NWB Workshops and Hackathons
Welcome to the 2022 NWB-DANDI Remote Developer Hackathon!
- Report
- Dates and Location
- Overview
- Registration
- Logistics
- Organizing Committee
- How to prepare?
- Projects
- Breakout Sessions
- Matchmaking Chat
- Objective
- Agenda
- Code of Conduct
Report
The final report for the 2022 NWB-DANDI Developer Hackathon is now available on GitHub (PDF) (LaTeX).
Dates and Location
- Pre-hackathon project pitch session: Tuesday, February 8, 2021, 10am PST (1pm EST)
- Dates: Tuesday, February 15, 2022 - Friday, February 18, 2022, 8am - 3pm PST (11am - 6pm EST)
- Location: Anywhere with an internet connection
Overview
Neurodata Without Borders (NWB) and the DANDI neurophysiology data archive development teams are joining together to create a remote hackathon event for developers. In contrast to the User Days hackathons that focus on training users, this event will focus on bringing together the developers of the NWB data standard, the DANDI development team, and developers of tools in the NWB ecosystem.
This hackathon will enable participants to work intensively on an NWB or DANDI-related project with the assistance of core developers and others in the community. We will share updates with each other on NWB, DANDI, and related community projects. Together, we can develop and discuss ideas for solving technical problems that impact the broader community. Our goal is to foster collaboration and community among developers working on and with NWB and DANDI.
Registration
Please complete the registration form to attend the event. There is no cost to attend.
Logistics
We will be using the Gather spatial chat platform for most of the meeting. We will be using the Zoom videoconferencing platform for the breakout sessions. We will send an email in the week before the workshop with the meeting links.
Gather Platform
In Gather, you control a video-game-like avatar with your arrow keys. When your avatar is near another attendee’s avatar, their video will appear and you will be able to speak with them. This platform allows for many small-group or one-on-one conversations to occur simultaneously and spontaneously. We hope that Gather will emulate the free-flowing social interactions of an in-person hackathon better than having everyone in a single Zoom meeting or messaging over Slack.
We have a few tips for using Gather, especially if it is your first time:
- Sign in to the space before the meeting and practice using the controls.
- Use a desktop/laptop computer, not a mobile device. Chrome seems to works best. The desktop app also works.
- This is not a 20+ person Zoom call. You can “walk” up to different people and communicate with only the people within a few tiles from your avatar.
- Shaded areas are “private spaces” - only people inside the private space can see and hear you. There are private spaces for each breakout room, each table/desk, and the main stage area.
- While you are hacking, we recommend that you keep Gather open in the background with your speakers/audio on, so that others can more easily reach you. This will help us better emulate an in-person hackathon where everyone is approachable. Feel free to mute yourself and turn off your video when you are not interacting with anyone.
- Click on a name in the People panel (bottom-left button) to send them a message or locate them.
- We recommend that you keep the Chat panel on the left open in case someone messages you.
- If you are leaving your computer for a prolonged period, please close the browser to make your avatar leave the space.
- You can click the arrow icon in the top right of the video feed to make everyone’s videos bigger. You can also click your name at the bottom of the screen, User/Video preferences, and Use HD Video Quality for better video.
Zoom Platform
It is possible to use Zoom from the browser, but we recommend you install the Zoom app on your computer. See installation instructions here.
Organizing Committee
NWB POC: Ryan Ly (rly@lbl.gov)
DANDI POC: Satrajit S. Ghosh
Program Commitee: Ryan Ly, Benjamin Dichter, Matthew Avaylon, Andrew Tritt, Pam Baker, Oliver Rübel, Satrajit S Ghosh, Yaroslav O. Halchenko
Sponsored by The Kavli Foundation
How to prepare?
If you are not experienced with NWB, please watch this introduction to NWB and optionally the subsequent lessons in Python (or in MATLAB here). Install the Python or MATLAB software for NWB:
- PyNWB (Python): https://pynwb.readthedocs.io/en/stable/getting_started.html
- MatNWB (MATLAB): https://neurodatawithoutborders.github.io/matnwb/
If you are not experienced with DANDI, please read the DANDI documentation, browse the DANDI GitHub organization, and create an account on DANDI.
