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98 changes: 98 additions & 0 deletions HCK22_2025_DataConversion_Remote/README.md
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<img alt="NWB Data Conversion Workshop Banner" src="images/logo_brain_text_white_hor.png">

# NWB Data Conversion Workshop 2025

* [Dates and Location](#dates-and-location)
* [Registration](#registration)
* [Logistics](#logistics)
* [Organizing Committee](#organizing-committee)
* [Resources](#resources)
* [What to bring?](#what-to-bring)
* [Objective](#objective)
* [Agenda](#agenda)
* [Code of Conduct](#code-of-conduct)
* [Disclaimer](#disclaimer)


[//]: # (## Report)

[//]: # ()
[//]: # (The final report for the 2024 NWB Data Conversion Workshop is now available. You can also find recordings of the tutorials on the NeurodataWithoutBorders YouTube channel.)

[//]: # (- [Workshop report]&#40;https://drive.google.com/file/d/1rhgCXs_N1OLFDI4VyEQ_vpWnvldzJW31/view?usp=sharing&#41;)

[//]: # (- [Recorded tutorials]&#40;https://www.youtube.com/watch?v=xZiSesEVA3o&list=PL5wPNhoBP0ZB2sLuRKWqwgXf9V3FRl1bw&#41;)

## Dates and Location

- **Dates:** May 12-14, 2025
- **Location:** Virtual

## Registration

Registration has not opened yet.

[//]: # (Register for the event [here]&#40;https://forms.gle/pTsjRMEqsgCRo3VD8&#41;.)

## Logistics

We will be using Gather and Zoom for the meeting and will send an email in the days before the workshop with links.

## Organizing Committee

**Program chair:** [Steph Prince](https://crd.lbl.gov/divisions/scidata/computational-biosciences/members/staff/stephanie-prince/) and [Oliver Rübel](https://crd.lbl.gov/divisions/scidata/mla/staff/oliver-ruebel/)

## 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)
* 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 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.

## 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.


## Disclaimer

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.


7 changes: 7 additions & 0 deletions HCK22_2025_DataConversion_Remote/agenda/AGENDA.md
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Below is the current draft of the agenda. All times are in Pacific Time (PT, UTC-7). [Download Agenda](agenda/2025_data_conversion_workshop_agenda.pdf)

### Agenda

<a href="agenda/2025_data_conversion_workshop_agenda.pdf">
<img align="center" alt="Agenda for 2024 NWB Data Conversion Workshop" src="agenda/2025_data_conversion_workshop_agenda.png" width="870">
</a>
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148 changes: 148 additions & 0 deletions HCK24_2025_Janelia_NDRH/README.md
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[//]: # (<img alt="NeuroDataReHack banner" src="images/NDRH2025_banner.png">)

# NeuroDataReHack 2025
## *Generate new insights from existing neurophysiology data through secondary analysis*

[//]: # (* [Report]&#40;#report&#41;)
* [Dates and Location](#dates-and-location)
* [Objective](#objective)
* [Logistics](#logistics)
* [Organizing Committee](#organizing-committee)
* [Resources](#resources)
* [What to bring?](#what-to-bring)
* [Schedule](#schedule)
* [Disclaimer](#disclaimer)
* [Eligibility](#eligibility)
* [Application](#application)

[//]: # (## Report)

[//]: # ()
[//]: # (The final report for NeuroDataReHack 2024 is now available online at [[PDF]&#40;https://drive.usercontent.google.com/u/0/uc?id=1QYw9jmIpKPXPMLmhTnVIIWgbWHL5tPS3&export=download&#41;].)



## Dates and Location

- **Dates:** July 14-18, 2025
- **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)

## 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.


Prior to the workshop, we are organizing [Open Neurodata Showcase](../HCK23_2025_OpenNeurodataShowcase/README.md) where
attendees can meet the contributors behind the neurophysiology datasets and explore virtual posters. Visit the
[event page](../HCK23_2025_OpenNeurodataShowcase/README.md#application) 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.
* Create educational content that uses open data.

<!--
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 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.

## 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.


## Application

Space for the event is limited. Apply to attend NeuroDataReHack 2025 [here](https://forms.gle/cR9sm5wjAt8oqTaT7).

[//]: # ()
[//]: # (* Application deadline: Feb 15)

[//]: # (* Notification of admission decisions: April 1)


## 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.

## Organizing Committee

**Program chairs:**
* Benjamin Dichter, CatalystNeuro
* Oliver Rübel, Lawrence Berkeley National Laboratory
* Ryan Ly, Lawrence Berkeley National Laboratory
* Steph Prince, Lawrence Berkeley National Laboratory

## Resources

Resources will be posted here to help participants prepare for the event.

* Slides from the 2024 NeuroDataReHack: [Google Drive](https://drive.google.com/drive/folders/1DAmQr4qWCamhj_2Zyke0kkHGvV8Kyq13?usp=sharing)
* Search API tutorials
* [Basic API tutorial](tutorials/simple_dandiset_search.ipynb)
* [Advanced API tutorial](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](../HCK14_2022_Seattle_RH/report/Report_Neurodata_Rehack_v2.pdf))
* A report of the second NeuroDataReHack event: ([PDF](../HCK16_2023_Granada_RH/report/Report__NeuroDataReHack_2023.pdf))
* A report of the third NeuroDataReHack event: ([PDF](https://drive.usercontent.google.com/u/0/uc?id=1QYw9jmIpKPXPMLmhTnVIIWgbWHL5tPS3&export=download))
* Recordings of talks will be made available on the [NWB Youtube channel](https://www.youtube.com/channel/UCfD_mU-EFz135a9TpNFJP5A).

[//]: # (## Schedule)

[//]: # (Tentative schedule:)

[//]: # ()
[//]: # (<img align="center" alt="Agenda NeuroDataReHack 2025" src="AgendaNeuroDataReHack2025.png" width="870">)

[//]: # ()
[//]: # ([PDF]&#40;AgendaNeuroDataReHack2024.pdf&#41;)

## Disclaimer

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.
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