From 434cfeef23f63522cec2b1ea8d97ceb091546e15 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Mon, 11 Mar 2024 16:20:53 +0100 Subject: [PATCH] SG 2024 updates (#366) * SG 2024 updates * fix weird chars * remove duplicate table --- _posts/2024-01-11-Steering-Group-minutes.md | 222 +++++++++++++ _posts/2024-02-01-Steering-Group-minutes.md | 325 ++++++++++++++++++++ _posts/2024-02-22-Steering-Group-minutes.md | 191 ++++++++++++ tools/convert_to_md.sh | 2 +- 4 files changed, 739 insertions(+), 1 deletion(-) create mode 100644 _posts/2024-01-11-Steering-Group-minutes.md create mode 100644 _posts/2024-02-01-Steering-Group-minutes.md create mode 100644 _posts/2024-02-22-Steering-Group-minutes.md diff --git a/_posts/2024-01-11-Steering-Group-minutes.md b/_posts/2024-01-11-Steering-Group-minutes.md new file mode 100644 index 00000000..8f4ab767 --- /dev/null +++ b/_posts/2024-01-11-Steering-Group-minutes.md @@ -0,0 +1,222 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2024/01/11 + +Date: Thursday, January 11th, 2024 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links + +
+ April maintainers meeting in Seattle + +
+ BIDS 2.0 next baby steps + +

+ + + + https://github.com/orgs/bids-standard/projects/10 + + + +

+

+ + + + https://github.com/bids-standard/bids-2-devel/issues/54 + + + +

+
+ Open science prize - how to pass on to community? +
+ - prize +
+ - salary money + 		+ +
+ How to improve adoption of BIDS? + +
+ +
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+
+ +
+ +
+ + + +[[https://utexas.zoom.us/my/kimray]{.underline}](https://utexas.zoom.us/my/kimray) + +**Present:** Dora Hermes, Kimberly Ray, Ariel Rokem, Cyril Pernet, +Camille Maumet, Yaroslav Halchenko, Stefan Appelhoff + +**Guest:** + + +BIDS Meeting Notes: + +**April Maintainers Meeting in Seattle**: April 11-12, Arial can +currently fund travel within the US (NSF funding), the OS Prize can fund +non-US travel. They have a meeting space at the E-science institute and +can provide space. + +Ariel needs: meeting attendees list, meeting agenda, + +Stefan to pass on to the maintainers to see if someone is up to making +the program/defining attendees list + +**BIDS 2.0** + +Github project is established with many ideas but there aren\'t many +\'takers' on completing the suggested items. + +- Creating a more flexible hierarchy for BIDS + ([[https://github.com/bids-standard/bids-2-devel/issues/54]{.underline}](https://github.com/bids-standard/bids-2-devel/issues/54) + ) + +- What are the most important items that should be attended to? + +- Long term goal should be to make BIDS adoption easier, will a 2.0 + version create more confusion between versions or how can we make + BIDS 2.0 improve adoption from community + + - While presenting 2.0 we would like to accent that to be + developed in 2.0 features would help ? + +- Revisiting how BIDS is defined beyond MRI may be a path to improving + adoption within the neuroscience community. I.e. BIDS started with + MRI and some of the BIDS spec might be more complicated than could + have been if we had focused on all modalities from the start. + + - iEEG, MEG,\... - + + - Perhaps a tool for automatic BIDS conversions would help, but + there are at least 20 different file formats for + electrophysiology data + +- + +**Open Science Prize!** + +- What should we do with the physical prize? We could 3D print + replicate the model to share among the maintainers/steering + committee. + +- What to do with the prize money? + + - How do we receive the money? - \$5k CAD per person or \$55k CAD + to be spent as needed for BIDS + +- \$55k CAD will be split with U Washington and Cyril (sub-contract + with xx Institution) so funds will be in both US and Europe + +- + +```{=html} + +``` +- + +**BIDS Steering Committee Theme for the year: Improve adoption** + +- Web presence (already in process - meeting established for Jan 12th) + +- Training and dissemination + + - How do we poll non-BIDS users to understand barriers to BIDS + adoption? + + - Big consortia (OHBM, SfN, INCF, \...) + + - People who have adopted BIDS but not fully + + - Openneuro bidsignore files + + - Should we target specific regions such as Asia which has + historically provided few contributions to BIDS + +- First steps: create and agree on a survey for non-BIDS users + + - Create a pull request for this survey: + + - Are they aware of BIDS? + + - Was it hard to convert data? + + - Do you use data that do not yet fit within BIDS? + + - Had questions, but could not find answers + + - + + - [[Yaroslav Halchenko]{.underline}](mailto:yarikoptic@gmail.com) + will create a pull request on github: + [[https://github.com/bids-standard/bids-starter-kit/pull/376]{.underline}](https://github.com/bids-standard/bids-starter-kit/pull/376) + + - + + - diff --git a/_posts/2024-02-01-Steering-Group-minutes.md b/_posts/2024-02-01-Steering-Group-minutes.md new file mode 100644 index 00000000..a2db6544 --- /dev/null +++ b/_posts/2024-02-01-Steering-Group-minutes.md @@ -0,0 +1,325 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2024/02/01 + +Date: Thursday, February 1st, 2024 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links and to do + +
+ April maintainers meeting in Seattle + +

