NWB Workshops and Hackathons

Welcome to the 6th NWB:N Developer Hackathon and User Days!!

• Report
• Dates and Location
• Attendees
• Registration
• Logistics
• Organizing Committee
  • Additional Organizational Support
• Resources
• What to bring?
• Objective
• Agenda
  • User Days
  • Developer Days
  • Calendar
• Projects
  • Creating a New Project
• Registrants
• Attending Remotely
• Resources
• Disclaimer

Report

The final report for the 6th NWB:N Developer Hackathon and User Days is now available on GitHub (PDF)(LaTeX)

Dates and Location

• Dates: May 13-16, 2019
  • User Days: May 13-14, 2019
  • Developer Days: May 15-16, 2019
• Location: HHMI Janelia Research Campus, 19700 Helix Dr, Ashburn, VA 20147, Openstreetmap Directions
• Meeting Rooms: For the meeting we have two rooms. The main room is Synapse and the breakout room is Spectrum. For details about the room locations see the building map.

Attendees

NWB:N User Days

Credits: Photo by Matt Staley (HHMI Janelia)

NWB:N Developer Days

Credits: Photo by Matt Staley (HHMI Janelia)

• …

Registration

Registration for the NWB:N User Days is closed. Space at the event is limited and registration was on a first-come basis.

To attend the meeting remotely, please complete the remote attendee registration form. Remote attendance is for the the talks and tutorials only. Local attendance is required in order to actively participate in hacking and project sessions.

Logistics

Housing: Housing will be onsite on the Janelia research campus. For details about transportation and logistics please see here

Travel: Travel support is being provided by the Kavli foundation. As housing will be onsite on the Janelia research campus, travel support is intended for flights (not housing). Funds available to support attendee travel are limited! Travel arrangements must be pre-approved by the Foundation’s Executive Assistant. If you use the Kavli travel services (recommended) then please CC Stephanie Albin (salbin@kavlifoundation.org) to get approval for the travel cost. Also, if you are planing to book your own flights then please make sure to get PRE-APPROVAL from Stephanie Albin (salbin at kavlifoundation.org). Please see the Kavli reimbursement guidelines for details. The traveler profile form is available here.

Directions: The Janelia Research Campus is located in Loudoun County, Virginia – just 30 miles from Washington, DC, and about eight miles north of Dulles International Airport (IAD). For directions see https://www.janelia.org/directions

Organizing Committee

Site chair: Karel Svoboda

Program chair (Developer Days): Oliver Rübel and Michael Grauer

Program chair (User Days): Oliver Rübel and Ben Dichter

Administrative Support: Janine Stevens

Additional Organizational Support

• The Kavli Foundation
• Janelia HHMI

Resources

Talks

The slides for the talks presented during the User Days are available here.

Code

Ben Dichter’s electrophysiology tutorial (Day 1):

• python jupyter notebook
• matlab code

Tom Davidson’s ‘early adopter experiences’ talk (Day 1):

• Repo containing notebooks in talk

What to bring?

• Create the outline for your project at the hackathon. For further details and instructions on how to create a project see here
• Bring any example data sets needed for your project with you to the hackathon. For any lab-specific data (i.e., data not in NWB:N) you should know how to read the data using Python and ideally have scripts ready for reading the data.
• Bring your laptop with appropriate software installed. For instructions on how to install PyNWB see http://pynwb.readthedocs.io/en/latest/getting_started.html#installation
• For an overview of NWB:N see also: https://neurodatawithoutborders.github.io/

Objective

The Neurodata Without Borders: Neurophysiology project (NWB:N, https://neurodatawithoutborders.github.io/) is an effort to standardize the description and storage of neurophysiology data and metadata. NWB:N 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:N. The community needs to join forces to achieve data standardization in neurophysiology.

The purpose of the hackathon is to bring the experimental neurophysiology community together to further adoption and the development of NWB:N, the NWB:N software libraries, and the progress of the scientific workflows that rely on NWB:N. Members of the community will exchange ideas and best practices for using NWB:N and the libraries, share NWB:N 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:N developers and users to interact with each other to facilitate communication, gather requirements, and train users.

The event is planned for 4 days, where the first two days will focus on user training and use-cases followed by two days focused on core development. Work involves collaborative, open source software development, with a focus on use cases, tools, and core development.

Note: This event is meant to foster community and collaboration around NWB:N, not competition. As such, this is really more of a “workshop” or “tutorial” than a “hackathon.” There will be no judges nor prizes. Participants will be expected to bring data from their own lab and/or collaborate with others to build integration with NWB:N.

