diff --git a/archetypes/events.md b/archetypes/events.md new file mode 100644 index 0000000..fd70fa0 --- /dev/null +++ b/archetypes/events.md @@ -0,0 +1,20 @@ +--- +title: "{{ replace .Name "-" " " | title }}" +date: {{ .Date }} +endDate: {{ .Date }} +location: "" +eventType: "Hackathon" # or Workshop, Conference, etc. +image: "/images/events/default-event-banner.png" +weight: {{ dateFormat "20060102" .Date }} # YYYYMMDD format for sorting +summary: "" +draft: false +organizers: + - "Organizer 1" + - "Organizer 2" +registration: "Registration details here" +resources: + "Resource 1": "https://example.com" + "Resource 2": "https://example.com" +--- + +Event content goes here. This will be displayed on the event page. diff --git a/config/_default/menus.yaml b/config/_default/menus.yaml index 30fa44a..be2c05d 100644 --- a/config/_default/menus.yaml +++ b/config/_default/menus.yaml @@ -50,16 +50,21 @@ main: weight: 1 url: "news/" parent: "Community" - - name: "Enhancement Proposals" + - name: "Events" weight: 2 + url: "events/" + parent: "Community" + parent: "Community" + - name: "Enhancement Proposals" + weight: 4 url: "https://github.com/nwb-extensions/nwbep-review/" parent: "Community" - name: "Working Groups" - weight: 3 + weight: 5 url: "working-groups/" parent: "Community" - name: "Team" - weight: 4 + weight: 6 url: "team/" parent: "Community" @@ -105,11 +110,17 @@ community_links: - name: "News & Updates" weight: 1 url: "/news" - - name: "Working Groups" + - name: "Events" weight: 2 + url: "/events" + - name: "About Events" + weight: 3 + url: "/about-events" + - name: "Working Groups" + weight: 4 url: "/working-groups" - name: "Contact Us" - weight: 3 + weight: 5 url: "/contact-us" resources: diff --git a/content/about-events.md b/content/about-events.md new file mode 100644 index 0000000..03bed95 --- /dev/null +++ b/content/about-events.md @@ -0,0 +1,53 @@ +--- +title: "About NWB Events" +bg_image: "/images/events/default-event-banner.png" +image: "/images/events/default-event-banner.png" +summary: "Information about Neurodata Without Borders (NWB) events, including their purpose, types, and history." +draft: false +type: "page" +--- + +## What are NWB events? + +The [Neurodata Without Borders](https://www.nwb.org/) (NWB) events are hands-on gatherings lasting several days in which neurophysiology researchers create solutions using the open source NWB 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 these events is to provide a venue for creators and users of neurophysiology open-source software to collaboratively work on related research projects. + +## Types of NWB Events + +Over the course of the NWB endeavor, the NWB team has created a range of different event types to address different needs: + +- **NeurodataReHack**: Focused on training and projects to generate new insights from existing neurophysiology data through secondary analysis. +- **User Days**: Focused on training and engagement with the NWB user community and integration of data and lab processes with NWB. +- **Developer Days**: Focused on engagement with the broader developer community and on integration and development of NWB-enabled tools and core software. +- **Docathon**: Focused on enhancing documentation for NWB and associated software. +- **NWB Core Hackathons**: These hackathons focus on development of the core NWB data standard and software. This includes in particular the 1st, 2nd, and 3rd hackathon. +- **Workshops and Tutorials**: Focused on introducing NWB to new users and providing hands-on training in specific contexts, such as at conferences or institutions. + +## History of NWB Events + +The NWB 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 and other events are a way for us to collaborate and develop NWB as well as to engage with the NWB user community. + +### NWB 1.x (2014-2017) +The NWB initiative began with the development of NWB 1.x, during which two hackathons were held at Janelia Research Campus in Ashburn, Virginia: +- The first hackathon on November 20–22, 2014 +- The second hackathon on May 14-16, 2015 + +### NWB 2.0 and Beyond (2017-Present) +As part of the development of NWB 2.0, a third hackathon was held at Janelia Research Campus on July 31 - August 1, 2017. The primary focus of the first three hackathons was on development of the NWB format as well as on development of a software strategy for NWB. + +To encourage the development, growth and use of NWB as a unified data format for cellular-based neurophysiology data, the Allen Institute for Brain Science, Lawrence Berkeley National Lab, and Kitware organized 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, 2018). + +Since then, the NWB team has continued to organize various types of events to support the growing NWB community, including: + +- Regular User Days and Developer Days events +- Docathons to improve documentation +- NeurodataReHack events focused on data reuse +- Conference tutorials and workshops +- Virtual events during the COVID-19 pandemic + +As of 2025, the NWB ecosystem has grown significantly, with over 300 datasets on the DANDI Archive in NWB format, including data from the Allen Institute, the International Brain Laboratory, and many individual labs. The hackathons and other events continue to play a crucial role in the development and adoption of NWB as a standard for neurophysiology data. + +## Upcoming Events + +For information about upcoming NWB events, please visit our [Events page](/events/). diff --git a/content/event-cards/_index.md b/content/event-cards/_index.md deleted file mode 100644 index f4c073a..0000000 --- a/content/event-cards/_index.md +++ /dev/null @@ -1,17 +0,0 @@ ---- -title: Events -intro_section: - enable: true - image: /images/hackathons.png - title: NWB Hackathons - content: The NWB Hackathons are hands-on activities lasting several days in - which neurophysiology researchers and software developers create solutions - using the open source NWB software ecosystem.

Participants work - collaboratively on solutions that use the NWB unified data format for - cellular-based neurophysiology data. In contrast to conferences and - workshops where the primary focus is to report results, the objective of the - Hackathons is to provide a venue for creators and users of neurophysiology - open-source software to collaboratively work on NWB-related research - projects.

For more information about past and upcoming hackathons, - see here. ---- diff --git a/content/event-cards/nwb-dandi.md b/content/event-cards/nwb-dandi.md deleted file mode 100644 index e95ed7d..0000000 --- a/content/event-cards/nwb-dandi.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: "2022 NWB-DANDI Remote Developer Hackathon!" -date: 2024-07-15 -lastDate: 2024-07-18 -comments: 12 -time: "9:00 - 3:00" -register_btn: / -weight: 1 ---- \ No newline at end of file diff --git a/content/event-cards/nwb-dandi2.md b/content/event-cards/nwb-dandi2.md deleted file mode 100644 index f26d397..0000000 --- a/content/event-cards/nwb-dandi2.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: "2022 NWB-DANDI Remote Developer Hackathon!" -date: 2024-07-15 -lastDate: 2024-07-22 -comments: 12 -time: "9:00 - 3:00" -register_btn: / -weight: 2 ---- \ No newline at end of file diff --git a/content/event-cards/nwb-dandi3.md b/content/event-cards/nwb-dandi3.md deleted file mode 100644 index 8ef14d9..0000000 --- a/content/event-cards/nwb-dandi3.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: "2022 NWB-DANDI Remote Developer Hackathon!" -date: 2024-07-20 -lastDate: 2024-07-22 -comments: 12 -time: "9:00 - 3:00" -register_btn: / -weight: 3 ---- \ No newline at end of file diff --git a/content/event-cards/nwb-dandi4.md b/content/event-cards/nwb-dandi4.md deleted file mode 100644 index a82940f..0000000 --- a/content/event-cards/nwb-dandi4.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: "2022 NWB-DANDI Remote Developer Hackathon!" -date: 2024-07-15 -lastDate: 2024-07-18 -comments: 12 -time: "9:00 - 3:00" -register_btn: / -weight: 4 ---- \ No newline at end of file diff --git a/content/event-cards/nwb-dandi5.md b/content/event-cards/nwb-dandi5.md deleted file mode 100644 index 7764c9a..0000000 --- a/content/event-cards/nwb-dandi5.md +++ /dev/null @@ -1,9 +0,0 @@ ---- -title: "2022 NWB-DANDI Remote Developer Hackathon!" -date: 2024-07-28 -lastDate: 2024-07-30 -comments: 12 -time: "9:00 - 3:00" -register_btn: / -weight: 5 ---- \ No newline at end of file diff --git a/content/events/_index.md b/content/events/_index.md index e87a38f..2404eba 100644 --- a/content/events/_index.md +++ b/content/events/_index.md @@ -1,43 +1,8 @@ --- -title: "NeuroDataReHack" -subtitle: "Generate new insights from existing neurophysiology data through secondary analysis" -date: 2023-09-12 -hero_image: "/images/essentials/eventsImg.png" - -### Insights -insight_section: +title: "NWB Events" +banner: enable: true - list_title: "NeuroDataReHack 2023" - title: "Generate new insights from existing neurophysiology data through secondary analysis" - insights: - - title: "Report" - content: "The final report for NeuroDataReHack 2023 is now available online at [PDF (GitHub)] [LaTeX (Overleaf)]." - - title: "Dates and Location" - content: "Dates: September 5-8, 2023

Location: Hotel Andalucia Center in Granada, Spain (google maps)" - - title: "Objective" - content: "The DANDI Archive now has 110+ neurophysiology datasets in the Neurodata Without Borders format spanning many species, brain areas, task types, and imaging modalities. These include high-value datasets, e.g. from The Allen Institute, the MICrONS project, and the International Brain Laboratory, as well as diverse contributions from neuroscience labs around the world. In this workshop, we will teach attendees about the open neurophysiology datasets available on the DANDI Archive and train them on how to maximally utilize the archive and the NWB standard to incorporate existing data into their scientific workflows. Feedback from attendees will be used to improve the software and data standard to better enable reanalysis workflows.

Prior to the workshop, we are organizing Open Neurodata Showcase where attendees can meet the contributors behind the neurophysiology datasets and explore virtual posters. Visit the event page to sign up and read more about this feature event.

Example projects include but are not limited to:
  • Determine whether your result is present in another species or brain area.
  • Showcase the capabilities of your tool or analysis on existing data from another lab.
  • Explore follow-up questions to a study.


    • Following the event, participants will be invited to apply for a Kavli Foundation Neurodata Discovery Award, which awards $50,000 (USD) of funding to continue data reanalysis projects that come out of the NeuroDataReHack event. Details about the Kavli Foundation Neurodata Discovery Award will be provided closer to the event.

    This event is held as a satellite of the IBRO World Congress 2023 with the goal of making it more accessible to diverse participants who might not otherwise have the opportunity to participate in this workshop. Attendance of IBRO 2023 is not a requirement for application.

    This event will primarily focus on analyzing existing data in NWB and on DANDI, not converting data to NWB. If you are interested in learning how to convert data, consider signing up for an NWB User Days event." - - title: "Eligibility" - content: "This course is intended for PhD students, postdoctoral researchers, principal investigators, or similar. Applicants should have basic programming experience in Python or MATLAB and experience with neurophysiology research." - - title: "Application" - subtitle: "Applications are now closed." - content: "Space for the event is limited. Apply to attend NeuroDataReHack 2023 here.
  • Application deadline: May 8
  • Notification of admission decisions: June 1
    • " - - title: "Logistics" - subtitle: "Thanks to the generous sponsorship of The Kavli Foundation, this event will be free to participants:" - content: "Space for the event is limited. Apply to attend NeuroDataReHack 2023 here.
  • There is no registration or application fee.
  • Participants will be provided a private room at the Hotel Andalucia Center Hotel for the duration of this event, checking in on Monday, September 4 and checking out on Saturday, September 9th, the day that the IBRO conference starts. Note that we previously stated that check out would be on Friday, September 8th.
    • " - - title: "Organizing Committee" - subtitle: "Program chairs:" - content: "
  • Benjamin Dichter, CatalystNeuro
  • Oliver Rübel, Lawrence Berkeley National Laboratory
  • Ryan Ly, Lawrence Berkeley National Laboratory
  • Stephanie Albin, The Kavli Foundation
    • " - - title: "Resources" - subtitle: "Resources will be posted here to help participants prepare for the event." - content: "
  • A report of the first NeuroDataReHack event: (PDF)
  • Recordings of talks will be made available on the NWB Youtube channel.
    • " - - title: "What to bring?" - content: "Bring a laptop with appropriate software installed. Python should be installed and MATLAB is optional. For instructions on how to install PyNWB, see the PyNWB documentation. For instructions on how to install MatNWB, see the MatNWB documentation
  • A report of the first NeuroDataReHack event: (PDF)
  • Recordings of talks will be made available on the NWB Youtube channel.