+ Updates? + + + https://github.com/bids-standard/202404-seattle-maintainer-meeting + + +

+

+ + + https://bids-standard.github.io/202404-seattle-maintainer-meeting/ + + +

+
+ BIDS steering ways of working, onboarding? + +

+ Right now pure catching up, but maybe good idea to have a +plan +

+

+ We got an + + + onboarding + + + folder +for maintainers (probably overlap with onboarding steering) in the +google drive and a + + + BIDS +accounts and onboarding + + + and + + + CONTENT + + + for +the whole google drive +

+

+ -- proof the website and info needs updated :-) lol +

+
+

+ OPM BEP proposal ?? seems wrong given test performed -- MEG +updates needed +

+

+ + + https://github.com/bids-standard/bids-specification/issues/1676 + + +

+ 		+
+ Cyril/Ariel, train the trainers idea as part of outreach + +
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    + Possibly develop software carpentry module +

    +
    • +
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    + Give certifications/badges for different levels of +experience +

    +
    • +
  • +

    + Ariel recommended software carpentry as in general pedagogical +training +

    +
    • +
+
+ Updates on plan for website + +

+ See + + + BIDS +Online Presence Working Group: Working Document + + +

+

+ + To be discussed next time + +

+
+ Cooperation with DICOM standard + + YOH pointed David Clunie to our + + + DICOMs +deficits table + + + , he forwarded to WG-16 to consider at the next +meeting. + + To be discussed next time + +
+