Agenda

We are planing to have this be a full-day event for May 13 - 16, 2019 consisting of 2 days for user training and engagement (May 13-14) followed by 2 days for developer hackathon (May 15-16). On May 14 (late afternoon) we will have a joint user & developer social. The event will begin early in the morning on May 13, i.e., if you are attending the user days, please plan to arrive on May 12 and depart in the evening on May 14 after the social. If you are attending the developer days, then plan to arrive in the afternoon on May 14 to attend the social and plan to depart in the evening on May 16 after completion of the event. Below the current draft of the agenda. The agenda is work in progress! Further details will be announced here as they become available Download Agenda

Agenda: User Days

Agenda: Developer Days

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.

User Days

• Abf and Dat to NWB:N
• Chang lab to NWB:N
• Neuromodulation Research Center to NWB:N
• Integrate Thorlabs 2p calcium data into NWB
• Tandon lab to NWB:N
• Rutishauser lab to NWB:N
• Lazy cross-file links
• Use case gathering
• Zuckerman Institute NWB:N demos
• Simultaneously recorded physiology and imaging data from single cells in slice
• Convert Buzsaki lab data formats to NWB
• Mesoscale Activity Project to NWB
• Bender Lab - Neuronal Model Optimization
• Brain Modeling Toolkit to NWB

Developer Days

• Integrate NWB:N with RAVE
• Integrate ZARR with PyNWB/HDMF
• Integrate Exdir with PyNWB/HDMF
• Evaluate avenues for NIX + NWB:N
• NWB:N Jupyter notebook widgets
• NWB:N Explorer and Open Source Brain
• Import data from acquisition systems
• Extension sharing
• Lazy cross-file links
• DataJoint-NWB-Interoperability
• Import data from acquisition systems
• NWBIndex
• NWB Query
• Vastly improve documentation
• Validation enhancements
• Interactive PyNWB course

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

  • Add default ProcessingModules: see nwb-schema issue
  • Schema validator: We need a way to ensure that the schema yaml files follow the schema language. This will be particularly useful as part of an extension sharing infrastructure, where users will be creating these yaml files and we would like to validate them before sharing them with the community. This could be done using the HDMF data structures or JSON-schema.
  • Alternate storage backends: While NWB:N and pynwb were designed to support multiple backends, the only one currently implemented is HDF5. Possible options may be:
    • Exdir: See issue 629
    • Zarr: See issue 230
    • Nix: Nix is another neural data standard, and it would be useful to be able convert back and forth between NWB:N and Nix.
  • Parallel I/O Test and improve support for MPI parallel HDF5 I/O and create parallel I/O tutorial (see, e.g., https://github.com/NeurodataWithoutBorders/pynwb/pull/847)
  • Visualization and documentation tools:
    • Documentation Utils: Improve organization and visualizations of the documentation utils used to generate Sphinx docs and figures from the YAML schema files. See also https://github.com/NeurodataWithoutBorders/nwb-docutils
  • Support for regular ontology: See previous work here. There is also ongoing work in this space by LBNL and AIBS. If you are interested in this please contact oruebel@lbl.gov .
  • Add support for other data analysis/visualization/management packages
    • Add ONE API
    • DataJoint support
    • Neo support: Neo is a community standard for representing neural data in memory that several analysis and visualization tools use. We would like to have methods that convert from pynwb objects to neo objects:

pynwb	neo
TimeSeries	AnalogSignal, AnalogSignalArray, or IrregularlySampledSignal
SpikeEventSeries	Spike
Units.spike_times	SpikeTrain
AnnotationSeries	EventArray
trials, epochs	EpochArray

• MatNWB
  • Continuous Integration (CI): CI is a tool for running tests automatically every time you merge a pull request, which makes sure the tests and up-to-date and prevents the addition of bugs. We have this working in pynwb, and it would be great to also have this working in matnwb.
  • Data compression: HDF5 has robust data compression capabilities, but matnwb cannot currently take advantage of them. We need a way to tell the neurodata_type constructors whether/how a dataset should be chunked and compressed. Issue here. See the pynwb implementation of this for inspiration.
  • Data append: see issue here
  • Support MATLAB table: see issues for in and out
  • DataJoint support
  • Support for other analysis/visualization packages

• Data acquisition

  • ScanImage
  • TDT
  • Plexon
  • OpenNeurophys
  • …

Attending Remotely

We are using Zoom for remote participation.There are multiple ways to join this meeting.

1. Use the following link to Join the meeting from your desktop or cell: https://hhmi.zoom.us/j/122156921 (This will load the Zoom client and is recommended for the best audio quality!)

2. From a cell phone if you are not able to use the first link : US: +19294362866,,122156921# or +16699006833,,122156921#

3. From a standard telephone : Dial(for higher quality, dial a number based on your current location): US: +1 929 436 2866 or +1 669 900 6833 or 877 853 5257 (Toll Free) or 855 880 1246 (Toll Free) Meeting ID: 122 156 921 (Find your local number: https://zoom.us/u/acHwiXLxGC)

4. If you are in an HHMI conference room, use the touch panel to dial 2800. When prompted, type #122 156 921#

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