Merge branch 'main' into bf-codespell

HCK18_2024_Dev_Hackathon_DataJoint/README.md

@@ -33,37 +33,36 @@ This is our first NWB hackathon event hosted by DataJoint. Working in the DataJo
 ## Dates and Location
 
 - **Pre-hackathon project pitch session:** TBD
-- **Dates:** Wednesday, April 17, 2024, 9 AM to Friday, April 19, 2024, 5 PM
+- **Dates:** Wednesday, April 17, 2024, 9 AM to Friday, April 19, 2024, 6 PM
 - **Location:** DataJoint headquarters, [4265 San Felipe St #1025, Houston, TX 77027](https://www.google.com/maps/place/4265+San+Felipe+St+%231025,+Houston,+TX+77027/data=!4m2!3m1!1s0x8640c15d907d761d:0x38a7f7a077419384?sa=X&ved=2ahUKEwih_8ykk_GAAxVzEEQIHb_sBvIQ8gF6BAgcEAA&ved=2ahUKEwih_8ykk_GAAxVzEEQIHb_sBvIQ8gF6BAgdEAI)
 
-We encourage participants to stay at the hackathon until Friday at 5 PM to participate in the final project presentations.
+We encourage participants to stay at the hackathon until Friday at 5:30 PM to participate in the final project presentations.
 
-Immediately prior to the NWB Developer Hackathon, DataJoint will be organizing a two-day workshop at the same location.
+Immediately prior to the NWB Developer Hackathon, DataJoint will be organizing the SciOps Summit 2024 at the same location.
 If you are interested in this DataJoint event, we encourage you to register for it as well.
-More details about this event are to come.
 
-DataJoint will also be organizing a social mixer event on the late afternoon of Tuesday, April 16
+DataJoint will also be organizing a social mixer event on Tuesday, April 16 at 5:30pm
 for DataJoint workshop participants to mix with NWB Developer Hackathon participants. We encourage participants to arrive early
 enough on Tuesday to attend this mixer.
 
 You can start attending the event(s) on different days for different experiences:
 
-- Start on Monday: full DJ + NWB
-- Tuesday: half DJ + NWB
-- Tuesday afternoon: DJ mixer + NWB
-- Wed-Fri: just NWB
-
+- NWB Developer Hackathon only: Join Wednesday to Friday
+- SciOps Summit 2024 and NWB Developer Hackathon: Join Monday to Friday
 
 ## Registration
 
-Register for the NWB Developer Hackathon and/or the DataJoint Workshop here: [https://forms.gle/xqDYeMy1rCQpRnYU9](https://forms.gle/xqDYeMy1rCQpRnYU9)
+[Register for the NWB Developer Hackathon](https://try.datajoint.com/nwb-hackathon2024)
 
+You can also register for the SciOps Summit 2024 [here](https://try.datajoint.com/sciops-summit-2024).
 
 ## Logistics
 
 ### Housing
 
-TBD
+Housing support is not provided, but we will organize a room block at the 
+[Hampton Inn Houston-Near The Galleria](https://www.hilton.com/en/hotels/houpohx-hampton-houston-near-the-galleria/), 
+which is a short walk to the event. Details TBD.
 
 ### Travel
 
@@ -74,12 +73,12 @@ the hackathon.
 
 ### Dining
 
-TBD
+Breakfast and lunch will be generously provided by DataJoint. 
 
 
 ## Organizing Committee
 
-**Site Chair:** TBD
+**Site Chair:** Kushal Bakshi
 
 **Program chairs:** [Ryan Ly](https://crd.lbl.gov/divisions/scidata/mla/staff/ryan-ly/) and [Ben Dichter](http://bendichter.com/)
 

HCK18_2024_Dev_Hackathon_DataJoint/agenda/AGENDA.md

@@ -1 +1,15 @@
-TBD
+ Below the current draft of the agenda.
+[Download Agenda](agenda/2024_developer_hackathon_agenda.pdf)
+
+### Agenda
+
+<a href="agenda/2024_developer_hackathon_agenda">
+    <img align="center" alt="Agenda for 2024 NWB Developer Hackathon" src="agenda/2024_developer_hackathon_agenda.png" width="870">
+</a>
+
+<!---### Agenda: Calendar--->
+
+<!---We will update the below calendar once the agenda has been finalized.--->
+
+<!---<iframe src="https://calendar.google.com/calendar/embed?mode=AGENDA&amp;height=600&amp;wkst=1&amp;bgcolor=%23FFFFFF&amp;src=lbl.gov_6b2ckprkr6s7eojvefua4a89a4%40group.calendar.google.com&amp;color=%23333333&amp;ctz=America%2FNew_York" style="border-width:0" width="800" height="600" frameborder="0" scrolling="no"></iframe>
+[How to add this calendar to your own?](CALENDAR_INSTRUCTIONS.md)--->

