Bidsme -- bidsifier for multimodal datasets
Opened this issue · 9 comments
Project info
Title:
bidsme
Project lead:
Nikita Beliy, @nbeliy
UTC+2, Bussels
Hub:
Europe, Middle East and Africa
Description:
One of the great ideas behind BIDS is unification of various modalities in the same dataset, sharing common metadata and providing a self-sufficient dataset ready to analyse. However various bidsificators target only one or two modalities.
Bidsme project has been developed to provide a bidsificator as universal as possible, both in modalities and data formats. The project is based on two main ideas:
- everything that is laboratory-depending (log files, events, demographic info, psychological assessments, format conversions) must be treated via plugins
- Data treated in object-oriented way: master class do the bidsifications, modality sub-class defines the BIDS-related parameters (entities, JSON fields etc...), data-format sub-sub-class implements how to read metadata
Using this approach it is possible to integrate a new modality from scratch in one week, and fully create plugins for a given dataset in few days.
Link to project:
https://github.com/CyclotronResearchCentre/bidsme
Mattermost handle:
nbeliy
Goals for the OHBM Brainhack
The minimum program is to get some long-term collaborators, for now it is one man project, but it becomes too big to be handled alone.
Program maximum is to implement few new modalities, namely MEG, probably create a neat GUI.
Good first issues:
- Incorporate MEG and most popular corresponding data formats
- Rework how sidecar JSON file are created and filled
- Improve plugin framework
- Incorporate bidsified dataset versioning
- Incorporate checks for dataset completeness
Skills:
| Language | Level |
|---|---|
| Python3 | confirmed |
| Unix command line | beginner |
Advanced Python3 skills, with understanding of object-oriented programming, including virtual functions
If working on modality, knowledge of such modality, corresponding BIDS section and knowledge of data format
Chat channel:
Mattermost channel
Video channel:
Please have a look at the Mattermost channel for the URL of the video channel, or alternatively, please contact to @nbeliy.
Slides for project pitch
bidsme.pdf
Project submission
Submission checklist
Once the issue is submitted, please check items in this list as you add under 'Additional project info'
Please include the following above (all required):
- Link to your project: could be a code repository, a shared document, etc. See here
- Include your Mattermost handle (i.e. your username). If you do not have an account, please sign up here.
- Goals for the OHBM Brainhack: describe what you want to achieve during this brainhack. See here.
- Flesh out at least 2 "good first issues": those are tasks that do not require any prior knowledge about your project, could be defined as issues in a GitHub repository, or in a shared document, cf here.
- Skills: list skills that would be particularly suitable for your project. We ask you to include at least one non-coding skill, cf. here.
- Chat channel: A link to a chat channel that will be used during the OHBM Brainhack. This can be an existing channel or a new one. We recommend using the Brainhack space on mattermost, cf. here.
- Video channel: Please create a video channel that will be used during the OHBM Brainhack and share it in your chat channel above. This can be an existing channel or a new one. For instance a jitsi meet room, cf. here.
You can also include information about (all optional):
- Number of participants, cf. here
- Twitter-size summary of your project pitch, cf. here
- Provide an image of your project for the OHBM brainhack website
- Set up a kanban board on your repository to better divide the work and keep track of things, cf here
- Project snippet for the OHBM Brainhack website, cf. here
We would like to think about how you will credit and onboard new members to your project. We recommend reading references from this section. If you'd like to share your thoughts with future project participants, you can include information about (recommended):
- Specify how will you acknowledge contributions (e.g. listing members on a contributing page).
- Provide links to onboarding documents if you have some.
🎉 Welcome to the 2020 OHBM Hackathon! 🎉 We're really excited to have your input on this repository and welcome your idea! 💖 If you haven't done so already, please make sure you check out our Code of Conduct. Did you issue a new hackathon project? Please check if you have provided all relevant information and an image for the website.
hey @nbeliy
I added some labels to this issue.
Make sure you are fine with those or if you want to change or add more.
Hi Remi, tags looks fine, there no much more than bids
hi @ohbm/project-monitors: My project is ready!
Hi @nbeliy, thanks for adding this project!! I've added the MEG label as well since you mentioned it in the description. If you by any chance have a logo that you'd like us to use for project advertisement, let me know :)
Hi @nbeliy, is there an image for your project that you would like to be displayed on the hackathon website? Thanks in advance!
Hi all, I took an initiative to attach slides for pitch to the project description. Please tell if it's ok for you.
Also, can you add a tag data-managment, I've seen some projects that have it.
Thanks
Hi @nbeliy, is there an image for your project that you would like to be displayed on the hackathon website? Thanks in advance!
Hi @DorienHuijser, I don't have any image, but Matthias made a make-shift one for me
Dear @nbeliy I removed the video link in your issue to avoid any unwanted interference.
I guess you already shared the video link in your Mattermost channel so your issue seems ready to go! Thank you very much 🤗