Projects
Working on a project related to NWB, individually or as part of a team, is encouraged. There is dedicated time during the hackathon to work on your project and seek ask questions to the NWB and DANDI development teams.
For instructions on how to create a project, see here
Assigned Projects
Please see the Projects GoogleDoc for the list of hackathon projects.
Projects are collaborative in nature. If you are attending the hackathon and are interested in participating in any of the existing projects, then please contact the team listed on the project page and add your name to the list of participants for the project.
Breakout Sessions
Breakout sessions are collaborative meetings focused on topics of common interest. Each breakout session has an assigned session chair to help coordinate the meeting.
Please see the Breakout GoogleDoc for the list of breakout sessions.
Proposing breakout sessions
To propose additional breakout sessions, please contact the hackathon organizing team to request edit access to the Breakout GoogleDoc.
Matchmaking Chat
Successful collaborations often begin from casual social interactions. To facilitate networking and social interactions during the hackathon, we will have a session of 2 one-on-one 15-minute chats between participants. Please fill out the form you received by email to let us know your interests, and we will pair you up during the hackathon.
Prior to the chat, please take a quick look at your partner’s webpage, GitHub page, or list of publications (a link will be included in the email we send you), but there is no expectation that you will read their papers. Please also think about how to quickly describe your research interests bearing in mind your partner’s background.
During the chat, we recommend the following, but feel free to structure your meeting however you like.
- Start by each of you talking for 1 - 2 minutes about your general interests and approach.
- If you immediately see a point of connection, go for it and talk about that.
- Feel free to use screen-sharing and your slides if you think they help.
- If not, try each of you describing briefly one or two projects that you think would be relevant or interesting to the other one, and see if that sparks an interesting discussion.
- Keep in mind, the idea is to give yourselves the best chance of finding an unexpected and useful connection, so think broadly and try to get across a range of ideas until you find something that gets you both excited that you can talk about in more detail.
- Please be kind and respectful during your meeting (see more on our code of conduct page).
- Don’t worry if you don’t find something, our algorithms aren’t perfect and you’re not being judged on how well you do - have fun!
These tips are largely adapted from the successful mindmatching from the neuromatch conference. See also this paper on the format and a matching algorithm.
Objective
The Neurodata Without Borders: Neurophysiology project (NWB, https://www.nwb.org/) is an effort to standardize the description and storage of neurophysiology data and metadata. NWB enables data sharing and reuse and reduces the energy barrier to applying data analysis both within and across labs. Several laboratories, including the Allen Institute for Brain Science, have wholeheartedly adopted NWB. The community needs to join forces to achieve data standardization in neurophysiology.
The Distributed Archives for Neurophysiology Data Integration (DANDI, https://www.dandiarchive.org/) is a platform for publishing, sharing, and processing neurophysiology data funded by the BRAIN Initiative. The platform is now available for data upload and distribution.
The purpose of the NWB+DANDI Developer Hackathon is to bring the neurophysiology developer community together to further the development NWB and DANDI and integration of NWB and DANDI with tools. Members of the community will work jointly on coding projects, exchange ideas and best practices, surface common needs, resolve coding issues, make feature requests, brainstorm about future collaboration, and make progress on current blockages.
