Welcome to the 5th NWB:N Hackathon!
The final report for the 5th NWB:N Hackathon at LBNL is now available on GitHub (PDF)(LaTeX)
After the hackathon
- All participants of the hackathon, please complete the following short survey
- Update your project pages with progress from (and after) the hackathon
- If you have data that you are willing to share, then please do so (see below)
Add your publicly sharable NWB:N files
Please register a user in the Girder web data sharing instance and add your publicly sharable data to the
NWB Hackathon 5 sharing folder.
- Agenda [PDF]
- Online Tutorials, The online tutorials for PyNWB that were used and mentioned in the talks are available here
- Welcome to the NWB:N Hackathon @ LBNL, Oliver Ruebel, 04/26/2018, 8am [PDF]
- Neurodata Without Borders, Kris Bouchard, 04/26/2018, 8:10am [PDF]
- Introduction to NWB:N – An ecosystem for standardizing neurophysiology data, Oliver Ruebel, 04/26/2018, 8:20am [PDF]
- NWB:N and PyNWB – A Python API for standardizing neurophysiology data Andrew Tritt, 04/26/2018, 8:40am [PDF]
- Overview of MatNWB, Lawrence Niu / Nathan Clack, 04/26/2018 , 9:40am [Slides coming soon]
- NWB:N I/O – ophys, Nick Cain, 04/26/2018, 10:25am [Slides coming soon][Online Tutorials]
- NWB:N I/O – ephys, Ben Dichter, 04/26/2018, 11:10am [PDF]
- Welcome to Day 2 of the NWB:N Hackathon @ LBNL, Oliver Ruebel, 04/27/2018, 9am [PDF]
- PyNWB Software Process and How to Contribute, Michael Grauer and Jean-Christophe Fillion-Robin, 04/27/2018, 9:15am, [PDF]
- Writing Extensions, Ben Dichter, 04/27/2018, 9:30am, [PDF] (see the second part of the slide deck)
- PyNWB Containers – Front-end objects for NWB data, Andrew Tritt, 04/27/2018, 10:45am, [PDF]
- PyNWB: Advanced Data I/O, Oliver Ruebel, 04/27/2018, 12:30pm [PDF]
Dates and Location
- Registration for in person attendence is CLOSED Deadline was March 2nd, 2018. Registration for remote attendance is still open (see below). Please contact Oliver Ruebel firstname.lastname@example.org in case you have questions.
- Other Guests: This event is invitation-only. If you have not received an invitation but would like to attend then please contact Oliver Ruebel email@example.com.
- Remote Attendance: If you are planing to attend remotely, then please register via the follwing registration form for remote attendees
- NOTE: We expect that significant portions of this event will be involve hacking/coding on problems and working on projects. Remote attendance is for the talks and tutorials only! Local attendance is required in order to actively participate in hacking and project sessions.
- Registration Deadline for Remote Attendance: None
Hotel: A block of 15 rooms has been reserved at the LBNL Guest House for this event for April 25-27. For details on how to reserve your room see here. Availability of rooms is limited. Please reserve your room 30 days prior to arrival.
Alternate Hotels: LBNL operates a shuttle service from Downtown Berkeley to LBNL. Alternate hotels in Berkeley near LBNL shuttle stops are e.g.:
Lawrence Berkeley National Laboratory (LBNL) is located in Berkeley on the hillside directly above the campus of the University of California at Berkeley. The Labs address is 1 Cyclotron Road, Berkeley CA 94720. To make LBNL easily accessible, the Lab has its own shuttle service that takes people around the site and to downtown Berkeley and the BART station there.
Getting to LBNL: Detailed instructions for how to get to the Lawrence Berkeley National Laboratory campus from the San Francisco Internal Ariport and the Oakland Internal Airport are available here.
LBNL Shuttle: The LBNL Shuttle service is available to all attendees. For a detailed schedule and routes see here. Building 59 is located near the Building 65 shuttle stop. As a visitor you will need your photo ID and a visitor bus pass, email, or permission from Lab host, written on official letterhead. TIP: When you see a shuttle bus approaching WAVE AT THE DRIVER so the driver knows you want to board the bus. LBNL shuttle stops are marked with this sign:
- Car: Parking is available to all guests of the LBNL Guest House. Guest house parking is located directly across from the LBNL guest house (Parking Lot Z in the below map). For attendees staying at offsite locations, parking spaces are difficult to find at LBNL and if you need to park onsite then additional reserved parking must be requested 2 weeks ahead of the meeting.
