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Allen Institute for Brain Science

Welcome to the web page for the 4th Hackathon !


Table of Contents

Preparatory Videoconferences

Local Organizing Committee

Additional Organizational Support


How to add this calendar to your own?

Projects (How to add a new project?)

  1. Experimental Structure Viewer (Roni Choudhury, Nicholas Cain, and others)
  2. Neuropixels (Josh Siegle, Xiaoxuan Jia, Nile Graddis)
  3. ChangeIsTheOnlyConstant (Justin Kiggins, Marina Garrett)
  4. SlicerDicer (Doruk Ozturk, and others)
  5. GalleryOfExamples (Andrew Tritt, Oliver Ruebel, Jean-Christophe Fillion-Robin, and others)
  6. ExtensionSharing (Andrew Tritt, Oliver Ruebel, Jean-Christophe Fillion-Robin, and others)
  7. Advanced Data I/O (Oliver Ruebel, Andrew Tritt, and others)
  8. Storage of large-scale network simulation output (Kael Dai, Ben Dichter, Yazan Billeh, and others)
  9. PatchmasterToNWBConverter (Sándor Bordé)
  10. StimulusMetadata (Luke Campagnola)
  11. SpatialCoordinates (Luke Campagnola)
  12. NWB Explorer (Matteo Cantarelli, Giovanni Idili)

Breakout Sessions

Next Hackathon

5th Hackathon, April 25-29, 2018, Berkeley


Do not add your name to this list - it is maintained by the organizers based on your registration.


  1. Grauer, Michael (@mgrauer) - Kitware Inc. - michael.grauer@kitware.com
  2. Fillion-Robin, Jean-Christophe (@jcfr) - Kitware Inc. - jchris.fillionr@kitware.com
  3. Tritt, Andrew (@ajtritt) - Lawrence Berkeley National Laboratory - ajtritt@lbl.gov
  4. Dichter, Ben (@bendichter) - Stanford University - ben.dichter@gmail.com
  5. Millman, Dan (@everythingevolves) - Allen Institute - danielm@alleninstitute.org
  6. Feng, David (@dyf) - Allen Institute - davidf@alleninstitute.org
  7. Steuerman, David (@davidsteuerman) - Kavli Foundation - dsteuerman@kavlifoundation.org
  8. Ozturk, Doruk (@dorukozturk) - Kitware Inc. - doruk.ozturk@kitware.com
  9. Idili, Giovanni (@gidili) - Metacell - giovanni@metacell.us
  10. Perkins, Jed (@JFPerkins) - Allen Institute - jedp@alleninstitute.org
  11. Siegle, Josh (@jsiegle) - Allen Institute - joshs@alleninstitute.org
  12. Kiggins, Justin (@neuromusic) - Allen Institute - justink@alleninstitute.org
  13. Dai, Kael (@kaeldai) - Allen Institute - kaeld@alleninstitute.org
  14. Campagnola, Luke (@campagnola) - Allen Institute - lukec@alleninstitute.org
  15. Ng, Lydia (@lydiang) - Allen Institute - lydian@alleninstitute.org
  16. Becker, Lynne (@lynnebecker13) - Allen Institute - lynneb@alleninstitute.org
  17. Garrett, Marina (@matchings) - Allen Institute - marinag@alleninstitute.org
  18. Cantarelli, Matteo (@tarelli) - Metacell - matteo@metacell.us
  19. Cain, Nick (@nicain) - Allen Institute - nicholasc@alleninstitute.org
  20. Graddis, Nile (@nilegraddis) - Allen Institute - nileg@alleninstitute.org
  21. Ruebel, Oliver (@oruebel) - Lawrence Berkeley National Laboratory - oruebel@lbl.gov
  22. Choudhuri, Roni (@ronichoudhury) - Kitware Inc. - roni.choudhury@kitware.com
  23. Bordé, Sándor (@sborde) - University of Szeged - borde@inf.u-szeged.hu
  24. Braun, Thomas (@t-b) - byte physics - thomas.braun@byte-physics.de
  25. Davidson, Tom (@tjd2002) - UCSF - Thomas.Davidson@ucsf.edu
  26. Schroeder, Will (@wschroed) - Kitware Inc. - will.schroeder@kitware.com
  27. Jia, Xiaoxuan (@jiaxx) - Allen Institute - xiaoxuanj@alleninstitute.org
  28. Billeh, Yazan (@CellAssembly) - Allen Institute - yazanb@alleninstitute.org

Frequently Asked Questions


The Neurodata Without Borders: Neurophysiology (NWB:N) Hackathon is a hands-on activity lasting several days in which neurophysiology researchers create solutions using the open source NWB:N software packages.