Agenda
All times are in Pacific Standard Time (PST; UTC-8)
All breakout sessions will be held in Room 1 of the Gather space unless noted otherwise.
| Day 1 | Tuesday, February 15 | |
|---|---|---|
| 7:50 - 8am |
 Log in to Gather, learn controls, and explore the space |
|
| 8 - 8:30am |
 Welcome and Introduction (Main Stage) |
|
| 8:30 - 9am |
 Project presentations (2-3 min presentation each) (Main Stage)
|
|
| 9 - 9:30am |
 Breakout: Conversion of Proprietary Formats to NWB
|
 Open Hacking
|
| 9:30 - 10am |
Breakout: Data Overlays in NWB
|
|
| 10 - 11am |
Breakout: Best Practices and Validation
|
|
| 11am - 12pm |
|
|
| 12 - 12:30pm |
 Coffee Break (Fountain)
|
|
| 12:30 - 3pm |
|
|
| Day 2 | Wednesday, February 16 | |
|---|---|---|
| 8 - 8:30am |
Breakout: BIDS-ephys
|
Open Hacking
|
| 8:30 - 9am |
Breakout: Data Acquisition API for NWB
|
|
| 9 - 10am |
Breakout: External Links in NWB and DANDI
|
|
| 10 - 11am |
Breakout: Ontologies and External Resources
|
|
| 11am - 12pm |
|
|
| 12 - 12:30pm |
Coffee Break (Fountain)
|
|
| 12:30 - 1pm |
|
|
| 1 - 2pm |
Breakout: MatNWB Working Group
|
|
| 2 - 3pm |
|
|
| Day 3 | Thursday, February 17 | |
|---|---|---|
| 8 - 8:10am |
 Project check-in (Main Stage)
|
|
| 8:10am - 12pm |
|
Open Hacking
|
| 12 - 12:30pm |
 Matchmaking chats (optional)
|
|
| 12:30 - 1pm |
 Group games and social hour (Yoh's Island Bar)
|
|
| 1 - 3pm |
|
|
| Day 4 | Friday, February 18 | |
|---|---|---|
| 8 - 9am |
|
Open Hacking
|
| 9 - 9:30am |
Breakout: NWB Trials and Events Working Group
|
|
| 9:30 - 10am |
Breakout: NWB Documentation
|
|
| 10 - 11am |
Breakout: The Future of NWB
|
|
| 11am - 12pm |
|
|
| 12 - 12:30pm |
Coffee Break (Fountain)
|
|
| 12:30 - 2pm |
|
|
| 2 - 3pm |
Final presentations (Main Stage)
|
|
| 3 - 4pm |
 Social hour (Yoh's Island Bar)
|
|
Code of Conduct
We are dedicated to providing a harassment-free hackathon experience for everyone, regardless of gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. We do not tolerate harassment of event participants in any form. Sexual language and imagery is not appropriate for any event venue, including talks. event participants violating these rules may be sanctioned or expelled from the event without a refund at the discretion of the event organizers.
Harassment includes, but is not limited to:
Verbal comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, disability, physical appearance, body size, race, age or religion. Sexual images in public spaces Deliberate intimidation, stalking, or following Harassing photography or recording Sustained disruption of talks or other events Inappropriate physical contact Unwelcome sexual attention Advocating for, or encouraging, any of the above behaviour Enforcement Participants asked to stop any harassing behavior are expected to comply immediately.
Organizers and presenters are also subject to the anti-harassment policy. In particular, they should not use sexualized images, activities, or other material.
Event organisers may take action to redress anything designed to, or with the clear impact of, disrupting the event or making the environment hostile for any participants.
If a participant engages in harassing behaviour, event organisers have the responsibility to remind the offender about our Code of Conduct, and warn them that repeated inappropriate, uncivil, threatening, offensive, or harmful behavior can lead to a temporary or permanent ban from the event with no refund. The offending person(s) may also see affected their participation in future NWB and DANDI events.
We expect participants to follow these rules at all event venues and event-related social activities. We think people should follow these rules outside event activities too!
Reporting
If someone makes you or anyone else feel unsafe or unwelcome, please report it as soon as possible to the events organizers. Harassment and other code of conduct violations reduce the value of our event for everyone. We want you to be happy at our event. People like you make our event a better place.
You can make a report either with your personal email or using an anonymous email.
NWB Contributor Code of Conduct
When directly contributing to the NWB project, contributors are expected to follow the NWB Contributor Code of Conduct
Credit
This hackathon code of conduct is adapted from the Brainhack Code of Conduct.
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