    • " - - title: "What to bring?" - subtitle: "Tentative schedule:" - pdf: "/images/time.pdf" - -### Disclaimer -discalimer: - enable: true - content: "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." ---- \ No newline at end of file + title: "NWB Events" + content: "Explore past and upcoming events related to Neurodata Without Borders (NWB). These events include workshops, hackathons, tutorials, and conferences aimed at advancing the NWB data standard and fostering collaboration within the neuroscience community." + image: "/images/events/events-banner.png" +--- diff --git a/content/events/cosyne-2019.md b/content/events/cosyne-2019.md new file mode 100644 index 0000000..325fcd9 --- /dev/null +++ b/content/events/cosyne-2019.md @@ -0,0 +1,46 @@ +--- +title: "Cosyne 2019, NWB Tutorial" +date: 2019-03-04 +endDate: 2019-03-04 +location: "Hotel Miragem Cascais, Cascais, Portugal" +eventType: "Tutorial" +image: "/images/events/default-event-banner.png" +weight: 20190304 +summary: "A tutorial session on the NWB:N data standard and on using PyNWB and MatNWB at the Computational and Systems Neuroscience (Cosyne) 2019 Workshops." +draft: false +organizers: + - "Ben Dichter" + - "Oliver Ruebel, LBNL" + - "Stephanie Albin, Kavli Foundation" +registration: "Registration is now closed." +resources: + "NWB:N 2.0: Overview": "https://drive.google.com/open?id=1Dq7zhQ4weiGv-3m6zD11ZrHQcObuddik" + "Electrophysiology tutorial slides": "https://docs.google.com/presentation/d/1Q03wU6NzMTOwuWaZIANtldNT-8ZKeM0fk3b0mEI-JFc/edit?usp=sharing" + "Python jupyter notebook": "http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/master/Cosyne_2019/cosyne_NWB_tutorial_2019_python.html" + "MATLAB code": "http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/master/Cosyne_2019/cosyne_NWB_tutorial_2019_matlab.html" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/Cosyne_2019" +--- + +## Dates and Location + +- **Date/Time:** March 4, 2019, 1-4pm +- **Location:** Hotel Miragem Cascais, Av.Marginal n.8554 ​ 2754-536 Cascais, Portugal +- **Room:** Sala XVI + +## Overview + +The [Neurodata Without Borders: Neurophysiology (NWB:N)](https://neurodatawithoutborders.github.io/) team held a tutorial on the NWB:N data standard and on using [PyNWB](https://neurodatawithoutborders.github.io/pynwb) and [MatNWB](https://neurodatawithoutborders.github.io/matnwbemb) at the Cosyne 2019 Workshops. + +The [NWB:N project](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. NWB:N is more than just a file format but it defines an [ecosystem](https://neurodatawithoutborders.github.io/overview) of tools, methods, and standards for storing, sharing, and analyzing complex neurophysiology data. + +The team had recently released [NWB:N 2.0](https://neurodatawithoutborders.github.io/news), and was excited to teach the user-base and potential new users about NWB:N and the software tools. + +## Tutorial Program + +- NWB:N 2.0: Overview +- Electrophysiology tutorial +- Python and MATLAB code examples + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/cosyne-2023.md b/content/events/cosyne-2023.md new file mode 100644 index 0000000..d0e8877 --- /dev/null +++ b/content/events/cosyne-2023.md @@ -0,0 +1,59 @@ +--- +title: "DANDI+NWB Tutorial at COSYNE 2023" +date: 2023-03-09 +endDate: 2023-03-09 +location: "Fairmont The Queen Elizabeth, Montreal, Canada" +eventType: "Tutorial" +image: "/images/events/cosyne-2023/dandi-logo.png" +weight: 20230309 +summary: "A tutorial on the DANDI Archive and NWB data standard, teaching participants how to find relevant data, stream NWB data, and process and analyze neurophysiology data using popular tools." +draft: false +organizers: + - "Ryan Ly, LBNL" + - "Cody Baker, CatalystNeuro" + - "Stephanie Albin, Kavli Foundation" +registration: "There is NO additional fee to attend. When registering for the main meeting, select the Dandi Archive for Neurophysiology Data and the Neurodata Without Borders Data Standard Tutorial." +resources: + "DANDI Search (PDF)": "/images/events/cosyne-2023/COSYNE 2023 DANDI Search.pdf" + "Optical Physiology (PDF)": "/images/events/cosyne-2023/COSYNE 2023 Optical Physiology.pdf" + "Pose Estimation (PDF)": "/images/events/cosyne-2023/COSYNE 2023 Pose Estimation.pdf" + "NWB Documentation": "https://nwb-overview.readthedocs.io/en/latest/index.html" +--- + +## Welcome to the DANDI+NWB Tutorial at COSYNE 2023! + +The [Neurodata Without Borders (NWB)](https://www.nwb.org/) team is holding a tutorial on the [DANDI Archive](https://www.dandiarchive.org/) and NWB data standard and on using [PyNWB](https://pynwb.readthedocs.io/en/stable/) and [MatNWB](https://neurodatawithoutborders.github.io/matnwb) at the COSYNE 2023 tutorial session. + +The DANDI Archive now has 100+ publicly available neurophysiology datasets stored using the NWB data standard. + +The NWB project 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. NWB is more than just a file format but it defines an [ecosystem](https://nwb-overview.readthedocs.io/en/latest/tools/tools_home.html) of tools, methods, and standards for storing, sharing, and analyzing complex neurophysiology data. + +## What You'll Learn + +At this tutorial, we'll teach you how to: + +- Find relevant data on the DANDI Archive and use the DANDI compute resources +- Stream NWB data from DANDI and read an NWB file in Python and MATLAB +- Process NWB data using popular tools such as SpikeInterface and suite2p +- Analyze NWB data using tools such as Pynapple, SSM, or your own scripts + +Bring your laptop to work along with the demonstration. To get familiar with NWB and DANDI prior to attending, please refer to this [documentation](https://nwb-overview.readthedocs.io/en/latest/index.html). + +## Tutorial Program + +- **8:00 - 8:30**: Introduction to the NWB data standard and DANDI Archive +- **8:30 - 8:55**: How to find relevant data on the DANDI archive and use the DANDI Hub +- **8:55 - 9:00**: Break +- **9:00 - 9:20**: How to read and explore an NWB file in Python and MATLAB +- **9:20 - 9:50**: How to analyze NWB data using popular data processing and visualization tools + - Using [SpikeInterface](https://github.com/SpikeInterface/spikeinterface#spikeinterface-a-unified-framework-for-spike-sorting) to sort raw extracellular electrophysiology recording data streamed from DANDI & write the output back to NWB + - Storing [DeepLabCut](http://www.mackenziemathislab.org/deeplabcut) and [SLEAP](https://sleap.ai/) pose estimation data in NWB + - Using calcium imaging analysis tools, such as [CaImAn](https://github.com/flatironinstitute/CaImAn#caiman) and [suite2p](https://www.suite2p.org/) to process and segment raw imaging data and write the output to NWB + +## Survey + +If you attended the tutorial, please fill out this [2-minute survey](https://bit.ly/nwb-cosyne-survey) to give us feedback on what your data needs are and how did this tutorial go for you. Thank you. + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/cosyne-2024.md b/content/events/cosyne-2024.md new file mode 100644 index 0000000..c18bb76 --- /dev/null +++ b/content/events/cosyne-2024.md @@ -0,0 +1,53 @@ +--- +title: "NWB & DANDI Tutorial at COSYNE 2024" +date: 2024-02-29 +location: "Lisbon Conference Center, Lisbon, Portugal" +eventType: "Tutorial" +image: "/images/events/cosyne-2024/nwb+dandi_logo.png" +weight: 20240229 +summary: "The NWB team held a tutorial on the NWB data standard and DANDI Archive during the tutorial session of COSYNE 2024, teaching attendees how to convert neurophysiology data to NWB, publish it on DANDI, find relevant data, and analyze NWB data using popular tools." +draft: false +organizers: + - "Ryan Ly, LBNL" + - "Ben Dichter, CatalystNeuro" + - "Alessio Buccino, CatalystNeuro and Allen Institute for Neural Dynamics" +--- + +# Welcome to the NWB & DANDI Tutorial at COSYNE 2024! + +The [Neurodata Without Borders (NWB)](https://www.nwb.org/) team held a tutorial on the NWB data standard and [DANDI Archive](https://www.dandiarchive.org/) during the [tutorial session of COSYNE 2024](https://www.cosyne.org/tutorials). + +The [NWB](https://www.nwb.org/) project 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 analyzing data both within and across labs. NWB is more than just a file format; it defines an [ecosystem](https://nwb-overview.readthedocs.io/en/latest/tools/analysis_tools_home.html) of tools, methods, and standards for storing, sharing, and analyzing neurophysiology data, including extracellular electrophysiology, intracellular electrophysiology, optical physiology, and behavior. + +The [DANDI Archive](https://www.dandiarchive.org/) now has 175+ publicly available neurophysiology datasets stored using the NWB data standard, including from the Allen Institute, International Brain Laboratory, MICRONS project, and over 100 individual labs. + +At this tutorial, we taught attendees how to: + +- Convert neurophysiology data to NWB and publish it on the DANDI Archive +- Find relevant data on the DANDI Archive and use the DANDI compute resources +- Read NWB data streamed from DANDI or downloaded locally +- Process and analyze NWB data using popular tools such as SpikeInterface and Pynapple + +## Dates and Location + +* **Date/Time:** February 29, 2024, 8:00 - 9:30 AM +* **Location:** Lisbon Conference Center, Lisbon, Portugal + +## Tutorial Program + +8:00 - 8:30: Lecture: Introduction to the NWB data standard and DANDI Archive + +8:30 - 8:45: Follow along: Convert common neurophysiology data formats to NWB and publish NWB data to DANDI + +8:45 - 9:00: Follow along: Use the DANDI Archive and community tools, such as [Neurosift](https://github.com/flatironinstitute/neurosift) and [NWB Widgets](https://nwb-widgets.readthedocs.io/en/latest/), to find and visualize relevant data + +9:00 - 9:30: Follow along: Read NWB data streamed from DANDI and downloaded locally, and analyze NWB data using popular tools, such as: + +- [SpikeInterface](https://github.com/SpikeInterface/spikeinterface#spikeinterface-a-unified-framework-for-spike-sorting) to spike sort raw extracellular electrophysiology recording data streamed from DANDI & write the output back to NWB +- [Pynapple](https://pynapple-org.github.io/pynapple/) to perform common analysis functions on NWB data, such as compute tuning curves and cross-correlograms + +## Learn more! + +Learn more about upcoming and past NWB events on our [main page](https://neurodatawithoutborders.github.io/nwb_hackathons/). + +New to NWB? Learn more about the NWB software ecosystem, how to convert data to NWB, how to read data in NWB, and much more in our [NWB Overview website](https://nwb-overview.readthedocs.io/). diff --git a/content/events/cosyne-2025.md b/content/events/cosyne-2025.md new file mode 100644 index 0000000..bb837cf --- /dev/null +++ b/content/events/cosyne-2025.md @@ -0,0 +1,47 @@ +--- +title: "NWB & DANDI Tutorial at COSYNE 2025" +date: 2025-03-27 +location: "Agora-Centreville Room, Fairmont Queen Elizabeth, Montreal, QC, Canada" +eventType: "Tutorial" +image: "/images/events/cosyne-2025/nwb+dandi_logo.png" +weight: 20250327 +summary: "A tutorial on the NWB data standard and DANDI Archive during COSYNE 2025, teaching participants how to share neurophysiology data using NWB and DANDI, and how to use NWB data available on DANDI." +draft: false +organizers: + - "Ryan Ly, LBNL" + - "Ben Dichter, CatalystNeuro" +--- + +# NWB & DANDI Tutorial at COSYNE 2025 + +The [Neurodata Without Borders (NWB)](https://www.nwb.org/) team is holding a tutorial on the NWB data standard and [DANDI Archive](https://www.dandiarchive.org/) during the [tutorial session of COSYNE 2025](https://www.cosyne.org/tutorials). + +The goal of this tutorial is to teach you how to share your neurophysiology data using the [Neurodata Without Borders (NWB)](https://www.nwb.org/) data standard and the [DANDI Archive](https://www.dandiarchive.org/) and how to use NWB data available on DANDI. NWB standardizes the storage of neurophysiology data and metadata to facilitate data analysis, sharing, and reuse. The DANDI Archive now has 300+ TB of neurophysiology data across 300+ publicly available datasets in NWB, including from the Allen Institute, International Brain Laboratory, MICRONS project, and over 150 individual labs. In this tutorial, we will introduce several new tools to convert data to NWB, publish data to DANDI, and stream data from DANDI. We will also introduce new community tools for data analysis and management that are integrated with NWB, so this tutorial will be useful for both new and returning attendees. + +## What You'll Learn + +At this tutorial, we will teach you how to: +- Convert neurophysiology data to NWB and publish it on DANDI using the new [NWB GUIDE app](https://nwb-guide.readthedocs.io/en/stable/) and other tools +- Read local NWB data using Python and MATLAB, and efficiently stream remote NWB data on DANDI using the new LINDI tool +- Process, analyze, and manage NWB data using popular community tools, including tools that have not previously presented as part of this tutorial + +Bring your laptop to work along with the demonstration. To get familiar with NWB and DANDI prior to attending, please refer to this [documentation](https://nwb-overview.readthedocs.io/en/latest/index.html). + +## Dates and Location + +- **Date/Time:** March 27, 2025, 9:00 - 10:30 AM +- **Location:** Agora-Centreville Room, Fairmont Queen Elizabeth, Montreal, QC, Canada + +## Registration + +There is NO additional fee to attend. When registering for the main meeting, select the "NWB Data Standard and DANDI Archive for Neurophysiology Tutorial". + +## Tutorial Program + +The detailed program will be announced closer to the event date. + +## Learn More + +Learn more about upcoming and past NWB events on our [main page](https://neurodatawithoutborders.github.io/nwb_hackathons/). + +New to NWB? Learn more about the NWB software ecosystem, how to convert data to NWB, how to read data in NWB, and much more in our [NWB Overview website](https://nwb-overview.readthedocs.io/). diff --git a/content/events/docathon-2025.md b/content/events/docathon-2025.md new file mode 100644 index 0000000..c624bd3 --- /dev/null +++ b/content/events/docathon-2025.md @@ -0,0 +1,71 @@ +--- +title: "NWB Docathon 2025" +date: 2025-05-01 +endDate: 2025-05-02 +location: "Virtual" +eventType: "Docathon" +image: "/images/events/default-event-banner.png" +weight: 20250501 +summary: "A virtual event focused on updating, improving, and expanding NWB documentation to ensure it is up-to-date and accessible to new and existing users." +draft: false +organizers: + - "NWB Team" +registration: "Register for the event [here](https://forms.gle/YA5LBR4iSG8UVgpf6)." +resources: + "NWB Documentation Survey": "https://forms.gle/ihC8xLDeSX5XKyXN8" + "PyNWB Issues": "https://github.com/NeurodataWithoutBorders/pynwb/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22topic%3A%20docs%22&page=1" + "MatNWB Issues": "https://github.com/NeurodataWithoutBorders/matnwb/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22topic%3A%20docs%22" + "NWB Schema Issues": "https://github.com/NeurodataWithoutBorders/nwb-schema/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22topic%3A%20docs%22" +--- + +## Dates and Location + +- **Dates:** May 1-2, 2025 +- **Location:** Virtual + +## Objective + +The [Neurodata Without Borders](https://nwb.org) project 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. NWB has seen wide adoption in the neurophysiology community, and there are now over 300 datasets on the DANDI Archive in NWB, including data from the Allen Institute and the International Brain Laboratory. + +One of the goals of NWB is to ensure that members of the neuroscience community have the resources and tools to easily interact with their data. We are hosting a dedicated docathon to invite members of the community to join us in updating, improving, and expanding our documentation. The goal of this workshop is to make sure our documentation and educational materials are up-to-date and accessible to new and existing users of NWB. + +Many types of contributions are welcome, including updates to: + +- Tutorials +- How-to guides +- Docstrings +- User documentation +- Developer documentation +- Recorded demo videos + +If you cannot attend but there is a particular gap or aspect of the documentation you think could use improvement, please submit a documentation issue on the relevant GitHub repo. + +**Note:** All levels of experience are welcome! We have several existing open issues and welcome new contributors. + +## Survey + +To let us know about your experience with NWB documentation, please feel free to complete the [NWB Documentation Survey](https://forms.gle/ihC8xLDeSX5XKyXN8) even if you are unable to participate in the Docathon. This survey is a great way to help