cyril will chat with +Melanie and Anthony and we should all think about the content to be +consolidated. + +Here is a list to get started with: + +- bids.neuroimaging.io (to go under bids-standard.org) + +- apps.neuroimaging.io + +- Starter kit + +- Specification (now on RTD) + +- Extension guidelines (now on RTD) + +- Awesome BIDS list + +- Governance documents that are now as a google doc + +- ... + +Things not to merge but to link + +- Google docs with draft BEPs + +- Github organization, issues and workflow + +- Support channels (google group, neurostars) + +- Announcement channels (mattermost, twitter) + +- Merchandize + +- ... + +Things that are not for public display + +- Maintainers folder on Google Drive + +- Slack + +- Meeting notes (at least some are not for public display) diff --git a/_posts/2023-11-30-Steering-Group-minutes.md b/_posts/2023-11-30-Steering-Group-minutes.md new file mode 100644 index 00000000..421eeeeb --- /dev/null +++ b/_posts/2023-11-30-Steering-Group-minutes.md @@ -0,0 +1,205 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2023/11/30 + +Date: Thursday, November 30th, 2023 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    + + Topic + + + + Relevant Links + +
    + Welcome new steering group members! + +
    + Finalize OHBM submissions + + + + https://docs.google.com/document/d/1sYXI_uUmkMMZg4OqYRSOCRkb66IZ_qQJbvI-nP3Z024/edit?usp=sharing + + + -- change again of people, no multiple submissions, Dora/Camille not +going +
    + Aperture Neuro further steps + + + + https://apertureneuro.org/for-authors + + + , see + + + https://github.com/bids-standard/bids-website/issues/359 + + +
    + Update on TOSI prize funds + +
    + BIDS history timeline + + + + BIDS +history timeline + + +
    + Website + + Maybe spend some cash with +https://www.ericholscher.com/roadmap/ +
    + +
    + +[[https://utexas.zoom.us/my/kimray]{.underline}](https://utexas.zoom.us/my/kimray) + +**Present:** Guio, Robert, Cyril, Camille, Ariel, Dora, Ross + +**Guest:** none + +BIDS Meeting Notes: + +From Renzo Huber email (November 21st): + +"I had reported back to the executive time of Aperture about what we had +discussed at the BIDS Steering Group meeting. + +We have implemented a few of the suggestions that were discussed: + +-\> The [[author +guidelines]{.underline}](https://urldefense.com/v3/__https://apertureneuro.org/for-authors__;!!K-Hz7m0Vt54!hYrc_zwV6CSxP10J0AQf_OWGR-doFt3PFZa5wXdfyjjCfaOkc1qp5qGN32AwaXFKD9fv3uoZD2omdBKU8W3m$) +now explicitly state that we recommend people to share their data in +BIDS. This needs to be mentioned in the manuscript with the respective +BIDS validator version. This is optional, though. If authors share their +data without a successful BIDS validation, the reviewers might ask for a +justification. But the Journal will not exclude the paper based on this +alone. + +-\> We recommend authors to include BIDS as one of the key-words. This +means that manuscripts can be sorted based on this flag. This then also +extends to 'tags' in URLs: as +[[https://apertureneuro.org/articles?tag=BIDS]{.underline}](https://urldefense.com/v3/__https://apertureneuro.org/articles?tag=BIDS__;!!K-Hz7m0Vt54!hYrc_zwV6CSxP10J0AQf_OWGR-doFt3PFZa5wXdfyjjCfaOkc1qp5qGN32AwaXFKD9fv3uoZD2omdF3Fwu2O$). + +This feature is new for articles that are being typesetter via a +Apertures new vendor. Thus, there are no articles with this tag yet. + +-\> The manuscript submission form has an optional check box asking +whether shared data are in BIDS. + +-\> Aperture Neuro (as part of Schlasica journals) does not have the +flexibility of generating our own header fields in PDFs." + +**Notes:** + +Aperture Neuro followup: + +We can use Aperture Neuro as an example: How can journal editors +contribute to the BIDS ecosystem? This will give us a good basis for +further conversations with other journal editors. See +[[https://github.com/bids-standard/bids-website/issues/359]{.underline}](https://github.com/bids-standard/bids-website/issues/359) + +""" + +- For data documentation, it is advised to use the BIDS format + ([[https://bids.neuroimaging.io/]{.underline}](https://bids.neuroimaging.io/)). + It is recommended that the authors check the respective box in the + submission form. It is recommended that authors use 'BIDS' as one of + the key-words of the manuscript. And it is recommended that authors + mention the version of the BIDS validator that was used to ensure + BIDS compatibility. + +""" + +Maybe reach out to Simon Eickhoff for integration into Human Brain +Mapping (Cyril will do that). + +Ariel will reply to Renzo to say that we discussed and thank them, and +mention we will include this in the documentation for BIDS, and we will +point others to this as an example. + +Instructions for reviewers? Should we write a document that has a +checklist? Or something like that? Run the validator, of course. + +BIDS validator can tell users how many files are in the .bidsignore + +**TOSI funds:** + +**Website:** + +Could use some of the funds to improve the website. At least +conceptually. Could use a freelancer? E.g., from upwork? + +Need to think about different "persona": casual users, data +users/consumers, content contributors. + +In a maintainers meeting Christine mentioned google season of docs as an +approach for rewriting/updating documentation. She said the INCF had +used them with good success but finding and managing the technical +writer can be tricky. + +[[https://developers.google.com/season-of-docs]{.underline}](https://developers.google.com/season-of-docs) + +[[Timeline for Google Season of Docs +2023]{.underline}](https://developers.google.com/season-of-docs/docs/timeline) + +[[https://developers.google.com/season-of-docs/docs/2019/participants/project-incf-1]{.underline}](https://developers.google.com/season-of-docs/docs/2019/participants/project-incf-1) + +[[https://www.ericholscher.com/roadmap/]{.underline}](https://www.ericholscher.com/roadmap/) +he is the developer of ReadTheDocs and offers consultancy for 2,500 USD. diff --git a/tools/convert_to_md.py b/tools/convert_to_md.py index 5fdc53f1..e9116fc3 100644 --- a/tools/convert_to_md.py +++ b/tools/convert_to_md.py @@ -24,7 +24,7 @@ def prettify_html(input_folder): """Make html prettier.""" for file in input_folder.glob("*.html"): # Read the HTML file - with open(file, "r") as f: + with open(file, "r", encoding="utf8") as f: html = f.read() # Create BeautifulSoup object soup = BeautifulSoup(html, "html.parser")