+ OHBM roundtable/town hall plans +

+

+ + + OHBM +Round table + + +

+ 		+ Cyril to email Chinese and Korean chapters +
+ BIDS 2.0 going forward! + + + To be discussed next time + +
+ + + +[[https://washington.zoom.us/my/arokem]{.underline}](https://washington.zoom.us/my/arokem) + +**Present:** Cyril Pernet, Kimberly Ray, Ariel Rokem, Camille Maumet, +Yaroslav Halchenko, Rémi Gau + +**Guest:** + + +## BIDS Meeting Notes + +### April maintainers meeting in Seattle + +- Christine and Eric are pinging people to see if they want / can come + +- Maintainers need to be re-pinged + +- Meeting can support about 20-25 attendees + +- Scope: For maintainers and / or BEP? + +- ACTION: [[arokem@gmail.com]{.underline}](mailto:arokem@gmail.com) + contact maintainers to know what type of meetings and would be most + useful for them + +### BIDS steering ways of working + +- How can new steering group members \'catch up' on the previous years + progress and ongoing goals for the steering group? + +- Important docs: We got an + [[onboarding]{.underline}](https://drive.google.com/drive/folders/1yx6VWptjdv1JOe0Ybpb48iMB0bCoG_Ae?usp=drive_link)folder + for maintainers (probably overlap with onboarding steering) in the + google drive and a [[BIDS accounts and + onboarding]{.underline}](https://docs.google.com/document/d/1vxUglvS_mfqIpHOFUtxYAb79zQTYMYhajc7pQfSqSl0/edit) + +- The google drive is where everything lives, Remi has a + [[CONTENT]{.underline}](https://docs.google.com/document/d/1kNcuI-phF_N40m0Kuo9PTTD0K7atz5FOvxhYtQCR1ms/edit#heading=h.cr010sb0buzg) + file to help browse the google drive + +- What? + + - What was achieved by steering in past 2-3 years + + - Current projects in progress in the steering group. + + - A view of typical \"tasks\"/topics the steering is working on. + +- ACTION: Rémi set up a meeting to populate the onboarding docs above + +- ACTION: Kim added bookmark linking the BIDS Maintainers google drive + in the BIDS steering group slack channel for easier access + +### OPM BEP proposal + +- Optically Pumped Magnetometer-based Magnetoencephalography (OPM-MEG) + +- Suggestion: contact BEP leaders to address the concerns that it is + not following BEP protocols. + +- Could probably be PR? + +- In any case, we should point them to the bids BEP guidelines: + [[https://bids-extensions.readthedocs.io/en/latest/guide/#when-and-how-to-start-a-bids-extension-proposal]{.underline}](https://bids-extensions.readthedocs.io/en/latest/guide/#when-and-how-to-start-a-bids-extension-proposal) + + - BEP guidelines may require too high of a level of understanding + of BIDS for a novice user + +- ACTION: Rémi to point to BEP guidelines, mention that it is probably + not needed to go for a BEP but a PR should be enough. Mention that a + PR plus example should be enough. + +- ACTION: update BEP guidelines to make sure that the future \'BEP' + content cannot already fit into what BIDS raw can do. + +- ACTION: [Camille+Rém]{.mark}i to propose and update to the BEP + guidelines. Note would be good to ask people to ask to reach out + earlier to maintainers/steering w/ an example so that it can + illustrate why a BEP would be needed. + +### Train the trainers + +- Goal is to make BIDS more accessible and increase impact + +- Similar to data carpentries: + [[https://carpentries.org/become-instructor/]{.underline}](https://carpentries.org/become-instructor/) + +- Repronim fellowship: + [[https://www.repronim.org/fellowship]{.underline}](https://www.repronim.org/fellowship) + + - This is more geared to help fellows create material for their + own training + +- List "certified BIDS trainers" on the BIDS website + +- Having a way to "certify" trainers + +- Who will be the (meta)trainer to train the trainers? + +- Data carpentry BIDS "courses" in the carpentry incubator (**for + users not trainers**): + [[https://github.com/bids-standard/bids-starter-kit/issues/136#issue-666838055]{.underline}](https://github.com/bids-standard/bids-starter-kit/issues/136#issue-666838055) + +- Lighter version of an ambassador program: + [[https://www.softwareheritage.org/ambassadors/#becoming-an-ambassador]{.underline}](https://www.softwareheritage.org/ambassadors/#becoming-an-ambassador) + +- Carpentries instructor certification: + [[https://carpentries.org/become-instructor/]{.underline}](https://carpentries.org/become-instructor/), + and materials we can use/adapt: + [[https://carpentries.github.io/instructor-training/]{.underline}](https://carpentries.github.io/instructor-training/) + +### OHBM + +At this point, reach out to Christine to see what she needs in order to +get her started and going on her part of the presentation, which is the +"state of the BIDS" address. diff --git a/_posts/2024-02-22-Steering-Group-minutes.md b/_posts/2024-02-22-Steering-Group-minutes.md new file mode 100644 index 00000000..2a2a347b --- /dev/null +++ b/_posts/2024-02-22-Steering-Group-minutes.md @@ -0,0 +1,191 @@ +--- +title: Steering Group minutes +author: +display: true +--- + +# Steering Group minutes 2024/02/22 + +Date: Thursday, February 22nd, 2024 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + Topic + + + + Relevant Links and to do + +