us better understand your experience with the NWB documentation and how we can improve! + +## Logistics + +We will use Zoom for the meeting and will send an email with a link to all registrants. + +## What to bring? + +If you have any particular documentation issues you are interested in working on, feel free to open a new issue or comment on an existing issue in advance: +- [PyNWB issues](https://github.com/NeurodataWithoutBorders/pynwb/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22topic%3A%20docs%22&page=1) +- [MatNWB issues](https://github.com/NeurodataWithoutBorders/matnwb/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22topic%3A%20docs%22) +- [NWB Schema issues](https://github.com/NeurodataWithoutBorders/nwb-schema/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22topic%3A%20docs%22) + +## Agenda + +The tentative agenda is below. All times are in Pacific Time (PT): + +### May 1st: +- 9:00AM - 9:30AM: Introduction to the docathon +- 9:30AM - 10:00AM: Project discussion +- 10:00AM - 5:00PM: Documenting / hacking + +### May 2nd: +- 9:00AM - 9:30AM: Project check-in and discussion +- 9:30AM - 5:00PM: Documenting / hacking diff --git a/content/events/docuthon-2022-september.md b/content/events/docuthon-2022-september.md new file mode 100644 index 0000000..ce0b056 --- /dev/null +++ b/content/events/docuthon-2022-september.md @@ -0,0 +1,48 @@ +--- +title: "Docathon: September 2022" +date: 2022-09-22 +endDate: 2022-09-23 +location: "Virtual" +eventType: "Docathon" +image: "/images/events/default-event-banner.png" +weight: 20220922 +summary: "A virtual event focused on improving documentation and tutorials for the NWB APIs, schema, and community tools that use NWB." +draft: false +organizers: + - "Oliver Ruebel" + - "Benjamin Dichter" + - "Ryan Ly" + - "Matthew Avaylon" +registration: "Registration is now closed." +resources: + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/Docuthon_2022_09" +--- + +## Dates and Location + +- **Dates:** September 22-23, 2022 +- **Location:** Virtual (Anywhere with an internet connection) + +## Overview + +The workshop focused primarily on improving documentation and tutorials for the NWB APIs, schema, and community tools that use NWB. + +## Objective + +The Neurodata Without Borders project (NWB, [https://www.nwb.org/](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 purpose of the NWB Docathon was to bring users and developers of the experimental neurophysiology community together to improve documentation and tutorials for the NWB APIs, schema, and community tools that use NWB. + +## How to prepare? + +Install the Python or MATLAB software for NWB: + * PyNWB (Python): [https://pynwb.readthedocs.io/en/stable/install_users.html](https://pynwb.readthedocs.io/en/stable/install_users.html) + * MatNWB (MATLAB): [https://neurodatawithoutborders.github.io/matnwb/#setup](https://neurodatawithoutborders.github.io/matnwb/#setup) + +## Projects + +Participants were encouraged to add their specific projects to a shared Google document to coordinate efforts during the event. + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/docuthon-2022-spring.md b/content/events/docuthon-2022-spring.md new file mode 100644 index 0000000..5937059 --- /dev/null +++ b/content/events/docuthon-2022-spring.md @@ -0,0 +1,49 @@ +--- +title: "Docathon Spring 2022" +date: 2022-03-10 +endDate: 2022-03-11 +location: "Virtual" +eventType: "Docathon" +image: "/images/events/default-event-banner.png" +weight: 20220310 +summary: "A virtual event focused on improving documentation and tutorials for the NWB APIs, schema, and community tools that use NWB." +draft: false +organizers: + - "Oliver Ruebel" + - "Benjamin Dichter" + - "Ryan Ly" + - "Matthew Avaylon" +registration: "Registration is now closed." +resources: + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/Docuthon_2022" + "NWB Documentation Survey": "https://forms.gle/TadZBRKJpwEWeErv8" +--- + +## Dates and Location + +- **Dates:** March 10-11, 2022 +- **Location:** Virtual (Anywhere with an internet connection) + +## Overview + +The workshop focused primarily on improving documentation and tutorials for the NWB APIs, schema, and community tools that use NWB. + +## Objective + +The Neurodata Without Borders project (NWB, [https://www.nwb.org/](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 purpose of the NWB Docathon was to bring users and developers of the experimental neurophysiology community together to improve documentation and tutorials for the NWB APIs, schema, and community tools that use NWB. + +## How to prepare? + +Install the Python or MATLAB software for NWB: + * PyNWB (Python): [https://pynwb.readthedocs.io/en/stable/install_users.html](https://pynwb.readthedocs.io/en/stable/install_users.html) + * MatNWB (MATLAB): [https://neurodatawithoutborders.github.io/matnwb/#setup](https://neurodatawithoutborders.github.io/matnwb/#setup) + +## Survey + +The organizers conducted a survey to learn about users' experience with the NWB documentation and to gather feedback on how to improve the experience with NWB. The survey was a great way to give back by helping the organizers better understand users' experience with the NWB documentation. + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/hck03-2017-janelia.md b/content/events/hck03-2017-janelia.md new file mode 100644 index 0000000..4259dc2 --- /dev/null +++ b/content/events/hck03-2017-janelia.md @@ -0,0 +1,37 @@ +--- +title: "3rd Hackathon" +date: 2017-07-31 +endDate: 2017-08-01 +location: "HHMI Janelia Research Campus, Ashburn, VA" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20170731 +summary: "A small gathering of active users and programmers of the NWB:Neurophysiology data format to discuss future development for the format and API, held at HHMI Janelia Research Campus." +draft: false +organizers: + - "The Kavli Foundation" +registration: "Registration is now closed." +resources: + "Event Page": "https://www.nwb.org/event/nwb-hackathon-july-2017/" +--- + +## Dates and Location + +- **Dates:** July 31, 2017 (9:00 am) - August 1, 2017 (4:00 pm) +- **Location:** HHMI Janelia Research Campus, 19700 Helix Dr, Ashburn, VA 20147 + +## Overview + +A small group of active users and programmers of the NWB:Neurophysiology data format representing a broad and deep range of interests and expertise gathered to discuss future development for the format and API. This small gathering was held at HHMI Janelia Research Campus near Washington, DC's Dulles Airport beginning at 9 am on Monday, July 31 and concluding at 4 pm on Tuesday, August 1, 2017. + +Since this was an active and interactive exchange of ideas and code, participants were asked to bring sample datasets and relevant documentation to the meeting so that issues could be raised and addressed in real-time. + +## Objective + +As part of the development of NWB 2.0, this hackathon was one of the core NWB hackathons that focused on the development of the NWB data standard and software. The primary focus was on the development of the NWB format as well as on the development of a software strategy for NWB. + +The Neurodata Without Borders: Neurophysiology project (NWB:N) 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 analysis both within and across labs. + +## Organizer + +- The Kavli Foundation diff --git a/content/events/hck04-2018-seattle.md b/content/events/hck04-2018-seattle.md new file mode 100644 index 0000000..b6fa3f5 --- /dev/null +++ b/content/events/hck04-2018-seattle.md @@ -0,0 +1,55 @@ +--- +title: "4th Hackathon" +date: 2018-04-03 +endDate: 2018-04-06 +location: "Allen Institute for Brain Science, Seattle, WA, USA" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20180403 +summary: "A hands-on event where neurophysiology researchers collaborated on solutions using the open source NWB:N software packages, hosted at the Allen Institute for Brain Science." +draft: false +organizers: + - "Lynne Becker" + - "Lydia Ng" + - "Nick Cain" + - "Justin Kiggins" +registration: "Registration is now closed." +resources: + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK04_2018_Seattle" +--- + +## Dates and Location + +- **Dates:** April 3 (12:00 PM)-6 (3:00 PM), 2018 +- **Location:** [Allen Institute for Brain Science, Seattle, WA](https://www.google.com/maps/place/Allen+Institute/@47.6251853,-122.3412859,17z/data=!3m1!4b1!4m5!3m4!1s0x5490150705cb5703:0x499c58d72a7bcf9!8m2!3d47.6251817!4d-122.3390919) + +## Objective + +The [Neurodata Without Borders: Neurophysiology](http://www.nwb.org/nwb-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. + +## Projects + +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 + +- Contributing to PyNWB, CI, and Development Process +- Visualization +- Read API +- User Adoption + +## Additional Organizational Support +- The Kavli Foundation diff --git a/content/events/hck05-2018-berkeley.md b/content/events/hck05-2018-berkeley.md new file mode 100644 index 0000000..c92ece3 --- /dev/null +++ b/content/events/hck05-2018-berkeley.md @@ -0,0 +1,49 @@ +--- +title: "User Days, 2018" +date: 2018-04-26 +endDate: 2018-04-27 +location: "Lawrence Berkeley National Laboratory, Berkeley, CA, USA" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20180426 +summary: "A two-day event at Lawrence Berkeley National Laboratory focused on training new users on NWB:N, promoting adoption, and facilitating communication between users and developers." +draft: false +organizers: + - "Oliver Ruebel" + - "Andrew Tritt" + - "Kristofer Bouchard" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK05_2018_Berkeley/report/report-5th-nwbn-hackathon-at-lbnl.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK05_2018_Berkeley" +--- + +## Dates and Location + +- **Dates:** April 26-27, 2018 +- **Location:** [Lawrence Berkeley National Laboratory, Berkeley, CA, USA](https://www.google.com/maps/place/Building+59+-+Shyh+Wang+Hall/@37.87585,-122.2540609,16.75z/data=!4m8!1m2!2m1!1sLBNL+Building+59!3m4!1s0x80857c3cbb4f1a65:0x8ba74e1cfa0e0623!8m2!3d37.8761533!4d-122.2530404), Building 59 - Shyh Wang Hall, Room 4102 + +## Objective + +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 invited experts from the neuroscience community to explore adopting NWB:N for their data sharing needs and lab use cases. The goal of this event was to: +- Train new users on NWB:N +- Promote adoption of NWB:N +- Work with users on programming projects, e.g, to integrate examples of their labs data into NWB:N +- Facilitate communication between users and developers and project teams +- Engage with the community + +## Slides and Materials + +- **Agenda** [[PDF]](https://drive.google.com/file/d/15epI5yUImoHcPYrsxSJQgR2d7AfLa52P/view?usp=sharing) +- **Online Tutorials**, The online tutorials for PyNWB that were used and mentioned in the talks are available [here](http://pynwb.readthedocs.io/en/latest/tutorials/index.html) +- **Welcome to the NWB:N Hackathon @ LBNL**, Oliver Ruebel, 04/26/2018, 8am [[PDF]](https://drive.google.com/file/d/1cb3qJyMqlR8ZQGZaka4IU5z5WVYkQ1KD/view?usp=sharing) +- **Neurodata Without Borders**, Kris Bouchard, 04/26/2018, 8:10am [[PDF]](https://drive.google.com/file/d/1FQg6fY-sPFAlPBd3HeUkG3uhfuvUsWz7/view?usp=sharing) +- **Introduction to NWB:N -- An ecosystem for standardizing neurophysiology data**, Oliver Ruebel, 04/26/2018, 8:20am [[PDF]](https://drive.google.com/file/d/1SIcMshEl_e-0Gz6F3AVCs8s7osvhz1FS/view?usp=sharing) +- **NWB:N and PyNWB -- A Python API for standardizing neurophysiology data** Andrew Tritt, 04/26/2018, 8:40am [[PDF]](https://drive.google.com/file/d/0B0OrtDJsFqMranF2eER2aTlvQmxXbmhaU2lrTjR5OXlYWlI4/view?usp=sharing) +- **NWB:N I/O -- ephys**, Ben Dichter, 04/26/2018, 11:10am [[PDF]](https://drive.google.com/file/d/19lDEY-qePtNATbqx8CpvzUNK89LFcgdq/view?usp=sharing) + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/hck06-2019-janelia.md b/content/events/hck06-2019-janelia.md new file mode 100644 index 0000000..d8e946e --- /dev/null +++ b/content/events/hck06-2019-janelia.md @@ -0,0 +1,58 @@ +--- +title: "Developer Days 2019 and User Days 2019" +date: 2019-05-13 +endDate: 2019-05-16 +location: "HHMI Janelia Research Campus, Ashburn, VA" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20190513 +summary: "A four-day event at Janelia Research Campus with two days focused on user training and use-cases followed by two days focused on core development, bringing the experimental neurophysiology community together to further adoption and development of NWB:N." +draft: false +organizers: + - "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" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK06_2019_Janelia/report/Report___6th_NWB_N_Hackathon.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK06_2019_Janelia" + "Slides": "https://drive.google.com/drive/folders/18oG1rRJpluXQJJQaH4xbz6u58LXPiZbI?usp=sharing" +--- + +## 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](https://www.janelia.org/), 19700 Helix Dr, Ashburn, VA 20147, [Directions](https://www.janelia.org/directions) +- **Meeting Rooms:** For the meeting we had two rooms. The main room was *Synapse* and the breakout room was *Spectrum*. + +## 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 was 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 exchanged ideas and best practices for using NWB:N and the libraries, shared NWB:N based tools, surfaced common needs, solved bugs, made feature requests, brainstormed about future funding and collaboration, and made progress on current blockages. The event also enabled NWB:N developers and users to interact with each other to facilitate communication, gather requirements, and train users. + +The event was planned for 4 days, where the first two days focused on user training and use-cases followed by two days focused on core development. Work involved collaborative, open source software development, with a focus on use cases, tools, and core development. + +## Resources + +### Talks +The slides for the talks presented during the User Days are available [here.](https://drive.google.com/drive/folders/18oG1rRJpluXQJJQaH4xbz6u58LXPiZbI?usp=sharing) + +### Code + +Ben Dichter's electrophysiology tutorial (Day 1): + +* [python jupyter notebook](http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/master/HCK06_2019_Janelia/NWB_tutorial_2019_python.html) +* [matlab code](http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/master/HCK06_2019_Janelia/NWB_tutorial_2019_matlab.html) + +Tom Davidson's 'early adopter experiences' talk (Day 1): + +* [Repo containing notebooks in talk](https://github.com/LorenFrankLab/franklab-nwb-hack/tree/master/hackathon-6) + +## Additional Organizational Support + +- The Kavli Foundation +- Janelia HHMI diff --git a/content/events/hck07-2020-seattle.md b/content/events/hck07-2020-seattle.md new file mode 100644 index 0000000..e1a171d --- /dev/null +++ b/content/events/hck07-2020-seattle.md @@ -0,0 +1,37 @@ +--- +title: "Developer Days 2020" +date: 2020-02-03 +endDate: 2020-02-06 +location: "Allen Institute for Brain Science, Seattle, WA, USA" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20200203 +summary: "A development-focused hackathon centered around core NWB development, held at the Allen Institute for Brain Science in Seattle." +draft: false +organizers: + - "Site Chair: Lydia Ng and Pam Baker (Allen Institute for Brain Science)" + - "Program Chair: Oliver Ruebel (Lawrence Berkeley National Laboratory)" +registration: "Registration for this event is closed." +resources: + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK07_2020_Seattle" +--- + +## Dates and Location + +- **Dates:** Mon, Feb. 3 (12:00 PM) -- Thur. Feb. 6 (3:00 PM), 2020 +- **Location:** [Allen Institute for Brain Science, Seattle, WA](https://www.google.com/maps/place/Allen+Institute/@47.6251853,-122.3412859,17z/data=!3m1!4b1!4m5!3m4!1s0x5490150705cb5703:0x499c58d72a7bcf9!8m2!3d47.6251817!4d-122.3390919) + +## Objective + +This event was centered around core NWB development, bringing together developers and users to collaborate on improving the NWB ecosystem. The hackathon focused on development projects, breakout sessions, and advancing the NWB format and associated tools. + +## Logistics + +- **Hotel:** The Allen Institute organized a special rate at the Staybridge Suites, just 3 blocks from the institute. +- **Transportation:** Attendees were encouraged to use public transportation or park at a local garage. Additional details on getting to the Allen Institute are available [here](https://alleninstitute.org/events-training/getting-allen-institute/). +- **Food:** Lunch was provided at the Allen Institute. Breakfast and dinner were on attendees' own. + +## Additional Organizational Support + +- The Kavli Foundation +- Allen Institute for Brain Science diff --git a/content/events/hck08-2020-remote.md b/content/events/hck08-2020-remote.md new file mode 100644 index 0000000..9184e52 --- /dev/null +++ b/content/events/hck08-2020-remote.md @@ -0,0 +1,47 @@ +--- +title: "User Days Spring 2020" +date: 2020-05-12 +endDate: 2020-05-15 +location: "Virtual" +eventType: "Workshop" +image: "/images/events/default-event-banner.png" +weight: 20200512 +summary: "A virtual training workshop bringing together the experimental neurophysiology community to further adoption and development of NWB, the NWB software libraries, and scientific workflows that rely on NWB." +draft: false +organizers: + - "Benjamin Dichter" + - "Ryan Ly" + - "Andrew Tritt" + - "Pam Baker" + - "Oliver Rübel" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK08_2020_Remote/report/Report___8th_NWB_Hackathon.