HCK19_2024_Remote/README.md

@@ -0,0 +1,91 @@
+<img alt="NWB Data Conversion Workshop Banner" src="images/logo_brain_text_white_hor.png">
+
+# NWB Data Conversion Workshop 2024
+
+  * [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)
+
+
+## Dates and Location
+
+- **Dates:** June 12-14, 2024
+- **Location:** Virtual
+
+## Registration
+
+Register for the event [here](https://forms.gle/pTsjRMEqsgCRo3VD8).
+
+## Logistics
+
+We will be using Zoom for the meeting. We will send an email in the days before the workshop with Zoom 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?
+
+* 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:
+  * [**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/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 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. During this workshop, we will also introduce and train users on NWB GUIDE, a 
+no-code user interface for data conversion. 
+
+**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.
+
+## Agenda
+
+{% include_relative agenda/AGENDA.md %}
+
+## 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.
+
+

HCK19_2024_Remote/agenda/AGENDA.md

@@ -0,0 +1,11 @@
+**The agenda is a work in 
+progress! Further details will be announced here as they become available**
+
+
+<!---### Agenda: Calendar--->
+
+<!---We will update the below calendar once the agenda has been finalized.--->
+
+<!---<iframe src="https://calendar.google.com/calendar/embed?mode=AGENDA&amp;height=600&amp;wkst=1&amp;bgcolor=%23FFFFFF&amp;src=lbl.gov_6b2ckprkr6s7eojvefua4a89a4%40group.calendar.google.com&amp;color=%23333333&amp;ctz=America%2FNew_York" style="border-width:0" width="800" height="600" frameborder="0" scrolling="no"></iframe>
+[How to add this calendar to your own?](CALENDAR_INSTRUCTIONS.md)--->
+

HCK20_2024_OpenNeurodataShowcase/README.md

@@ -0,0 +1,91 @@
+<img alt="OpenNeuroDataShowcase banner" src="images/open_neurodata_showcase_banner.png">
+
+# Open Neurodata Showcase 2024
+## *Meet the scientists who have publicly shared neurophysiology data.*
+
+* [Dates and Location](#dates-and-location)
+* [Objective](#objective)
+* [Eligibility](#eligibility)
+* [Application](#application)
+* [Virtual Data Showcase Agenda](#agenda)
+* [Organizing Committee](#organizing-committee)
+* [Disclaimer](#disclaimer)
+
+## Report
+
+The combined report for NeuroDataReHack 2023 and the Open Neurodata Showcase 2023 is now available online at [[PDF (GitHub)](../HCK16_2023_Granada_RH/report/Report__NeuroDataReHack_2023.pdf)] [[LaTeX (Overleaf)](https://www.overleaf.com/read/gzpkpyzcrvfr#1400b0)].
+
+## Dates and Location
+
+- **Dates:** July 2, 9 - 10:30AM PDT (UTC-7) 2024
+- **Location:** Virtual in Gather (link to be shared closer to the event date)
+
+## Objective
+[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.
+
+## 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
+
+## Application
+
+If you are interested in **attending** the event, register [here](https://forms.gle/amPd4h5kN9BPLX4g7). 
+
+If you are interested in **presenting** your dandiset(s), register as a presenter at Open Neurodata Showcase 2024 [here](https://forms.gle/FwMEEtvQUtzFiEhg7).
+
+## Virtual Data Showcase Agenda
+
+| Session                                   | Speakers          | Time: Pacific |
+|-------------------------------------------|-------------------|---------------|
+| Gather space opens to participants        |                   | 8:55am        |
+| Introduction to the virtual data showcase | Organizers        | 9:00-9:20am   |
+| Virtual poster session                    | Data Contributors | 9:20-10:30am  |
+
+<!--
+## Presenters
+
+-->
+
+## Organizing Committee
+
+**Program chairs:**
+* 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
+
+
+## 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.