Local Organizing Committee
- Oliver Ruebel
- Andrew Tritt
- Kristofer Bouchard
Additional Organizational Support
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 labtop 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/
The Neurodata Without Borders: Neurophysiology project (NWB:N, www.nwb.org) is an effort to standardize the description and storage of neurophysiology data and metadata. NWB:N enables data sharing/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. This hackathon event invites experts from the neuroscience community to explore adopting NWB:N for their data sharing needs and lab use cases. The goal of this event is to a) train new users on NWB:N, b) promote adoption of NWB:N, c) work with users on programming projects, e.g, to integrate examples of their labs data into NWB:N, d) facilitate communication between users and developers and project teams, and e) engage with the community.
We are planing to have this be a full-day event for both days (April 26 and 27), starting at ~8am in the morning and ending at ~6pm in the evening. Further details will be announced here as they become available. The agenda is work in progress! Stay Tuned.
How to add this calendar to your own?
For instructions on how to create a project see here
Do not add your name to this list - it is maintained by the organizers. Click on the name of a registrant to view their hackathon project.
- Oliver Ruebel (LBNL)
- Andrew Tritt (LBNL)
- Max Dougherty (LBNL, NSE Lab)
- Tom Davidson (UCSF - Frank Lab)
- Karen Lavi (UCSF)
- Ali Mohebi (UCSF)
- Dylan Paiton (UCB)
- Evan Lyall (UCB)
- Jeff Teeters (UCB)
- Stephanie Albin (The Kavli Foundation)
- Kevin Brown (New York University)
- David Tingley (NYU)
- Sam McKenzie (NYUMC)
- Sebi Rolotti (Columbia University, Losonczy Lab)
- Jochen Weber (Columbia University, Zuckerman Mind Brain Behavior Institute)
- David Thibodeaux (Columbia University)
- Ben Dichter (Stanford)
- Aaron Milstein (Stanford University)
- Ivan Raikov (Stanford University)
- Kei Masuda (Stanford University, Giocomo Lab)
- Jason Bant (Stanford University)
- Adam Granger (Harvard Medical School)
- Duo Xu (Johns Hopkins University)
- Eric Finkel (Johns Hopkins School of Medicine, O’Connor Lab)
- Michael Grauer (Kitware)
- Jean-Christophe Fillion-Robin (Kitware)
- Michael Wulf (Cold Spring Harbor Laboratory, Kepecs Lab)
- Torben Ott (Cold Spring Harbor Laboratory)
- Nathan Clack (Vidrio Technologies)
- Lawrence Niu (Vidrio Technologies)
- Nicholas Cain (Allen Institute for Brain Science)
We will use Zoom for remote attendance. For information on how to get started with Zoom see here.
Join from PC, Mac, Linux, iOS or Android: https://lbnl.zoom.us/j/952481719
Or iPhone one-tap : US: +16699006833,,952481719# or +16465588656,,952481719#
- Dial(for higher quality, dial a number based on your current location): US: +1 669 900 6833 or +1 646 558 8656
- Meeting ID: 952 481 719
- International numbers available: https://lbnl.zoom.us/zoomconference?m=7mjcuSAZBd4DW6HDXaRAaR09FHQ1lQ8k
Or an H.323/SIP room system:
- 22.214.171.124 (US West)
- 126.96.36.199 (US East)
- 188.8.131.52 (China)
- 184.108.40.206 (India)
- 220.127.116.11 (EMEA)
- 18.104.22.168 (Australia)
- 22.214.171.124 (Hong Kong)
- 126.96.36.199 (Brazil)
- 188.8.131.52 (Canada)
- Meeting ID: 952 481 719
- SIP: firstname.lastname@example.org
This website and related content were prepared as an account of or to expedite work sponsored at least in part by the United States Government. While we strive to provide correct information, neither the United States Government nor any agency thereof, nor The Regents of the University of California, nor any of their employees, makes any warranty, express or implied, or assumes any legal responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.
Reference herein to any specific commercial product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or The Regents of the University of California. Use of the Laboratory or University’s name for endorsements is prohibited.
The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof or The Regents of the University of California. Neither Berkeley Lab nor its employees are agents of the US Government.
Berkeley Lab web pages link to many other websites. Such links do not constitute an endorsement of the content or company and we are not responsible for the content of such links.