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK08_2020_Remote" +--- + +## Dates and Location + +- **Dates:** May 12-15, 2020 +- **Location:** Virtual (due to COVID-19) + +## Objective + +The Neurodata Without Borders: Neurophysiology project (NWB, [https://www.nwb.org/](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 was 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 exchanged ideas and best practices for using NWB and the libraries, shared NWB-based tools, surfaced common needs, solved bugs, made feature requests, brainstormed about future funding and collaboration, and made progress on current blockages. The event also enabled 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 was 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 was meant to foster community and collaboration around NWB, not competition. Participants were 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. + +## How to prepare? + +* Create a project page with an outline for your workshop project. +* 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](https://pynwb.readthedocs.io/en/stable/getting_started.html) + * MatNWB (MATLAB): [https://neurodatawithoutborders.github.io/matnwb/](https://neurodatawithoutborders.github.io/matnwb/) +* For an overview of NWB, see also: [https://www.nwb.org/](https://www.nwb.org/) + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/hck09-2020-remote.md b/content/events/hck09-2020-remote.md new file mode 100644 index 0000000..037a3f2 --- /dev/null +++ b/content/events/hck09-2020-remote.md @@ -0,0 +1,54 @@ +--- +title: "User Days Fall 2020" +date: 2020-09-21 +endDate: 2020-09-23 +location: "Virtual" +eventType: "Workshop" +image: "/images/events/default-event-banner.png" +weight: 20200921 +summary: "A virtual training workshop focused on user training for both beginners and advanced users of NWB, with breakout sessions featuring state-of-the-art data analysis, visualization, and management tools." +draft: false +organizers: + - "Ryan Ly" + - "Benjamin Dichter" + - "Andrew Tritt" + - "Pam Baker" + - "Oliver Rübel" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK09_2020_Remote/report/Report___9th_NWB_Hackathon.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK09_2020_Remote" +--- + +## Dates and Location + +- **Dates:** September 21-23, 2020 +- **Location:** Virtual (Anywhere with an internet connection) +- **Time:** 9am-6pm Central European Time (UTC+2) + +## Overview + +The workshop focused primarily on user training, including lessons for complete beginners to NWB and training in more advanced usage of NWB. There were breakout sessions where the developers of state-of-the-art data analysis, visualization, and management tools (e.g., CaImAn, SpikeInterface, DANDI, suite2p, DataJoint, and more) demonstrated their tools and showed how to use NWB with their tools. There was also time for attendees to work on NWB-related projects, such as converting data to NWB, using NWB-compatible software tools, or going through the NWB online tutorials. + +To accommodate researchers in Europe, the Middle East, and Africa, the workshop was held 9am-6pm Central European Time (UTC+2). + +## Objective + +The Neurodata Without Borders: Neurophysiology project (NWB, [https://www.nwb.org/](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 purpose of the NWB User Days training workshops is to bring the experimental neurophysiology community together to further the adoption and development of NWB, the NWB software libraries, and scientific workflows that rely on NWB. Members of the community exchange ideas and best practices for using NWB, share NWB-based tools, surface common needs, resolve coding issues, make feature requests, brainstorm about future collaboration, and make progress on current blockages. The event also enables NWB developers and users to interact with each other to facilitate communication, gather requirements, and train users. + +## Projects + +During the workshop, there was time to work on NWB-related projects to practice using the NWB software and ask questions to the NWB developers. Working on a project was optional but encouraged for attendees to get the most out of the workshop. + +Project suggestions included: +- Convert some of your or a collaborator's data to NWB +- Convert data from a public archive to NWB +- Integrate a software tool with NWB +- Work through NWB online tutorials +- Practice using NWB-compatible tools on publicly available NWB data, e.g., on [DANDI](https://dandiarchive.org/) + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/hck10-2021-remote.md b/content/events/hck10-2021-remote.md new file mode 100644 index 0000000..cd9613e --- /dev/null +++ b/content/events/hck10-2021-remote.md @@ -0,0 +1,55 @@ +--- +title: "Developer Days 2021 (NWB+DANDI)" +date: 2021-03-30 +endDate: 2021-04-01 +location: "Virtual" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20210330 +summary: "A remote hackathon event bringing together developers of the NWB data standard, the DANDI development team, and developers of tools in the NWB ecosystem to work intensively on NWB or DANDI-related projects." +draft: false +organizers: + - "NWB POC: Oliver Rübel" + - "DANDI POC: Satrajit S. Ghosh" + - "Program Committee: Ryan Ly, Benjamin Dichter, Andrew Tritt, Pam Baker, Oliver Rübel, Satrajit S Ghosh, Yaroslav O. Halchenko" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK10_2021_Remote/report/Report___10th_NWB_and_DANDI_Hackathon.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK10_2021_Remote" +--- + +## Dates and Location + +- **Pre-hackathon project pitch session:** Friday, March 19, 2021, 9am PST (12pm EST) +- **Dates:** Tuesday, March 30, 2021 - Thursday, April 1, 2021, 8am - 3pm PST (11am - 6pm EST) +- **Location:** Virtual (Anywhere with an internet connection) + +## Overview + +Neurodata Without Borders (NWB) and the DANDI neurophysiology data archive development teams joined together to create a remote hackathon event for developers. In contrast to the User Days hackathons that focus on training users, this event focused on bringing together the developers of the NWB data standard, the DANDI development team, and developers of tools in the NWB ecosystem. + +This hackathon enabled participants to work intensively on an NWB or DANDI-related project with the assistance of core developers and others in the community. Participants shared updates with each other on NWB, DANDI, and related community projects. Together, they developed and discussed ideas for solving technical problems that impact the broader community. The goal was to foster collaboration and community among developers working on and with NWB and DANDI. + +## Objective + +The Neurodata Without Borders: Neurophysiology project (NWB, [https://www.nwb.org/](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/](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 was 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 worked jointly on coding projects, exchanged ideas and best practices, surfaced common needs, resolved coding issues, made feature requests, brainstormed about future collaboration, and made progress on current blockages. + +## Project Themes + +- Information standards, Ontologies, NWB extensions +- NWB and/or DANDI-enabled tools +- Contributions to NWB and/or DANDI core software +- Interfacing with data acquisition systems and building tools for data conversion +- Documentation and diagrams + +## Sponsored by + +The Kavli Foundation + +## Code of Conduct + +This hackathon followed a code of conduct to provide a harassment-free experience for everyone. The organizers were 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. diff --git a/content/events/hck11-2021-remote.md b/content/events/hck11-2021-remote.md new file mode 100644 index 0000000..db4a0df --- /dev/null +++ b/content/events/hck11-2021-remote.md @@ -0,0 +1,52 @@ +--- +title: "User Days 2021" +date: 2021-08-25 +endDate: 2021-08-27 +location: "Virtual" +eventType: "Workshop" +image: "/images/events/default-event-banner.png" +weight: 20210825 +summary: "A virtual training workshop focused on user training for both beginners and advanced users of NWB, with breakout sessions featuring state-of-the-art data analysis, visualization, and management tools." +draft: false +organizers: + - "Benjamin Dichter" + - "Ryan Ly" + - "Andrew Tritt" + - "Pam Baker" + - "Oliver Ruebel" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK11_2021_Remote/report/Report___11th_NWB_User_Days_at_INCF.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK11_2021_Remote" + "INCF Event Page": "https://www.incf.org/neurodata-without-borders-nwb-user-training-workshop" +--- + +## Dates and Location + +- **Dates:** August 25-27, 2021 +- **Location:** Virtual (Anywhere with an internet connection) + +## Overview + +The workshop focused primarily on user training, including lessons for complete beginners to NWB and training in more advanced usage of NWB. There were breakout sessions where the developers of state-of-the-art data analysis, visualization, and management tools (e.g., CaImAn, SpikeInterface, DANDI, suite2p, DataJoint, and more) demonstrated their tools and showed how to use NWB with their tools. There was also time for attendees to work on NWB-related projects, such as converting data to NWB, using NWB-compatible software tools, or going through the NWB online tutorials. + +## Objective + +The Neurodata Without Borders project (NWB, [https://www.nwb.org/](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 purpose of the NWB User Days training workshops is to bring the experimental neurophysiology community together to further the adoption and development of NWB, the NWB software libraries, and scientific workflows that rely on NWB. Members of the community exchange ideas and best practices for using NWB, share NWB-based tools, surface common needs, resolve coding issues, make feature requests, brainstorm about future collaboration, and make progress on current blockages. The event also enables NWB developers and users to interact with each other to facilitate communication, gather requirements, and train users. + +## Projects + +During the workshop, there was time to work on NWB-related projects to practice using the NWB software and ask questions to the NWB developers. Working on a project was optional but encouraged for attendees to get the most out of the workshop. + +Project suggestions included: +- Convert some of your or a collaborator's data to NWB +- Convert data from a public archive to NWB +- Integrate a software tool with NWB +- Work through NWB online tutorials +- Practice using NWB-compatible tools on publicly available NWB data, e.g., on [DANDI](https://dandiarchive.org/) + +## Additional Organizational Support + +- The Kavli Foundation diff --git a/content/events/hck12-2022-remote.md b/content/events/hck12-2022-remote.md new file mode 100644 index 0000000..06babbe --- /dev/null +++ b/content/events/hck12-2022-remote.md @@ -0,0 +1,51 @@ +--- +title: "Developer Days 2022 (NWB+DANDI)" +date: 2022-02-15 +endDate: 2022-02-18 +location: "Virtual" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20220215 +summary: "A remote hackathon event bringing together developers of the NWB data standard, the DANDI development team, and developers of tools in the NWB ecosystem to work intensively on NWB or DANDI-related projects." +draft: false +organizers: + - "NWB POC: Ryan Ly" + - "DANDI POC: Satrajit S. Ghosh" + - "Program Committee: Ryan Ly, Benjamin Dichter, Matthew Avaylon, Andrew Tritt, Pam Baker, Oliver Rübel, Satrajit S Ghosh, Yaroslav O. Halchenko" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK12_2022_Remote/report/Report___12th_NWB_and_DANDI_Hackathon.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK12_2022_Remote" +--- + +## Dates and Location + +- **Pre-hackathon project pitch session:** Tuesday, February 8, 2022, 10am PST (1pm EST) +- **Dates:** Tuesday, February 15, 2022 - Friday, February 18, 2022, 8am - 3pm PST (11am - 6pm EST) +- **Location:** Virtual (Anywhere with an internet connection) + +## Overview + +Neurodata Without Borders (NWB) and the DANDI neurophysiology data archive development teams joined together to create a remote hackathon event for developers. In contrast to the User Days hackathons that focus on training users, this event focused on bringing together the developers of the NWB data standard, the DANDI development team, and developers of tools in the NWB ecosystem. + +This hackathon enabled participants to work intensively on an NWB or DANDI-related project with the assistance of core developers and others in the community. Participants shared updates with each other on NWB, DANDI, and related community projects. Together, they developed and discussed ideas for solving technical problems that impact the broader community. The goal was to foster collaboration and community among developers working on and with NWB and DANDI. + +## Objective + +The Neurodata Without Borders: Neurophysiology project (NWB, [https://www.nwb.org/](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/](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 was 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 worked jointly on coding projects, exchanged ideas and best practices, surfaced common needs, resolved coding issues, made feature requests, brainstormed about future collaboration, and made progress on current blockages. + +## Matchmaking Chat + +To facilitate networking and social interactions during the hackathon, there was a session of 2 one-on-one 15-minute chats between participants. This format was adapted from the successful mindmatching from the neuromatch conference. + +## Sponsored by + +The Kavli Foundation + +## Code of Conduct + +This hackathon followed a code of conduct to provide a harassment-free experience for everyone. The organizers were 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. diff --git a/content/events/hck13-2022-janelia.md b/content/events/hck13-2022-janelia.md new file mode 100644 index 0000000..302c32f --- /dev/null +++ b/content/events/hck13-2022-janelia.md @@ -0,0 +1,53 @@ +--- +title: "User Days 2022" +date: 2022-07-25 +endDate: 2022-07-27 +location: "HHMI Janelia Research Campus, Ashburn, VA" +eventType: "Workshop" +image: "/images/events/default-event-banner.png" +weight: 20220725 +summary: "A three-day event at HHMI Janelia Research Campus focused on bringing the experimental neurophysiology community together to further adoption and development of NWB, the NWB software libraries, and scientific workflows that rely on NWB." +draft: false +organizers: + - "Program chair: Oliver Rübel and Ben Dichter" + - "Administrative Support: Janine Stevens" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK13_2022_Janelia/report/Report___13th_NWB_and_User_Days_at_HHMI_Janelia.