HCK21_2024_Janelia_NDRH/README.md

@@ -3,7 +3,7 @@
 # NeuroDataReHack 2024
 ## *Generate new insights from existing neurophysiology data through secondary analysis*
 
-* [Report](#report)
+[//]: # (* [Report](#report))
 * [Dates and Location](#dates-and-location)
 * [Objective](#objective)
 * [Eligibility](#eligibility)
@@ -32,10 +32,10 @@ them on how to maximally utilize the archive and the NWB standard to incorporate
 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](../HCK16_2023_OpenNeuroDataShowcase/README.md) where attendees can meet the contributors behind the neurophysiology datasets and explore virtual posters. Visit the [event page](../HCK16_2023_OpenNeuroDataShowcase/README.md#application) to sign up
+
+Prior to the workshop, we are organizing [Open Neurodata Showcase](../HCK20_2024_OpenNeurodataShowcase/README.md) where attendees can meet the contributors behind the neurophysiology datasets and explore virtual posters. Visit the [event page](../HCK20_2024_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.
@@ -60,7 +60,7 @@ Applicants should have basic programming experience in Python or MATLAB and expe
 
 Space for the event is limited. Apply to attend NeuroDataReHack 2024 [here](https://forms.gle/tzumwuVgrkdD4zm36). 
 
-* Application deadline: March 1
+* Application deadline: March 10
 * Notification of admission decisions: April 1
 
 ## Logistics

README.md

@@ -3,14 +3,17 @@
 ## Hackathon Events
 
 ### Upcoming Events
-- [Brain Data Modeling Hackashop: February 2024](linkml_neurodata_hackashop_2024/README.md) - at the  [International Computer Science Institute (ICSI)](https://www.icsi.berkeley.edu) in Berkeley, CA, USA, **February 5-7 2024**.
-- [Cosyne: February 2024](Cosyne_2024/README.md) - A tutorial session on NWB and DANDI will be held during the
-  Computational and Systems Neuroscience (COSYNE) 2024 conference in Lisbon, Portugal on **February 29, 2024**.
-- [NWB Developer Hackathon: April 2024](HCK18_2024_Dev_Hackathon_DataJoint/README.md): **April 17 - 19, 2023** at DataJoint Headquarters in Houston, TX, USA
+- [NWB and DANDI Workshop: April 2024](Workshop_2024_BCM/README.md) - **April 15 - 16, 2024** at Baylor College of Medicine in Houston, TX, USA
+- [NWB Developer Hackathon: April 2024](HCK18_2024_Dev_Hackathon_DataJoint/README.md): **April 17 - 19, 2024** at DataJoint Headquarters in Houston, TX, USA
+- [NWB Data Conversion Workshop: June 2024](HCK19_2024_Remote/README.md) - **June 12 - 14, 2024** (virtual)
+- [Open Neurodata Showcase: Virtual, July, 2024](HCK20_2024_OpenNeurodataShowcase/README.md): **July 2, 2024** (virtual) 
 - [NeuroDataReHack: July 2024](HCK21_2024_Janelia_NDRH/README.md) - NeuroDataReHack 3 will be held at HHMI Janelia Research Campus in Ashburn, Virginia, USA **July 8-12, 2024**.
 
 
 ### Past Events
+- [Cosyne: February 2024](Cosyne_2024/README.md) - A tutorial session on NWB and DANDI was held during the
+  Computational and Systems Neuroscience (COSYNE) 2024 conference in Lisbon, Portugal on **February 29, 2024**.
+- [Brain Data Modeling Hackashop: February 2024](linkml_neurodata_hackashop_2024/README.md) - at the  [International Computer Science Institute (ICSI)](https://www.icsi.berkeley.edu) in Berkeley, CA, USA, **February 5-7 2024**.
 - [NWB and DANDI Workshop: September 2023](Workshop_2023_Princeton/README.md) - **September 14, 2023** at Princeton University, NJ, USA
 - [NeurodataReHack: September 2023](HCK16_2023_Granada_RH/README.md) - **Sept 5 - 8, 2023** NeuroDataReHack 2 was held in Granada, Spain as a satellite for the [IBRO World Congress](https://ibro2023.org/).
 - [Open NeuroData Showcase: Virtual, Aug 28, 2023](HCK17_2023_OpenNeuroDataShowcase/README.md): **Aug 28, 2023** (virtual)