Participants work collaboratively on solutions that use the NWB unified data format for cellular-based neurophysiology data, which is focused on the dynamics of groups of neurons measured under a large range of experimental conditions. In contrast to conferences and workshops where the primary focus is to report results, the objective of the Hackathon is to provide a venue for creators and users of neurophysiology open-source software to collaboratively work on any related research projects.

When, where, how much?

This year there will be a development focused Hackathon in Early April in Seattle, and then a user on-boarding tutorial Hackathon in late April in Berkeley. Ad-hoc meetings are added occasionally. We plan to have at least one more Hackathon in 2019. For this first Hackathon, breakfast and lunch will be covered and there will be no registration fee. These logistics are expected to evolve with the Hackathons.

How does it work?

Weekly videoconferences for preparation begin 8-12 weeks before an event. Potential participants propose projects during these meetings, and collaboratively create a list of projects that are of mutual interest. The projects include platform work, algorithm development, analytics, visualization, and neurophysiology applications and research tasks. Projects are not limited to code development, but can include creation of documentation and tutorial materials.

Through the course of the preparatory meetings, each participant selects one or more project teams and develops goals for the Hackathon. The first day of the Hackathon itself begins with a 2-hour in-person introduction to all projects and participants. The rest of the Hackathon consists of a mix of working sessions and breakout sessions on special topics, as decided by the participants during the preparatory meetings.

The projects should be something that can largely be accomplished in a few days, ideally fun, and can help your lab make progress on your research goals. The projects will be written up at the end in a publicly accessible resource that can be used by the community and can be referenced on grant proposals and reports. Projects could be coding, documentation, or tutorials.

Email announcements notifying of upcoming Hackathons are sent to the low-frequency Hackathon mailing list Hackathon mailing list (for continuity and permanence across hackathons), and communication specific to each event will happen on a dedicated Hackathon forum (see each Hackathon page for details).

Who can attend?

Due to limited space the hackathons participation is currently on an invitation-only basis. If you are interested in attending a hackathon then please contact the organizer of the hackathon directly. We are always excited to see new members join the NWB:N community. If space is available, we will try to accomodate the additional requests.

What is the history of NWB hackathons?

The NWB:N team consists of neuroscientists and software developers who recognize that creation and adoption of a unified data format is an important step toward breaking down the barriers to data sharing in neuroscience. Hackathons are a way for us to collaborate and develop NWB:N as well as to engage with the NWB:N user community. For an overview of NeurodataWithoutBorders see http://nwb.org/.

As part of the development of NWB:N 1.x two hackathons were held at Janelia Farm, in Ashburn, Virginia; the first hackathon on November 20 – 22, 2014 and the second one on May 14-16 at, 2015 (http://crcns.org/NWB/). As part of the development of NWB:N 2.0 a first hackathon was held at Janelia Farm, in Ashburn, Virginia on July 31 - August 1, 2017. The primary focus of the first three hackathons has been on development of the NWB:N format as well as on development of a software strategy for NWB:N.

To encourage the development, growth and use of NWB:N as a unified data format for cellular-based neurophysiology data, the Allen Institute for Brain Science, Lawrence Berkeley National Lab, and Kitware are organizing a development-focused hackathon at the Allen Institute for Brain Science (April 3-6, 2018) and a user-engagement and training hackathon at Lawrence Berkeley National Laboratory (April 25-27).

Who to contact?

Communication specific to this event will happen on a dedicated Hackathon forum (see Logistics for details).