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK13_2022_Janelia" + "Tutorial Materials": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK13_2022_Janelia/projects" +--- + +## Dates and Location + +- **Dates:** July 25-27, 2022 +- **Location:** [HHMI Janelia Research Campus](https://www.janelia.org/), 19700 Helix Dr, Ashburn, VA 20147, [Directions](https://www.janelia.org/directions) + +## Objective + +The Neurodata Without Borders project (NWB, 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 hackathon was 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 exchanged ideas and best practices for using NWB and the libraries, shared NWB based tools, surfaced common needs, solved bugs, made feature requests, brainstormed about future funding and collaboration, and made progress on current blockages. The event also enabled NWB developers and users to interact with each other to facilitate communication, gather requirements, and train users. + +Note: This event was meant to foster community and collaboration around NWB, not competition. As such, this was really more of a "workshop" or "tutorial" than a "hackathon." There were no judges nor prizes. Participants were expected to bring data from their own lab and/or collaborate with others to build integration with NWB. + +## Tutorial Materials + +* [BEADL Tutorial](https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK13_2022_Janelia/projects/beadl_tutorial) +* [NeuroConv Tutorial](https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK13_2022_Janelia/projects/neuroconv_tutorial) + +## Resources + +### Talks +Recordings of talks were made available on the [NWB Youtube channel](https://www.youtube.com/channel/UCfD_mU-EFz135a9TpNFJP5A). + +## What to bring? + +* Create the outline for your project at the hackathon. +* 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) you should know how to read the data using Python or MATLAB 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](http://pynwb.readthedocs.io/en/latest/getting_started.html#installation) + +## Additional Organizational Support + +- The Kavli Foundation +- Janelia HHMI diff --git a/content/events/hck14-2022-seattle-rh.md b/content/events/hck14-2022-seattle-rh.md new file mode 100644 index 0000000..1feb0fe --- /dev/null +++ b/content/events/hck14-2022-seattle-rh.md @@ -0,0 +1,79 @@ +--- +title: "NeuroDataReHack 2022" +date: 2022-10-03 +endDate: 2022-10-05 +location: "The Allen Institute, Seattle, WA, USA" +eventType: "Hackathon" +image: "/images/events/default-event-banner.png" +weight: 20221003 +summary: "A three-day event at the Allen Institute focused on generating new insights from existing neurophysiology data through secondary analysis, teaching attendees about open neurophysiology datasets available on the DANDI Archive." +draft: false +organizers: + - "Ben Dichter" + - "Oliver Rübel" + - "Satrjit Ghosh" + - "Jerome Lecoq" + - "Stephanie Albin" +registration: "Registration is now closed." +resources: + "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/raw/master/HCK14_2022_Seattle_RH/report/Report_Neurodata_Rehack_v2.pdf" + "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK14_2022_Seattle_RH" + "Allen Institute Event Page": "https://alleninstitute.org/what-we-do/brain-science/events-training/2022-neurodatarehack-hackathon/" +--- + +## Dates and Location + +- **Dates:** October 3-5, 2022 +- **Location:** [The Allen Institute](https://alleninstitute.org/) - 615 Westlake Ave N, Seattle, WA USA 98109 + +## Objective + +The DANDI Archive now has 89+ neurophysiology datasets in the NWB format spanning many different species, brain areas, task types, and imaging modalities. It is now time for us to shift our focus to reanalyzing these datasets. + +In this workshop, we taught attendees about the open neurophysiology datasets available on the DANDI Archive and trained them on how to maximally utilize the archive and the NWB standard to incorporate existing data into their scientific workflows. This was the first event of its type for NWB, so the team also learned about how to facilitate data reuse in the neuroscience community. + +## Schedule + +### Day 0: Thurs, Sept 29: NWB and DANDI Data Showcase (online) + +- 9 - 9:30am - Data blitz (1 min presentations) +- 9:30 - 11am - Poster session in Gather Town +- 11 - 11:30am - Introduction to NWB: Scope, APIs, tools +- 11:30 - 12pm - Introduction to DANDI: Scope, web interface, downloading data, DANDI Hub +- 12 - 12:30pm - Introduction to OpenScope: Scope, available datasets, high-level tour of existing analysis notebooks + +### Day 1: Monday, Oct 3: Advanced core training + +- 9 - 9:15am - Meet and greet +- 9:15 - 9:45am - Introduction to event: Goals, schedule, Kavli funding opportunities +- 9:45 - 10:15am - Round table discussion of project plans (2 minutes each) +- 10:15 - 11am - Hack and discuss +- 11 - 12pm - Advanced DANDI queries +- 12 - 1pm - Lunch +- 1 - 2pm - DANDI Hub: ros3, nwbwidgets, analysis, example-notebooks repo +- 2 - 3pm - OpenScope in-depth presentation of analysis notebooks +- 3 - 5pm - Hacking + +### Day 2: Tuesday, Oct 4: Hacking with breakouts + +Hacking all day with breakout sessions. + +### Day 3: Wednesday Oct 5: Hacking and final presentations + +- 3 - 4pm - Final project presentations (5 minutes each) +- 4 - 5pm - Feedback for organizers round table discussion + +## Resources + +### Talks +Recordings of talks were made available on the [NWB Youtube channel](https://www.youtube.com/channel/UCfD_mU-EFz135a9TpNFJP5A). + +## What to bring? + +* Create the outline for your project at the hackathon. +* Bring your laptop with appropriate software installed. For instructions on how to install PyNWB, see [the PyNWB documentation](http://pynwb.readthedocs.io/en/latest/getting_started.html#installation). For instructions on how to install MatNWB, see [the MatNWB documentation](https://github.com/NeurodataWithoutBorders/matnwb/blob/master/README.md) + +## Additional Organizational Support + +- The Kavli Foundation +- The Allen Institute diff --git a/content/events/hck15-2023-janelia.md b/content/events/hck15-2023-janelia.md new file mode 100644 index 0000000..ac6cac1 --- /dev/null +++ b/content/events/hck15-2023-janelia.md @@ -0,0 +1,111 @@ +--- +title: "NWB User Days and Developer Days 2023" +date: 2023-07-24 +endDate: 2023-07-29 +location: "HHMI Janelia Research Campus, Ashburn, VA" +eventType: "Hackathon" +image: "/images/events/hck15-2023-janelia/event_banner.png" +weight: 20230724 +summary: "The User Days trained users how to convert their data to NWB and publish it on the DANDI Archive. The Developer Days brought neuroscientists, tool builders, and research software engineers together to further the development of the NWB software ecosystem." +draft: false +organizers: + - "Site chair: Jakob Voigt" + - "Program chair (User Days): Oliver Rübel and Ben Dichter" + - "Program chair (Developer Days): Oliver Rübel and Ryan Ly" + - "Administrative Support: Janine Stevens" +registration: "Registration is now closed. If you would like to be added, please contact the organizers and we may be able to accommodate your request." +resources: + "Final Report (PDF)": "/images/events/hck15-2023-janelia/report/Report___15th_NWB_and_User_and_16th_Developer_Days_2023.pdf" + "Agenda (PDF)": "/images/events/hck15-2023-janelia/agenda/Agenda_NWB_hackathon_2023.pdf" + "User Days Projects": "https://docs.google.com/document/d/1SJOu-ze7L8QS-xJMLBwB42FrurA2Sbf2x8vy9TFMOx0/edit?usp=share_link" + "Developer Days Projects": "https://docs.google.com/document/d/1wXELFWmKnJu30_PsZdGw1F3TE9WNyBOvGEFLa-9uMP4/edit?usp=share_link" +--- + +## Dates and Location + +- **Dates:** July 24-29, 2023 + - **User Days:** July 24-26, 2023 + - **Developer Days:** July 27-29, 2023 +- **Location:** [HHMI Janelia Research Campus](https://www.janelia.org/), 19700 Helix Dr, Ashburn, VA 20147, + [Openstreetmap](https://www.openstreetmap.org/?mlat=39.0708&mlon=-77.4655#map=14/39.0708/-77.4655) + [Directions](https://www.janelia.org/directions) +- **Meeting Rooms:** For the meeting we have two rooms. The main room is *Axon-Dendrite* and the breakout room is *Spectrum*. + +## Agenda + + + Agenda NWB User and Developer Days + + +## Logistics + +**Housing:** Housing will be provided onsite on the Janelia research campus. + +**Travel:** Travel support is not provided. Limited funds may be available to support attendee travel. Once attendance has been confirmed, we will contact you to collect additional information regarding your travel details. + +* **User Days:** Attendees should plan to arrive Sunday afternoon and depart on Wednesday evening after the social or Thursday (depending on availability of flights). +* **Developer Days:** Attendees should plan to arrive Wednesday evening to attend the joint social with User Days participants and depart Saturday afternoon after conclusion of the meeting. + +**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](https://www.janelia.org/directions) + +## Organizing Committee + +**Site chair:** [Jakob Voigt](https://www.voigtslab.org/people) + +**Program chair (User Days):** [Oliver Rübel](https://crd.lbl.gov/divisions/scidata/mla/staff/oliver-ruebel/) and [Ben Dichter](http://bendichter.com/) + +**Program chair (Developer Days):** [Oliver Rübel](https://crd.lbl.gov/divisions/scidata/mla/staff/oliver-ruebel/) and [Ryan Ly](https://crd.lbl.gov/divisions/scidata/mla/staff/ryan-ly/) + +**Administrative Support:** [Janine Stevens](https://www.janelia.org/people/janine-stevens) + +### Additional Organizational Support + +- The Kavli Foundation +- Janelia HHMI + +## What to Bring + +* 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), you should know how to read the data using Python or MATLAB and ideally have scripts ready for + reading the data. +* Bring your laptop with appropriate software installed. For installation instructions see: + * [**PyNWB (Python)**](https://pynwb.readthedocs.io/en/stable/install_users.html). If you are a developer and want to contribute to PyNWB see the [**Installing PyNWB for Developers**](https://pynwb.readthedocs.io/en/stable/install_developers.html) instructions. + * [**MatNWB (Matlab)**](https://neurodatawithoutborders.github.io/matnwb/) +* For an overview of NWB software, see also: + * [**Glossary of Core NWB Tools**](https://nwb-overview.readthedocs.io/en/latest/core_tools/core_tools_home.html) + * [**Glossary of Analysis and Visualization Tools**](https://nwb-overview.readthedocs.io/en/latest/tools/tools_home.html) +* For an overview of NWB see the [**NWB Overview Docs**](https://nwb-overview.readthedocs.io) + +## Objective + +The [Neurodata Without Borders](nwb.org) project 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. NWB has seen wide adoption in the neurophysiology community, and there are now over 100 datasets on the +DANDI Archive in NWB, including data from the Allen Institute and the International Brain Laboratory. + +The **User Days** will train users how to convert their data to NWB and publish it on the DANDI Archive. +We will work with members of the neuroscience community that want to apply NWB to their datasets. We will train +attendees, starting from the basics and proceeding to advanced data engineering techniques to maximally utilize the +features of the HDF5 and Zarr backends. Attendees will also be trained in the creation of NWB extensions. + +The **Developer Days** will bring neuroscientists, tool builders, and research software engineers together to further the +development of the NWB software ecosystem, including the data standard, core software packages, official tools, and community tools. +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. + +**Note:** This event is meant to foster community and collaboration around NWB, 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, bring their own tool, or other relevant project and/or collaborate with others to +build integration with NWB. + +## Projects + +To ease collaborative editing of projects we are managing projects in the following Google Docs: + +* [**User Days Projects**](https://docs.google.com/document/d/1SJOu-ze7L8QS-xJMLBwB42FrurA2Sbf2x8vy9TFMOx0/edit?usp=share_link) +* [**Developer Days Projects**](https://docs.google.com/document/d/1wXELFWmKnJu30_PsZdGw1F3TE9WNyBOvGEFLa-9uMP4/edit?usp=share_link) + +## Code of Conduct + +Please see the [Code of Conduct](https://neurodatawithoutborders.github.io/nwb_hackathons/code_of_conduct) for all NWB events. diff --git a/content/events/hck16-2023-granada-rh.md b/content/events/hck16-2023-granada-rh.md new file mode 100644 index 0000000..137b444 --- /dev/null +++ b/content/events/hck16-2023-granada-rh.md @@ -0,0 +1,48 @@ +--- +title: "NeuroDataReHack 2023 in Granada" +date: 2023-09-05 +endDate: 2023-09-08 +location: "Hotel Andalucia Center, Granada, Spain" +eventType: "Hackathon" +image: "/images/events/hck16-2023-granada-rh/NDRH2023_banner.png" +weight: 20230905 +summary: "NeuroDataReHack 2023 was an event focused on generating new insights from existing neurophysiology data through secondary analysis, teaching attendees about open neurophysiology datasets available on the DANDI Archive and training them on how to utilize the archive and the NWB standard." +draft: false +organizers: + - "Benjamin Dichter, CatalystNeuro" + - "Oliver Rübel, Lawrence Berkeley National Laboratory" + - "Ryan Ly, Lawrence Berkeley National Laboratory" + - "Stephanie Albin, The Kavli Foundation" +--- + +# NeuroDataReHack 2023 +## *Generate new insights from existing neurophysiology data through secondary analysis* + +[The DANDI Archive](http://dandiarchive.org) now has 110+ neurophysiology datasets in the [Neurodata Without Borders](http://nwb.org) format spanning many species, brain areas, task types, and imaging modalities. These include high-value datasets, e.g. from The Allen Institute, the MICrONS project, and the International Brain Laboratory, as well as diverse contributions from neuroscience labs around the world. In this workshop, we taught attendees about the open neurophysiology datasets available on the DANDI Archive and trained them on how to maximally utilize the archive and the NWB standard to incorporate existing data into their scientific workflows. + +Example projects included but were not limited to: +* Determine whether your result is present in another species or brain area. +* Showcase the capabilities of your tool or analysis on existing data from another lab. +* Explore follow-up questions to a study. + +Following the event, participants were invited to apply for a Kavli Foundation Neurodata Discovery Award, which awards $50,000 (USD) of funding to continue data reanalysis projects that come out of the NeuroDataReHack event. + +This event was held as a satellite of the [IBRO World Congress 2023](http://ibro2023.org) with the goal of making it more accessible to diverse participants who might not otherwise have the opportunity to participate in this workshop. + +## Dates and Location + +- **Dates:** September 5-8, 2023 +- **Location:** [Hotel Andalucia Center in Granada, Spain](https://www.hotelescenter.es/en/hotel-andalucia-center-granada/) + +## Report + +The final report for NeuroDataReHack 2023 is available online at [[PDF (GitHub)](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK16_2023_Granada_RH/report/Report__NeuroDataReHack_2023.pdf)]. + +## Schedule + +Agenda NeuroDataReHack 2023 + +## Resources + +* A report of the first NeuroDataReHack event: ([PDF](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK14_2022_Seattle_RH/report/Report_Neurodata_Rehack_v2.pdf)) +* Recordings of talks are available on the [NWB Youtube channel](https://www.youtube.com/channel/UCfD_mU-EFz135a9TpNFJP5A). diff --git a/content/events/hck17-2023-openneurodata-showcase.md b/content/events/hck17-2023-openneurodata-showcase.md new file mode 100644 index 0000000..447db39 --- /dev/null +++ b/content/events/hck17-2023-openneurodata-showcase.md @@ -0,0 +1,53 @@ +--- +title: "Open Neurodata Showcase 2023" +date: 2023-08-28 +location: "Virtual (Gather)" +eventType: "Virtual Showcase" +image: "/images/events/hck17-2023-openneurodata-showcase/open_neurodata_showcase_banner.png" +weight: 20230828 +summary: "The Open Neurodata Showcase 2023 was a virtual event that brought together data contributors and researchers interested in reusing existing neurophysiology data, featuring a virtual poster session in the Gather platform." +draft: false +organizers: + - "Anna Szonja Weigl, CatalystNeuro" + - "Benjamin Dichter, CatalystNeuro" + - "Oliver Rübel, Lawrence Berkeley National Laboratory" + - "Ryan Ly, Lawrence Berkeley National Laboratory" + - "Stephanie Albin, The Kavli Foundation" +--- + +# Open Neurodata Showcase 2023 +## *Meet the scientists who have publicly shared neurophysiology data* + +[The DANDI Archive](http://dandiarchive.org) now has 175+ neurophysiology datasets in the [Neurodata Without Borders](http://nwb.org) format spanning many species, brain areas, task types, and imaging modalities. These include high-value datasets, e.g., from The Allen Institute, the MICrONS project, and the International Brain Laboratory, as well as diverse contributions from neuroscience labs around the world. + +In this event, we organized a virtual poster session in the Gather platform to bring together data contributors and anyone interested in reusing existing neurophysiology data. This virtual event offered a unique opportunity for participants to engage in discussions, explore dandisets, and allowed data contributors to showcase their projects. + +## Dates and Location + +- **Date:** August 28, 2023, 9:00 - 10:30 AM PDT (UTC-7) +- **Location:** Virtual in Gather + +## Report + +The combined report for NeuroDataReHack 2023 and the Open Neurodata Showcase 2023 is available online at [[PDF (GitHub)](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK16_2023_Granada_RH/report/Report__NeuroDataReHack_2023.pdf)]. + +## Virtual Data Showcase Agenda + +| Session | Speakers | Time: Pacific | +|-------------------------------------------|-------------------|---------------| +| Gather space opens to participants | | 8:55 AM | +| Introduction to the virtual data showcase | Organizers | 9:00-9:20 AM | +| Virtual poster session | Data Contributors | 9:20-10:30 AM | + +## Presenters + +| Posters | Speakers | +|----------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------| +| Allen Brain Observatory: Visual Coding Neuropixels Dataset | Josh Siegle, _Allen Institute_ | +| A Brain-Wide Map of Neural Activity during Complex Behaviour | Olivier Winter, _IBL_ | +| MICrONS Two Photon Functional Imaging | Paul Fahey, _Baylor College of Medicine_ | +| The OpenScope Databook | Carter Peene, _Allen Institute_ | +| Three datasets of human single-neuron electrophysiology recordings during working memory and long-term memory tasks | Michael Kyzar, _Rutishauser Lab_ | +| Challenges and neuroethical considerations in sharing human neural data | Angelique C Paulk, _Massachusetts General Hospital_ | +| Data on auditory cortex plasticity and oxytocin neuron responses in co-parental mice | Robert Froemke, _NYU_ | +| Esr1+ hypothalamic-habenula neurons shape aversive states | Pierre Le Merre, _Karolinska Institutet_ | diff --git a/content/events/hck18-2024-dev-hackathon-datajoint.md b/content/events/hck18-2024-dev-hackathon-datajoint.md new file mode 100644 index 0000000..9b5f576 --- /dev/null +++ b/content/events/hck18-2024-dev-hackathon-datajoint.md @@ -0,0 +1,40 @@ +--- +title: "2024 NWB Developer Hackathon hosted by DataJoint" +date: 2024-04-17 +endDate: 2024-04-19 +location: "DataJoint headquarters, Houston, TX, USA" +eventType: "Hackathon" +image: "/images/events/hck18-2024-dev-hackathon-datajoint/nwb_logo_brain_text_transp_hor.png" +weight: 20240417 +summary: "The 2024 NWB Developer Hackathon brought together developers of the NWB data standard and software ecosystem and developers of community tools who would like to integrate their tools with NWB, fostering collaboration and community among developers." +draft: false +organizers: + - "Kushal Bakshi (Site Chair)" + - "Ryan Ly (Program Chair)" + - "Ben Dichter (Program Chair)" +--- + +# 2024 NWB Developer Hackathon hosted by DataJoint + +The Neurodata Without Borders (NWB) team organized a hackathon event for developers. In contrast to NWB user training workshops, this event was focused on bringing together the developers of the NWB data standard and software ecosystem and developers of community tools who would like to integrate their tools with NWB. This hackathon enabled participants to work intensively on an NWB-related project with the assistance of the NWB development team and others in the community. + +This was the first NWB hackathon event hosted by DataJoint. Working in the DataJoint building and with their team facilitated projects at the intersection between DataJoint and NWB, such as Spyglass or building NWB export for custom DataJoint pipelines. The event also welcomed NWB projects that were not related to DataJoint. + +## Dates and Location + +- **Dates:** Wednesday, April 17, 2024, 9 AM to Friday, April 19, 2024, 5:30 PM +- **Location:** DataJoint headquarters, 4265 San Felipe St #1025, Houston, TX 77027 + +## Objective + +The [Neurodata Without Borders](https://www.nwb.org/) project 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. NWB has seen wide adoption in the neurophysiology community, and there are now over 175 datasets on the DANDI Archive in NWB, including data from the Allen Institute and the International Brain Laboratory. + +The NWB Developer Hackathon brought neuroscientists, tool builders, and research software engineers together to further the development of the NWB software ecosystem, including the data standard, core software packages, official tools, and community tools. Members of the community exchanged ideas and best practices for using NWB and the libraries, shared NWB based tools, surfaced common needs, solved bugs, made feature requests, brainstormed about future funding and collaboration, and made progress on current blockages. + +## Agenda + +Agenda for 2024 NWB Developer Hackathon + +## Report + +The final report for the 2024 NWB Developer Hackathon is available on GitHub ([PDF](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK18_2024_Dev_Hackathon_DataJoint/report/Report_18th_NWB_Developer_Hackathon.pdf)). diff --git a/content/events/hck19-2024-remote.md b/content/events/hck19-2024-remote.md new file mode 100644 index 0000000..50329ab --- /dev/null +++ b/content/events/hck19-2024-remote.md @@ -0,0 +1,58 @@ +--- +title: "NWB Data Conversion Workshop 2024" +date: 2024-06-12 +endDate: 2024-06-14 +location: "Virtual" +eventType: "Workshop" +image: "/images/events/hck19-2024-remote/logo_brain_text_white_hor.png" +weight: 20240612 +summary: "The NWB Data Conversion Workshop 2024 trained members of the neuroscience community on how to convert their data to NWB and publish it on the DANDI Archive, from basic to advanced techniques." +draft: false +organizers: + - "Steph Prince" + - "Oliver Rübel" +registration: "Register for the event [here](https://forms.gle/pTsjRMEqsgCRo3VD8)." +resources: + "NWB GUIDE": "https://nwb-guide.readthedocs.io/en/latest/installation.html" + "PyNWB (Python)": "https://pynwb.readthedocs.io/en/stable/install_users.html" + "MatNWB (Matlab)": "https://neurodatawithoutborders.github.io/matnwb/" + "NWB Overview Docs": "https://nwb-overview.readthedocs.io" +--- + +# NWB Data Conversion Workshop 2024 + +The [Neurodata Without Borders](https://nwb.org) project 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. NWB has seen wide adoption in the neurophysiology community, and there are now over 100 datasets on the DANDI Archive in NWB, including data from the Allen Institute and the International Brain Laboratory. + +The NWB Data Conversion Workshop trained members of the neuroscience community on how to convert their data to NWB and publish it on the DANDI Archive. We trained attendees starting from the basics of the NWB format and proceeding to domain-specific tutorials and advanced data engineering techniques to maximally utilize the features of the HDF5 and Zarr backends. During this workshop, we introduced multiple sets of tools with varying levels of flexibility for converting data, including NWB GUIDE, a new no-code user interface for data conversion. + +**Note:** All levels of experience were welcome! We had tutorials ranging from no-code, automated data conversion to more advanced, custom code conversion. + +## Dates and Location + +- **Dates:** June 12-14, 2024 +- **Location:** Virtual + +## Logistics + +We used Gather and Zoom for the meeting. + +## Report + +The final report for the 2024 NWB Data Conversion Workshop is available: +- [Workshop report](https://drive.google.com/file/d/1rhgCXs_N1OLFDI4VyEQ_vpWnvldzJW31/view?usp=sharing) +- [Recorded tutorials](https://www.youtube.com/watch?v=xZiSesEVA3o&list=PL5wPNhoBP0ZB2sLuRKWqwgXf9V3FRl1bw) + +## Agenda + +Agenda for 2024 NWB Data Conversion Workshop + +## What to Bring + +* Example datasets you would like to convert. For lab-specific data (i.e., data not in these [supported formats](https://nwb-guide.readthedocs.io/en/latest/format_support.html)), you should ideally have scripts for reading the data using Python or MATLAB. +* Your laptop with appropriate software installed. For installation instructions see: + * [**NWB GUIDE**](https://nwb-guide.readthedocs.io/en/latest/installation.html) + * [**PyNWB (Python)**](https://pynwb.readthedocs.io/en/stable/install_users.html) + * [**MatNWB (Matlab)**](https://neurodatawithoutborders.github.io/matnwb/) +* For an overview of NWB software, see also: + * [**Glossary of Core NWB Tools**](https://nwb-overview.readthedocs.io/en/latest/core_tools/core_tools_home.html) + * [**Glossary of Analysis and Visualization Tools**](https://nwb-overview.readthedocs.io/en/latest/tools/analysis_tools_home.html) diff --git a/content/events/hck20-2024-openneurodata-showcase.md b/content/events/hck20-2024-openneurodata-showcase.md new file mode 100644 index 0000000..697aabe --- /dev/null +++ b/content/events/hck20-2024-openneurodata-showcase.md @@ -0,0 +1,56 @@ +--- +title: "Open Neurodata Showcase 2024" +date: 2024-07-02 +location: "Virtual (Gather)" +eventType: "Virtual Showcase" +image: "/images/events/hck20-2024-openneurodata-showcase/open_neurodata_showcase_banner.png" +weight: 20240702 +summary: "The Open Neurodata Showcase 2024 is a virtual event that brings together data contributors and researchers interested in reusing existing neurophysiology data, featuring a virtual poster session in the Gather platform." +draft: false +organizers: + - "Alessandra Trapani, CatalystNeuro" + - "Anna Szonja Weigl, CatalystNeuro" + - "Benjamin Dichter, CatalystNeuro" + - "Oliver Rübel, Lawrence Berkeley National Laboratory" + - "Ryan Ly, Lawrence Berkeley National Laboratory" + - "Stephanie Albin, The Kavli Foundation" +registration: "Register for the event [here](https://forms.gle/amPd4h5kN9BPLX4g7)." +--- + +# Open Neurodata Showcase 2024 +## *Meet the scientists who have publicly shared neurophysiology data* + +[The DANDI Archive](http://dandiarchive.org) now has 199+ neurophysiology datasets in the [Neurodata Without Borders](http://nwb.org) format spanning many species, brain areas, task types, and imaging modalities. These include high-value datasets, e.g. from [Allen Institute OpenScope](https://dandiarchive.org/dandiset/search?search=openscope), the [MICrONS project](https://dandiarchive.org/dandiset/000402), and the [International Brain Laboratory Brain Wide Map](https://dandiarchive.org/dandiset/000409), as well as diverse contributions from neuroscience labs around the world. + +In this event, we organize a virtual poster session in the Gather platform to bring together data contributors and anyone interested in reusing existing neurophysiology data. This virtual event offers a unique opportunity for participants to engage in discussions, explore dandisets, and allows data contributors to showcase their projects. + +## Dates and Location + +- **Date:** July 2, 2024, 9:00 - 10:30 AM PDT (UTC-7) +- **Location:** Virtual in Gather (link to be shared closer to the event date) + +## Eligibility + +This virtual event is open to anyone interested in neurophysiology data, including but not limited to: +* Neuroscience graduate students, post-docs, and other researchers interested in using open data in their research +* Educators who want to use real datasets in their lessons +* Undergraduates and high school students interested in learning about neuroscience +* Open science advocates + +## Virtual Data Showcase Agenda + +| Session | Speakers | Time: Pacific | +|-------------------------------------------|-------------------|---------------| +| Gather space opens to participants | | 8:55 AM | +| Introduction to the virtual data showcase | Organizers | 9:00-9:20 AM | +| Virtual poster session | Data Contributors | 9:20-10:30 AM | + +## Presenters + +* Saskia de Vries, "Allen Institute Observatory - Visual Coding Calcium Imaging Datasets", [DANDI:000728](https://dandiarchive.org/dandiset/000728/draft), [DANDI:000039](https://dandiarchive.org/dandiset/000039), [DANDI:000049](https://dandiarchive.org/dandiset/000049) +* Alessio Buccino, "SpikeInterface, a unified framework for spike sorting", [DANDI:000034](https://dandiarchive.org/dandiset/000034/0.211030.0713) +* Xinyue Ma, "Patch-seq recordings from mouse visual cortex", [DANDI:000020](https://dandiarchive.org/dandiset/000020/0.210913.1639) +* Olivier Winter, "IBL - Brain Wide Map" and "IBL behavioral data", [DANDI:000409](https://dandiarchive.org/dandiset/000409), [DANDI:000045](https://dandiarchive.org/dandiset/000045), [DANDI:000049](https://dandiarchive.org/dandiset/000049) +* Michael Kyzar, "Data for: Control of working memory maintenance by theta-gamma phase amplitude coupling of human hippocampal neurons" and "Dataset of human-single neuron activity during a Sternberg working memory task.", [DANDI:000673](https://dandiarchive.org/dandiset/000673), [DANDI:000469](https://dandiarchive.org/dandiset/000469) +* Kevin Le, "Data for: Multimodal single-neuron, intracranial EEG, and fMRI brain responses during movie watching in human patients", [DANDI:000623](https://dandiarchive.org/dandiset/000623) +* Carolina Filipe, "Neurotask Benchmark Datasets", [DANDI:001055](https://dandiarchive.org/dandiset/001055), [DANDI:001056](https://dandiarchive.org/dandiset/001056), [DANDI:001057](https://dandiarchive.org/dandiset/001057), [DANDI:001058](https://dandiarchive.org/dandiset/001058), [DANDI:001059](https://dandiarchive.org/dandiset/001059), [DANDI:001060](https://dandiarchive.org/dandiset/001060) diff --git a/content/events/hck21-2024-janelia-ndrh.md b/content/events/hck21-2024-janelia-ndrh.md new file mode 100644 index 0000000..a2a3f24 --- /dev/null +++ b/content/events/hck21-2024-janelia-ndrh.md @@ -0,0 +1,73 @@ +--- +title: "NeuroDataReHack 2024 at Janelia" +date: 2024-07-08 +endDate: 2024-07-12 +location: "HHMI Janelia Research Campus, Ashburn, VA, USA" +eventType: "Hackathon" +image: "/images/events/hck21-2024-janelia-ndrh/NDRH2024_banner.png" +weight: 20240708 +summary: "NeuroDataReHack 2024 is an event focused on generating new insights from existing neurophysiology data through secondary analysis, teaching attendees about open neurophysiology datasets available on the DANDI Archive and training them on how to utilize the archive and the NWB standard." +draft: false +organizers: + - "Benjamin Dichter, CatalystNeuro" + - "Oliver Rübel, Lawrence Berkeley National Laboratory" + - "Ryan Ly, Lawrence Berkeley National Laboratory" +--- + +# NeuroDataReHack 2024 +## *Generate new insights from existing neurophysiology data through secondary analysis* + +[The DANDI Archive](http://dandiarchive.org) now has 199+ neurophysiology datasets in the [Neurodata Without Borders](http://nwb.org) format spanning many species, brain areas, task types, and imaging modalities. These include high-value datasets, e.g. from [Allen Institute OpenScope](https://dandiarchive.org/dandiset/search?search=openscope), the [MICrONS project](https://dandiarchive.org/dandiset/000402), and the [International Brain Laboratory Brain Wide Map](https://dandiarchive.org/dandiset/000409), as well as diverse contributions from neuroscience labs around the world. + +In this workshop, we will teach attendees about the open neurophysiology datasets available on the DANDI Archive and train them on how to maximally utilize the archive and the NWB standard to incorporate existing data into their scientific workflows. Feedback from attendees will be used to improve the software and data standard to better enable reanalysis workflows. + +Prior to the workshop, we are organizing [Open Neurodata Showcase](/events/hck20-2024-openneurodata-showcase/) where attendees can meet the contributors behind the neurophysiology datasets and explore virtual posters. + +Example projects include but are not limited to: +* Determine whether your result is present in another species or brain area. +* Showcase the capabilities of your tool or analysis on existing data from another lab. +* Explore follow-up questions to a study. +* Create educational content that uses open data. + +This event will primarily focus on analyzing existing data in NWB and on DANDI, **not** converting data to NWB. If you are interested in learning how to convert data, consider signing up for an NWB User Days event. + +## Dates and Location + +- **Dates:** July 8-12, 2024 +- **Location:** [HHMI Janelia Research Campus](https://www.janelia.org/), 19700 Helix Dr, Ashburn, VA 20147, [Directions](https://www.janelia.org/directions) + +## Logistics + +Thanks to the generous sponsorship of The Janelia Research Campus, this event will be free to participants: +* There is no registration or application fee. +* Participants will be provided a private room at Janelia Research Campus for the duration of this event, checking in on Sunday, July 7, and checking out on Friday, July 12 or Saturday, July 13. +* Breakfast, lunch, dinner, and coffee breaks will be provided. +* You will be responsible for booking your own flight and transportation to Janelia Research Campus. +* You will be responsible for determining visa and/or healthcare requirements for travel to the United States. + +## Report + +The final report for NeuroDataReHack 2024 is available online at [[PDF](https://drive.usercontent.google.com/u/0/uc?id=1QYw9jmIpKPXPMLmhTnVIIWgbWHL5tPS3&export=download)]. + +## Resources + +Resources to help participants prepare for the event: + +* All slides: [Google Drive](https://drive.google.com/drive/folders/1DAmQr4qWCamhj_2Zyke0kkHGvV8Kyq13?usp=sharing) +* Search API tutorials + * [Basic API tutorial](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK21_2024_Janelia_NDRH/tutorials/simple_dandiset_search.ipynb) + * [Advanced API tutorial](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK21_2024_Janelia_NDRH/tutorials/advanced_asset_search.ipynb) + +## What to Bring + +Bring a laptop with appropriate software installed. Python should be installed and MATLAB is optional. For instructions on how to install PyNWB, see [the PyNWB documentation](https://pynwb.readthedocs.io/en/stable/install_users.html#installing-pynwb). For instructions on how to install MatNWB, see [the MatNWB documentation](https://github.com/NeurodataWithoutBorders/matnwb/blob/master/README.md). + +## Past Events + +* A report of the first NeuroDataReHack event: ([PDF](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK14_2022_Seattle_RH/report/Report_Neurodata_Rehack_v2.pdf)) +* A report of the second NeuroDataReHack event: ([PDF](https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK16_2023_Granada_RH/report/Report__NeuroDataReHack_2023.pdf)) +* Recordings of talks are available on the [NWB Youtube channel](https://www.youtube.com/channel/UCfD_mU-EFz135a9TpNFJP5A). + +## Schedule + +Agenda NeuroDataReHack 2024 diff --git a/content/events/hck22-2025-dataconversion-remote.md b/content/events/hck22-2025-dataconversion-remote.md new file mode 100644 index 0000000..49c9487 --- /dev/null +++ b/content/events/hck22-2025-dataconversion-remote.md @@ -0,0 +1,59 @@ +--- +title: "NWB Data Conversion Workshop 2025" +date: 2025-05-12 +endDate: 2025-05-14 +location: "Virtual" +eventType: "Workshop" +image: "/images/events/hck22-2025-dataconversion-remote/logo_brain_text_white_hor.png" +weight: 20250512 +summary: "The NWB Data Conversion Workshop will train members of the neuroscience community on how to convert their data to NWB and publish it on the DANDI Archive, from basic to advanced techniques." +draft: false +organizers: + - "Steph Prince" + - "Oliver Rübel" +registration: "Register for the event [here](https://forms.gle/5Sewge3qpozxnrATA)." +resources: + "NWB GUIDE": "https://nwb-guide.readthedocs.io/en/latest/installation.html" + "PyNWB (Python)": "https://pynwb.readthedocs.io/en/stable/install_users.html" + "MatNWB (Matlab)": "https://neurodatawithoutborders.github.io/matnwb/" + "NWB Overview Docs": "https://nwb-overview.readthedocs.io" +--- + +## Objective + +The [Neurodata Without Borders](nwb.org) project 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. NWB has seen wide adoption in the neurophysiology community, and there are now over 100 datasets on the +DANDI Archive in NWB, including data from the Allen Institute and the International Brain Laboratory. + +The NWB Data Conversion Workshop will train members of the neuroscience community on how to convert their data to NWB and +publish it on the DANDI Archive. We will train attendees starting from the basics of the NWB format and proceeding to +domain-specific tutorials and advanced data engineering techniques to maximally utilize the features of the HDF5 and Zarr +backends. During this workshop, we will introduce multiple sets of tools with varying levels of flexibility for converting +your data, including NWB GUIDE, a new no-code user interface for data conversion. + +**Note:** All levels of experience are welcome! We will have tutorials ranging from no-code, automated data conversion to +more advanced, custom code conversion. + +## Logistics + +We will be using Gather and Zoom for the meeting and will send an email in the days before the workshop with links. + +## What to Bring + +* Please bring any example datasets you would like to convert. For lab-specific data (i.e., data not in these [supported formats](https://nwb-guide.readthedocs.io/en/latest/format_support.html)), you should ideally have scripts for reading the data using Python or MATLAB. +* Bring your laptop with appropriate software installed. For installation instructions see: + * [**NWB GUIDE**](https://nwb-guide.readthedocs.io/en/latest/installation.html) + * [**PyNWB (Python)**](https://pynwb.readthedocs.io/en/stable/install_users.html) + * [**MatNWB (Matlab)**](https://neurodatawithoutborders.github.io/matnwb/) +* For an overview of NWB software, see also: + * [**Glossary of Core NWB Tools**](https://nwb-overview.readthedocs.io/en/latest/core_tools/core_tools_home.html) + * [**Glossary of Analysis and Visualization Tools**](https://nwb-overview.readthedocs.io/en/latest/tools/analysis_tools_home.html) + +## Agenda + +The agenda will be shared at a later date. + +## Code of Conduct + +Please see the [Code of Conduct](https://neurodatawithoutborders.github.io/nwb_hackathons/code_of_conduct) for all NWB events. diff --git a/content/events/hck24-2025-janelia-ndrh.md b/content/events/hck24-2025-janelia-ndrh.md new file mode 100644 index 0000000..db58461 --- /dev/null +++ b/content/events/hck24-2025-janelia-ndrh.md @@ -0,0 +1,100 @@ +--- +title: "NeuroDataReHack 2025" +date: 2025-07-14 +endDate: 2025-07-18 +location: "HHMI Janelia Research Campus, Ashburn, VA" +eventType: "Hackathon" +image: "/images/events/hck24-2025-janelia-ndrh/NDRH2025_banner.png" +weight: 20250714 +summary: "Generate new insights from existing neurophysiology data through secondary analysis. This event will focus on analyzing existing data in NWB and on DANDI, with opportunities for funding through the Kavli Neurodata Discovery Award." +draft: false +organizers: + - "Benjamin Dichter, Ph.D. (Program Chair)" + - "Stephanie Prince, Ph.D. (Program Chair)" +registration: "Space for the event is limited. Apply to attend NeuroDataReHack 2025 [here](https://forms.gle/cR9sm5wjAt8oqTaT7). Application deadline: Feb 12. Notification of admission decisions: March 15." +resources: + "Event Flyer": "https://drive.google.com/file/d/1ptsGRa1sEMh-je7L_ff3CgtRTj-X11lO/view?usp=sharing" + "Slides from the 2024 NeuroDataReHack": "https://drive.google.com/drive/folders/1DAmQr4qWCamhj_2Zyke0kkHGvV8Kyq13?usp=sharing" + "PyNWB Documentation": "https://pynwb.readthedocs.io/en/stable/install_users.html#installing-pynwb" + "MatNWB Documentation": "https://github.com/NeurodataWithoutBorders/matnwb/blob/master/README.md" +--- + +## Objective + +[The DANDI Archive](http://dandiarchive.org) now has 300+ neurophysiology datasets in the +[Neurodata Without Borders](http://nwb.org) format spanning many species, brain areas, task types, and imaging +modalities. These include high-value datasets, e.g. from [Allen Institute OpenScope](https://dandiarchive.org/dandiset/search?search=openscope), the [MICrONS project](https://dandiarchive.org/dandiset/000402), and the +[International Brain Laboratory Brain Wide Map](https://dandiarchive.org/dandiset/000409), as well as diverse contributions from neuroscience labs around the world. In this +workshop, we will teach attendees about the open neurophysiology datasets available on the DANDI Archive and train +them on how to maximally utilize the archive and the NWB standard to incorporate existing data into their scientific +workflows. Feedback from attendees will be used to improve the software and data standard to better enable +reanalysis workflows. + +Example projects include but are not limited to: +* Determine whether your result is present in another species or brain area. +* Showcase the capabilities of your tool or analysis on existing data from another lab. +* Explore follow-up questions to a study. +* Create educational content that uses open data. + +This event will primarily focus on analyzing existing data in NWB and on DANDI, **not** converting data to NWB. If +you are interested in learning how to convert data, consider signing up for an NWB Data Conversion Workshop. + +## Kavli Neurodata Discovery Award + +Following the event, participants will be invited to apply for a Kavli Foundation Neurodata Discovery Awards, which awards $50,000 (USD) of funding to continue data reanalysis projects that come out of the NeuroDataReHack event. This is a funding opportunity exclusive to NeuroDataReHack participants. + +![Kavli Foundation Logo](/images/events/hck24-2025-janelia-ndrh/Kavli-Foundation-logo.png) + +## Instructors + +The event will feature a distinguished team of instructors, including: + +- **Benjamin Dichter, Ph.D.** - Program Chair, CatalystNeuro +- **Stephanie Prince, Ph.D.** - Program Chair, Lawrence Berkeley National Laboratory +- **Jeremy Magland, Ph.D.** - Senior Data Scientist, Flatiron Institute (Lead developer of Neurosift, FigURL, Dendro) +- **Carsen Stringer, Ph.D.** - Group Leader, HHMI Janelia Research Campus (Lead developer of rastermap, suite2p, facemap, cellpose) +- **Guillaume Viejo, Ph.D.** - Data Scientist, Flatiron Institute (Lead developer of pynapple) +- **Carter Peene** - Data Analyst I, Allen Institute for Neural Dynamics (Lead developer of OpenScope Databook) +- **Misha Ahrens, Ph.D.** - Group Leader, HHMI Janelia Research Campus +- **Jakob Voigts, Ph.D.** - Group Leader, HHMI Janelia Research Campus + +## Eligibility + +This course is intended for PhD students, postdoctoral researchers, principal investigators, or similar. +Applicants should have basic programming experience in Python or MATLAB and experience with neurophysiology research. + +## Logistics + +Thanks to the generous sponsorship of The Janelia Research Campus, this event will be free to participants: +* There is no registration or application fee. +* Participants will be provided a private room at Janelia Research Campus for the duration of this event, + checking in on Sunday, July 13, and checking out the evening of Friday, July 18 or the morning of Saturday, July 19. +* Breakfast, lunch, dinner, and coffee breaks will be provided. +* You will be responsible for booking your own flight and transportation to Janelia Research Campus. +* You will be responsible for determining visa and/or healthcare requirements for travel to the United States. + +## What to Bring + +Bring a laptop with appropriate software installed. Python should be installed and MATLAB is optional. For +instructions on how to install PyNWB, see +[the PyNWB documentation](https://pynwb.readthedocs.io/en/stable/install_users.html#installing-pynwb). For instructions +on how to install MatNWB, see +[the MatNWB documentation](https://github.com/NeurodataWithoutBorders/matnwb/blob/master/README.md) + +## Testimonials from NeuroDataReHack 2024 + +> "This workshop was enlightening, and I'm excited to bring these tools back to my research group and my university!" +> +> — Miles Martinez, Duke University + +> "The Hackathon was an incredible experience. I had the opportunity to get familiar with not only NWB but also the expanding NWB ecosystem. Additionally, the week was fantastic for connecting with others working on similar topics. I established potential collaborations and learned from people working on different topics as well." +> +> — Carolina Filipe, Champalimaud Foundation + +> "NeuroDataReHack 2024 is a inspiring tour to the ecosystem that the NWB and DANDI has supported, including a set of useful tools, datasets, and example notebook to hand on. Great opportunities to meet the organizers that make those things happen, and to connect with other researchers interested in dataset reuse." +> +> — Xinyue Ma, McGill University + +## Code of Conduct + +Please see the [Code of Conduct](https://neurodatawithoutborders.github.io/nwb_hackathons/code_of_conduct) for all NWB events. diff --git a/content/events/linkml-neurodata-hackashop-2024.md b/content/events/linkml-neurodata-hackashop-2024.md new file mode 100644 index 0000000..3c68eb6 --- /dev/null +++ b/content/events/linkml-neurodata-hackashop-2024.md @@ -0,0 +1,44 @@ +--- +title: "Brain Data Modeling Hackashop 2024" +date: 2024-02-05 +endDate: 2024-02-07 +location: "International Computer Science Institute (ICSI), Berkeley, CA, USA" +eventType: "Hackathon" +image: "/images/events/linkml-neurodata-hackashop-2024/banner_bdmh_2024.png" +weight: 20240205 +summary: "An invitation-only event bringing the neurophysiology data and standards developer community together to evaluate the use of LinkML to create common schema and facilitate integration of data across standards and resources." +draft: false +organizers: + - "Oliver Rübel (Site Chair)" + - "Satrajit Ghosh (Program Chair)" +--- + +# Brain Data Modeling Hackashop 2024 + +The objective of the event was to bring the neurophysiology data and standards developer community together to evaluate the use of LinkML to create common schema and facilitate integration of data across standards and resources. The goal was to create LinkML based schemas that integrate information across existing efforts in data modeling for neuroscience and leveraging existing standards and resources, e.g, NWB, AIND, OpenMINDS, DANDI, and BICAN. To support large scientific data, a second goal was to extend LinkML for array type data structures required, e.g, for NWB and OME-Zarr. This was an invitation-only event. + +## Dates and Location + +### Main Event +- **Dates:** February 5-7, 2024 + - **Note:** The main program started at noon on Feb. 5 to allow attendees taking morning flights to be able to get to ICSI on time. +- **Location:** [International Computer Science Institute (ICSI)](https://www.icsi.berkeley.edu), 2150 Shattuck Ave, Suite 250, Berkeley, CA 94704 + +### Optional Bonus Hacking Days +Participants could optionally choose to stay up to 2 extra days to continue working together in a free-form fashion. +- **Dates:** February 8-9, 2024 +- **Location:** [Building 59 (Shyh Wang Hall)](https://map.lbl.gov/#ctdl-UMAP_2012091840117,BLD_2013013161357), 1 Cyclotron Road, Lawrence Berkeley National Laboratory, Berkeley, CA + +## Agenda + +The main program started at noon on Feb. 5 to allow attendees taking morning flights to be able to get to ICSI on time. + + + Agenda Brain Data Modeling Hackashop 2024 + + +## Projects + +To ease collaborative editing of projects, projects were managed in the following Google Docs: + +* [**Brain Data Modeling Hackashop Projects 2024**](https://docs.google.com/document/d/1cvIr3FtUtxcsZJXKPbwiNtBctxNxnYnzU1xxSHkyg44/edit?usp=sharing) diff --git a/content/events/workshop-2023-princeton.md b/content/events/workshop-2023-princeton.md new file mode 100644 index 0000000..aeea997 --- /dev/null +++ b/content/events/workshop-2023-princeton.md @@ -0,0 +1,31 @@ +--- +title: "NWB and DANDI Workshop at Princeton Neuroscience Institute" +date: 2023-09-14 +endDate: 2023-09-14 +location: "Princeton Neuroscience Institute, Princeton, NJ" +eventType: "Workshop" +image: "/images/events/workshop-2023-princeton/nwb_dandi_princeton_banner.png" +weight: 20230914 +summary: "An interactive workshop on Neurodata Without Borders (NWB) and the DANDI Archive, teaching participants how to use these resources to maximize the impact of their data while complying with NIH data sharing policies." +draft: false +organizers: + - "Ryan Ly" + - "Ben Dichter" +registration: "RSVP for the talk and/or workshop [here](https://forms.gle/PnzdqpYW33TQ3Tz7A)" +--- + +## About the Workshop + +Join us for an interactive workshop on [Neurodata Without Borders (NWB)](https://nwb.org), a data standard for neurophysiology, and the [DANDI Archive](https://dandiarchive.org), a collaboration platform for publishing, sharing, and processing neurophysiology data. Learn how to use these resources to maximize the impact of your data while complying with the new NIH data sharing and management policies. + +Representatives from the NWB and DANDI teams, Ryan Ly and Ben Dichter, will provide an overview of the NWB software ecosystem and teach you how to convert data to NWB and publish data on DANDI. + +## Agenda + +- **1:45pm - 2:45pm**: PNI/PSH 101 - Introduction to NWB and DANDI +- **2:45pm - 3:00pm**: Coffee break +- **3:00pm - 5:00pm**: PNI/PSH 101 - Interactive workshop on NWB and DANDI + +## Registration + +RSVP for the talk and/or workshop [here](https://forms.gle/PnzdqpYW33TQ3Tz7A) diff --git a/content/events/workshop-2024-bcm.md b/content/events/workshop-2024-bcm.md new file mode 100644 index 0000000..d7cc364 --- /dev/null +++ b/content/events/workshop-2024-bcm.md @@ -0,0 +1,60 @@ +--- +title: "NWB and DANDI Workshop at Baylor College of Medicine" +date: 2024-04-15 +endDate: 2024-04-16 +location: "Baylor College of Medicine, Houston, TX, USA" +eventType: "Workshop" +image: "/images/events/workshop-2024-bcm/nwb_dandi_bcm_2024_banner.png" +weight: 20240415 +summary: "An interactive workshop on Neurodata Without Borders (NWB) and the DANDI Archive, hosted by the Baylor College of Medicine Neuroscience Department, teaching participants how to convert data to NWB and publish it on DANDI." +draft: false +organizers: + - "Ryan Ly" + - "Ben Dichter" +registration: "RSVP for the talk and/or workshop [here](https://forms.gle/rroCJtJBdSRuqft46). The