NWB Workshops and Hackathons
Welcome to the 8th NWB User Days Workshop!
- Report
- Dates and Location
- Registration
- Logistics
- Organizing Committee
- Resources
- How to prepare?
- Objective
- Projects
- Agenda
Report
The final report for the 8th NWB User Days is now available on GitHub (PDF)(LaTeX)
Dates and Location
- Dates: May 12-15, 2020
- Location: Your home!
Registration
The workshop is open to the public. Please complete our registration form to attend the event. Anyone interested in NWB may request an invitation.
Logistics
We will be using Zoom for the meeting. We will send an email the day before the workshop with Zoom links for each day.
It is possible to use Zoom from the browser, but we recommend you install the Zoom app on your computer or phone. See installation instructions here.
Organizing Committee
Program chairs: Benjamin Dichter, Ryan Ly, Andrew Tritt, Pam Baker, and Oliver Rübel
Additional organizational support is provided by the Kavli Foundation
Resources
Recorded talks will be uploaded after the talks are given.
How to prepare?
- Create a project page with an outline for your workshop project. For further details and instructions on how to create a project, see here
- Have example datasets that you need for your workshop project ready. For any lab-specific data (i.e., data not in NWB) you should know how to read the data using Python or MATLAB and ideally have scripts ready for reading the data.
- 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/
- For an overview of NWB, see also: https://www.nwb.org/
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 analytics 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 purpose of the NWB User Days training workshop is to bring the experimental neurophysiology community together to further adoption and the development of NWB, the NWB software libraries, and the progress of the scientific workflows that rely on NWB. Members of the community will exchange ideas and best practices for using NWB and the libraries, share NWB-based tools, surface common needs, solve bugs, make feature requests, brainstorm about future funding and collaboration, and make progress on current blockages. The event will also enable NWB developers and users to interact with each other to facilitate communication, gather requirements, and train users.
In contrast to conferences, where the primary focus is to report results, the objective of the Hackathon is to provide a venue for NWB users and tool developers to learn about NWB and collaboratively work on any NWB-related research projects. This event is meant to foster community and collaboration around NWB, not competition. There will be no judges nor prizes. Participants will be expected to bring data from their lab, software they would like to integrate with NWB, and/or collaborate with others to build integration with NWB.
Projects
For instructions on how to create a project see here
Assigned Projects
The lists below provide an overview of specific projects for which at least one or more attendees have signed up for to contribute to. Projects are collaborative in nature. If you are attending the hackathon and are interested in participating in any of the existing projets then please contact the team listed on the project page.
Data conversion projects
Tool development and integration projects
Project Suggestions
You are free to come to this event with your own ideas for a project, but if you want some inspiration, here are some areas we have identified where we could use some help:
-
Python/PyNWB
-
Data acquisition
- …
Agenda
All times are in PDT (US/Pacific time)
This calendar view shows the workshop agenda. Events in blue are highly recommended. Events in orange are optional. All times not marked are considered time for attendees to hack on their projects. Developers will be available to answer questions in the main Zoom room from 8:30am to 5pm PDT.
You can also add this Google Calendar to your calendar to see the workshop’s events with Zoom links in your time zone. https://bit.ly/2yBXU4V
| Tuesday, May 12 | Day 1: New User Training | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 8:30 - 9am | Call-in time, work out any technical issues | ||||||||||
| 9 - 9:10am | Introduction: How to get the most out of this workshop
YouTube Recording |
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| 9:10 - 10am | What is NWB, with short intro to NWB-enabled tools (Oliver Ruebel)
YouTube Recording |
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| 10am - 1pm | Elective tutorials / technical introductions (covers PyNWB and MatNWB).
|
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| 1 - 1:50pm |
Overview of NWB-enabled tools, Part 1:
- NWB Explorer / Open Source Brain - CaImAn - NWB Widgets - Brainstorm - SpikeInterface |
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| 2 - 2:40pm |
Overview of NWB-enabled tools, Part 2:
- DANDI - calciumImagingAnalysis - DataJoint - Frank Lab, UCSF |
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| 2:40 - 5pm | Hacking on projects |
| Wednesday, May 13 | Day 2 - Project Hacking | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| 8:30 - 9am |
Call-in time, work out any technical issues | ||||||||||
| 9 - 10am | Project overviews / lightning talks on proposed hacking projects | ||||||||||
| 10am - 5pm | Hacking on projects | ||||||||||
| 10am - 3pm |
Elective in-depth breakouts:
|
||||||||||
| 3 - 3:30pm | Check-in | ||||||||||
| 3:30 - 5pm | Hacking on projects |
| Thursday, May 14 | Day 3: Advanced Training | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 8:30 - 9am |
Call-in time, work out any technical issues | ||||||||
| 9 - 9:30am | How to build and share extensions (Ryan Ly)
YouTube Recording |
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| 9:30 - 10am | How to write custom API classes in PyNWB (Andrew Tritt)
YouTube Recording |
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| 10 - 10:30am | Advanced write in PyNWB (compression, chunking, iterative write, and parallel access) (Andrew Tritt)
YouTube Recording |
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| 10:30 - 11am | Advanced write in MatNWB (compression, chunking, and iterative write) (Ben Dichter)
YouTube Recording |
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| 11am - 5pm | Hacking on projects | ||||||||
| 11am - 3pm |
Elective in-depth breakouts:
|
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| 3 - 3:30pm | Check-in | ||||||||
| 3:30 - 5pm | Hacking on projects |
| Friday, May 15 | Final day: Project hacking and final presentation | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 8:30 - 9am |
Call-in time, work out any technical issues | ||||||||
| 9 - 9:10am | Introduction to final day | ||||||||
| 9:10am - 3pm | Hacking on projects | ||||||||
| 11am - 3pm |
Elective user discussions by data modality:
|
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| 3 - 4:30pm | Final check-in / lightning talks on hacking projects | ||||||||
| 4:30 - 5:30pm | Social happy hour |