+ BEP for dimensionality reduction-based networks + + Peer Herholz +
+ Avoiding BEP being stuck + + Issue with Atlas BEP - circulate the idea of revising BEP +development - one point missing in those discussions is how to get +unstuck if conflict (CP: item voting is my favourite option, we just +need the mechanism for it - like we do to elect this group) +
+ Cooperation with DICOM standard + + YOH pointed David Clunie to our + + + DICOMs +deficits table + + + , he forwarded to WG-16 to consider at the next +meeting. +
+ Updates on plan for website + + + + BIDS +Online Presence Working Group: Working Document + + +
+ BIDS 2.0 going forward! + +
+ BEP guidelines updating (Camille & Remi) + + + + https://github.com/bids-standard/bids-extensions/pull/28 + + +
+ + + +[[https://utexas.zoom.us/my/kimray]{.underline}](https://utexas.zoom.us/my/kimray) + +**Present:** Yarik, Kim, Ariel, Cyril, Eric, Christine, Camille + +**Apologies:** Dora + +**Guest:** Peer Herholz + +## BIDS Meeting Notes + +### Plan for website + +- Eric is chairing the BIDS Online Presence Working Group + + - Eric owes the open letter to the Steering Group + +- May use google season of docs (need to sign up for the program, + starts April 2nd for applications) + + - Will reach out to INCF to reconnect as the admin for google + season of docs + + - Mentors identified: Eric, Christine, and Remi (outlined in doc + linked in agenda) + +- Eric will reach out to the group to schedule a follow up meeting. + +- Yaroslav reminded the group that he has \$5k CAD to compensate for + work on this project + +BEP39 for dimensionality reduction-based networks + +[[https://docs.google.com/presentation/d/1SLvZ7um3RQAiDr6KeK8eO_mNoQ0qHl_bzx_gqIS169Y/edit#slide=id.g152266b1f78_0_45]{.underline}](https://docs.google.com/presentation/d/1SLvZ7um3RQAiDr6KeK8eO_mNoQ0qHl_bzx_gqIS169Y/edit#slide=id.g152266b1f78_0_45) + +- May need to introduce new terminology (something akin to an + \'index', param-mixing, param-components, something akin to + \'model') + + - Eric suggests instead of \'index' potentially like + [[\*\_aslcontext.tsv]{.underline}](https://bids-specification.readthedocs.io/en/stable/appendices/arterial-spin-labeling.html#_aslcontexttsv-three-possible-cases) + + - [[https://bids-specification.readthedocs.io/en/stable/appendices/arterial-spin-labeling.html#\_aslcontexttsv-three-possible-cases]{.underline}](https://bids-specification.readthedocs.io/en/stable/appendices/arterial-spin-labeling.html#_aslcontexttsv-three-possible-cases) + + - \map : discussion determined *modality* is a suffix + + - Related discussion + [[https://github.com/bids-standard/bids-2-devel/issues/58#issuecomment-1711758273]{.underline}](https://github.com/bids-standard/bids-2-devel/issues/58#issuecomment-1711758273) + + - \'model-ICA_description.json' : suggestion to rename file as + \'dataset_dscription.json' and include \'DatasetType: model" and + model-ICA_mfp.json similarly to \'task-xxx_bold.json + +- Current state is to build up and extend \'spatiotemporal + decompositions' introduced in BEP 012 + +- Interoperability : BIDS-Prov + + - [[https://github.com/bids-standard/BEP028_BIDSprov/blob/master/examples/from_parsers/spm/spm_default_batch.jsonld#L65-L77]{.underline}](https://github.com/bids-standard/BEP028_BIDSprov/blob/master/examples/from_parsers/spm/spm_default_batch.jsonld#L65-L77) + + - Software parameters is similar to BIDS-prov's Parameters + description (what is the specific file?) + +### Stalled BEPS + +Should there be a mechanism for addressing conflicts that halt BEP +progress? + +Suggestion: 1. a voting system similar to how the steering group is +elected. + +How would we want to implement something like this while addressing +concerns of FAIRness? + +2\. BEP leader determines how to move forward. + +**3. Could a technical committee make these decisions? (maintainers + +steering group) - if there is quorum possibility to vote one way or the +other** + +When do we modify the schema to address new ideas? + +### DICOM + +### BIDS 2.0 + +### BEP guidelines updating diff --git a/tools/convert_to_md.sh b/tools/convert_to_md.sh index d578d354..577d7397 100644 --- a/tools/convert_to_md.sh +++ b/tools/convert_to_md.sh @@ -7,7 +7,7 @@ set -eu -YEAR="2023" +YEAR="2024" # save current working directory to variable cwd=$(pwd)/inputs/${YEAR}