event is free and open to all, but registration is required for security purposes." +resources: + "Event Flyer": "/images/events/workshop-2024-bcm/nwb_dandi_bcm_2024_flyer.pdf" +--- + +# NWB and DANDI Workshop +## Hosted by the Baylor College of Medicine Neuroscience Department + +Join us for an interactive workshop on [Neurodata Without Borders (NWB)](https://nwb.org), a data standard for neurophysiology, and the [DANDI Archive](https://dandiarchive.org), a collaboration platform for publishing, sharing, and processing neurophysiology data. Learn how to use these resources to maximize the impact of your data while complying with the new NIH data sharing and management policies. + +Representatives from the NWB and DANDI teams, Ryan Ly and Ben Dichter, will provide an overview of the NWB software ecosystem and teach you how to convert data to NWB and publish data on DANDI. + +## Dates and Location + +- **Dates:** April 15-16, 2024 +- **Location:** [BCM Main (1 Baylor Plaza), Baylor College of Medicine, Houston, TX](https://maps.app.goo.gl/BNVgE71jAocqLQGr5) + +## Agenda + +### April 15, 11am - 3pm, [Cullen Building](https://maps.app.goo.gl/mfJwjmrHbM7ygEMT7) 111A: NWB and DANDI training + +* 11-12: Introduction to NWB and DANDI + * Core Format + * Extensions + * Analysis and visualization tools + * Other NWB Events +* 12-1: Networking lunch +* 1-2: Converting data to NWB + * NWB GUIDE + * NeuroConv + * PyNWB and MatNWB APIs + * Extensions +* 2-3: Publishing and accessing data on the DANDI Archive + * Uploading data + * DANDI Metadata + * Neurosift + * DANDI Hub + * Dendro + * DANDI API + +### April 16, 9am - 3pm, [DeBakey](https://maps.app.goo.gl/cmNxGjrzG2K8xF7m8) M303 & M305: NWB and DANDI hacking & office hours + +Participants will bring their own data and work with the NWB and DANDI teams to convert their data to NWB and publish it on DANDI. + +## Resources + +- [Event Flyer](/images/events/workshop-2024-bcm/nwb_dandi_bcm_2024_flyer.pdf) diff --git a/content/events/workshop-2024-incf.md b/content/events/workshop-2024-incf.md new file mode 100644 index 0000000..41d31eb --- /dev/null +++ b/content/events/workshop-2024-incf.md @@ -0,0 +1,61 @@ +--- +title: "NWB and DANDI Workshop at INCF Assembly 2024" +date: 2024-09-26 +endDate: 2024-09-27 +location: "INCF Assembly 2024" +eventType: "Workshop" +image: "/images/events/workshop-2024-incf/nwb+dandi_logo.png" +weight: 20240926 +summary: "An interactive workshop on Neurodata Without Borders (NWB) and the DANDI Archive, teaching participants how to use these resources to maximize the impact of their data while complying with the new NIH data sharing and management policies." +draft: false +organizers: + - "Ben Dichter" + - "Ryan Ly" + - "Oliver Rübel" +--- + +# NWB and DANDI Workshop at INCF Assembly 2024 + +Join us for an interactive workshop on [Neurodata Without Borders (NWB)](https://nwb.org), a data standard for neurophysiology, and the [DANDI Archive](https://dandiarchive.org), a collaboration platform for publishing, sharing, and processing neurophysiology data. Learn how to use these resources to maximize the impact of your data while complying with the new NIH data sharing and management policies. + +Representatives from the NWB and DANDI teams, Ben Dichter, Ryan Ly, and Oliver Rübel, will provide an overview of the NWB software ecosystem and teach you how to convert data to NWB and publish data on DANDI. + +## Dates and Location + +* **Dates:** September 26-27, 2024 +* **Location:** INCF Assembly 2024 + +## Agenda + +### Day 1: September 26, Lectures and Tutorials + +* **11:00 AM - 12:00 PM:** Introduction to NWB and DANDI + * Core Format + * Extensions + * Analysis and visualization tools + * Other NWB Events +* **12:00 PM - 1:00 PM:** Networking lunch +* **1:00 PM - 2:00 PM:** Converting data to NWB + * NWB GUIDE + * NeuroConv + * PyNWB and MatNWB APIs + * Extensions +* **2:00 PM - 3:00 PM:** Publishing and accessing data on the DANDI Archive + * Uploading data + * DANDI Metadata + * Neurosift + * DANDI Hub + * Dendro + * DANDI API +* **3:00 PM - 5:00 PM:** Hackathon + * Convert your own data to NWB + +### Day 2: September 27, Hackathon + +* **9:00 AM - 5:00 PM:** Hackathon + +Participants will bring their own data and work with the NWB and DANDI teams to convert their data to NWB and publish it on DANDI. + +## What to Bring + +Participants should bring their own laptops and data that they would like to convert to NWB and publish on DANDI. The NWB and DANDI teams will be available to help with the conversion process. diff --git a/content/events/workshop-2024-jhu.md b/content/events/workshop-2024-jhu.md new file mode 100644 index 0000000..7b50912 --- /dev/null +++ b/content/events/workshop-2024-jhu.md @@ -0,0 +1,80 @@ +--- +title: "NWB and DANDI Workshop at Johns Hopkins University" +date: 2024-06-20 +endDate: 2024-06-21 +location: "Johns Hopkins University, Baltimore, MD, USA" +eventType: "Workshop" +image: "/images/events/workshop-2024-jhu/nwb+dandi_logo.png" +weight: 20240620 +summary: "An interactive workshop hosted by the Kavli Neuroscience Discovery Institute at Johns Hopkins University on Neurodata Without Borders (NWB) and the DANDI Archive, teaching participants how to use these resources to maximize the impact of their data while complying with the new NIH data sharing and management policies." +draft: false +organizers: + - "Ben Dichter" + - "Ryan Ly" + - "Stephanie Prince" +--- + +# NWB and DANDI Workshop at Johns Hopkins University + +Join us for an interactive workshop on [Neurodata Without Borders (NWB)](https://nwb.org), a data standard for neurophysiology, and the [DANDI Archive](https://dandiarchive.org), a collaboration platform for publishing, sharing, and processing neurophysiology data. Learn how to use these resources to maximize the impact of your data while complying with the new NIH data sharing and management policies. + +Representatives from the NWB and DANDI teams, Ben Dichter, Ryan Ly, and Stephanie Prince, will provide an overview of the NWB software ecosystem and teach you how to convert data to NWB and publish data on DANDI. + +## Dates and Location + +* **Dates:** June 20-21, 2024 +* **Locations:** Shaffer Hall and Clark Hall, Johns Hopkins University, Baltimore, MD, USA + +## Agenda + +### Day 1: June 20, Lectures and Tutorials - Location: Shaffer 3 + +* **10:30 - 11:30 AM:** Introduction to NWB and DANDI + * Intro to Neurodata Without Borders (NWB) + * Intro to DANDI Archive + * NWB Extensions + * Analysis and visualization tools + * OpenScope DataBook + * Other NWB Events + * Download the GUIDE +* **11:30 AM - 12:15 PM:** NWB GUIDE tutorial. Follow a self-paced walk-through of converting data to NWB and uploading to DANDI using the new NWB GUIDE application. +* **12:30 - 1:15 PM:** Networking lunch +* **1:30 - 2:30 PM:** Walk-through of NeuroConv, PyNWB and MatNWB. These software libraries provide more flexibility than the GUIDE app. This session will walk through their usage and tutorials. +* **2:30 - 3:00 PM:** Interactive DANDI Demo. Explore the features of DANDI, including how to find and analyze datasets. Topics include: + * Navigating DANDI + * Neurosift + * Search + * DANDI Hub +* **3:00 - 3:15 PM:** Break +* **3:15 - 4:00 PM:** Interactive demos for analyzing data on DANDI Hub. + * Analysis of open data from the Moser Lab in Python on DANDI Hub + * Analysis of Dandiset 000011 in MATLAB on DANDI Hub +* **4:00 - 4:30 PM:** Interactive demo of Dendro. Follow this self-paced tutorial to learn how to automatically run data processing apps in Dendro, a cloud-based data analysis application. +* **4:30 - 5:00 PM:** BYOD (Bring Your Own Data) Hacking. Developers will be available for 1-1 support. + +### Day 2: June 21, Hackathon - Location: Clark Hall 316 + +* **10:00 AM - 4:00 PM:** BYOD (Bring Your Own Data) Hacking. + +Developers will be available for 1-1 support. Targeted break-outs in a second room based on participant interest. Topics might include: + * Details on specific experiment modalities + * Building and using NWB extensions + * Advanced data storage + +## Additional Session + +On Day 1, we will also host a separate event for early-stage trainees. + +### Day 1, Thursday, June 20 - Location: Clark Hall 110 + +* **6:00 - 6:45 PM:** Intro to Open Neurophysiology with NWB and DANDI. + +Early-year graduate students, research assistants, and advanced undergraduates are specially invited to an evening workshop to learn about the Neurodata Without Borders (NWB) data standard and DANDI Archive for neurophysiology. The session will be focused on how to get started with using the NWB data standard and reusing public NWB data in your research projects. **Pizza will be served.** + +Others are welcome to join but note that the session will repeat much of the same material presented during the morning/afternoon lectures and tutorials. + +* **6:45 - 7:00 PM:** Q+A and Discussion + +## Registration + +The event is free and open to all through the Kavli Neuroscience Discovery Institute. Please email sviswa10@jhmi.edu with any questions. diff --git a/content/events/workshop-2025-unam.md b/content/events/workshop-2025-unam.md new file mode 100644 index 0000000..8a5ea90 --- /dev/null +++ b/content/events/workshop-2025-unam.md @@ -0,0 +1,93 @@ +--- +title: "NWB and DANDI Workshop at UNAM" +date: 2025-02-19 +endDate: 2025-02-20 +location: "Universidad Nacional Autónoma de México, Mexico City, Mexico" +eventType: "Workshop" +image: "/images/events/workshop-2025-unam/nwb_logo_brain_text_transp_hor.png" +weight: 20250219 +summary: "An interactive workshop on Neurodata Without Borders (NWB) and the DANDI Archive, hosted by the Universidad Nacional Autónoma de México (UNAM), teaching participants how to use these resources to maximize the impact of their data." +draft: false +organizers: + - "Dr. Luis Lemus (Host)" + - "Benjamin Dichter, Founder & CEO, CatalystNeuro" + - "Ramon Heberto Martinez Mayorquin, Sr. Research Software Engineer, CatalystNeuro" +registration: "Registration is required for both in-person and remote attendance. Please fill out the registration form [here](https://docs.google.com/forms/d/e/1FAIpQLSdJ_CkRdeN02v1oU5SQFfhJ-v7MtkAna_OfAL7FmYjDqpdYrQ/viewform?usp=preview)." +--- + +# NWB and DANDI Workshop +## Hosted by the Universidad Nacional Autónoma de México (UNAM) + +Join us for an interactive workshop on [Neurodata Without Borders (NWB)](https://nwb.org), a data standard for neurophysiology, and the [DANDI Archive](https://dandiarchive.org), a collaboration platform for publishing, sharing, and processing neurophysiology data. Learn how to use these resources to maximize the impact of your data while complying with the new NIH data sharing and management policies. + +## Target Audience + +This workshop is designed for neuroscience researchers at all career stages, from undergraduate students working in labs to graduate students, post-doctoral researchers, and principal investigators. No prior programming experience is required. + +## Dates and Location + +- **Dates:** February 19-20, 2025 +- **Location:** Antonio Peña Auditorium, IFC, Universidad Nacional Autónoma de México, Mexico City, Mexico + +## Agenda + +### February 19, Day 1: NWB and DANDI Training +*Format: In-person + Remote* + +**11:00 AM - 12:00 PM: Open Neurophysiology with NWB and DANDI** + +*Overview session suitable for all attendees, including lab leaders* + +* Introduction to NWB and DANDI ecosystems +* NWB core format fundamentals +* Available conversion tools +* NWB extensions system +* Analysis and visualization toolkit +* Data reuse capabilities +* Upcoming NWB community events + +**12:00 PM - 1:00 PM: Lunch Break** + +**1:00 PM - 3:00 PM: Technical Implementation Session** + +*Detailed session for hands-on implementers* + +*Data Conversion* +* NWB GUIDE walkthrough +* NeuroConv tutorial +* PyNWB and MatNWB API usage +* Creating custom extensions + +*DANDI Publication* +* Data upload workflow +* DANDI metadata requirements +* Neurosift visualization tools +* DANDI Hub features +* Dendro integration +* DANDI API implementation + +*Data Analysis* +* DANDI dataset discovery +* NWB file handling +* Analysis workflow examples +* Visualization techniques +* Reproducibility best practices + +### February 20, Day 2, 10am - 4pm: NWB and DANDI Hacking +*Format: In-person Only* + +*Hands-on Workshop with Your Data* +* One-on-one assistance with: + * Data conversion to NWB + * Custom extension development + * DANDI data publication + * Data management optimization + +## Prerequisites + +* No prior programming experience is required +* For Day 2, participants should bring their own neurophysiology data they wish to convert to NWB format + +## Questions? + +For any questions about the workshop, please contact Luis Lemus. diff --git a/content/events/workshop-2025-uwashington.md b/content/events/workshop-2025-uwashington.md new file mode 100644 index 0000000..9341748 --- /dev/null +++ b/content/events/workshop-2025-uwashington.md @@ -0,0 +1,95 @@ +--- +title: "NWB and DANDI Workshop at University of Washington" +date: 2025-04-07 +endDate: 2025-04-08 +location: "University of Washington, Seattle, WA, USA" +eventType: "Workshop" +image: "/images/events/workshop-2025-uwashington/nwb+dandi_logo.png" +weight: 20250407 +summary: "An interactive workshop on Neurodata Without Borders (NWB) and the DANDI Archive, hosted by the University of Washington, teaching participants how to use these resources to maximize the impact of their data." +draft: false +organizers: + - "Benjamin Dichter, Founder & CEO, CatalystNeuro" + - "Oliver Ruebel, Staff Scientist, Lawrence Berkeley National Laboratory" +--- + +# NWB and DANDI Workshop +## Hosted by the University of Washington + +Join us for an interactive workshop on [Neurodata Without Borders (NWB)](https://nwb.org), a data standard for neurophysiology, and the [DANDI Archive](https://dandiarchive.org), a collaboration platform for publishing, sharing, and processing neurophysiology data. Learn how to use these resources to maximize the impact of your data while complying with the new NIH data sharing and management policies. + +## Target Audience + +This workshop is designed for neuroscience researchers at all career stages, from undergraduate students working in labs to graduate students, post-doctoral researchers, and principal investigators. No prior programming experience is required. + +## Dates and Location + +- **Dates:** April 7-8, 2025 +- **Location:** South Campus Center (SOCC) 354, University of Washington, Seattle, WA + +## Agenda + +### April 7, Day 1: NWB and DANDI Training + +#### 11am-12pm: Open Neurophysiology with NWB and DANDI + +*Overview session suitable for all attendees, including lab leaders* + +* Introduction to NWB and DANDI ecosystems +* NWB core format fundamentals +* Available conversion tools +* NWB extensions system +* Analysis and visualization toolkit +* Data reuse capabilities +* Upcoming NWB community events + +#### 1 - 3:30pm: Technical Implementation + +*Detailed session for hands-on implementers* + +**Data Conversion** +* NWB GUIDE walkthrough +* NeuroConv tutorial +* PyNWB and MatNWB API usage +* Creating custom extensions + +**DANDI Publication** +* Data upload workflow +* DANDI metadata requirements +* Neurosift visualization tools +* DANDI API implementation + +**Data Analysis** +* DANDI dataset discovery +* NWB file handling +* Analysis workflow examples +* Visualization techniques +* Reproducibility best practices + +#### 6 - 6:45pm: Undergrad-focused intro to NWB & DANDI (with pizza!) + +* Open data in neuroscience +* What is NWB and DANDI +* How to find and use relevant datasets + +### April 8, Day 2, 10am-3pm: NWB and DANDI Hacking + +**Hands-on Workshop with Your Data** +* One-on-one assistance with: + * Data conversion to NWB + * Custom extension development + * DANDI data publication + * Data management optimization + +## Prerequisites + +* No prior programming experience is required +* For Day 2, participants should bring their own neurophysiology data they wish to convert to NWB format + +## Registration + +Registration details will be announced soon. + +## Questions? + +For any questions about the workshop, please contact the organizers. diff --git a/hugo.yaml b/hugo.yaml index c6ef2fd..e0f505a 100644 --- a/hugo.yaml +++ b/hugo.yaml @@ -2,6 +2,9 @@ baseURL: https://neurodatawithoutborders.github.io/ languageCode: en title: Neurodata Without Borders +# Build Settings +buildFuture: true + # Pagination pagination: pagerSize: 10 diff --git a/layouts/events/list.html b/layouts/events/list.html index 1a0ff49..0f99373 100644 --- a/layouts/events/list.html +++ b/layouts/events/list.html @@ -1,101 +1,133 @@ {{ define "main" }} - {{/* Hero Section */}} -
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