Merge branch 'main' into add-ndrh-notebooks

HCK20_2024_OpenNeurodataShowcase/README.md

@@ -6,15 +6,11 @@
 * [Dates and Location](#dates-and-location)
 * [Objective](#objective)
 * [Eligibility](#eligibility)
-* [Application](#application)
+* [Registration](#registration)
 * [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
@@ -39,11 +35,11 @@ This virtual event is open to anyone interested in neurophysiology data, includi
 * Undergraduates and high school students interested in learning about neuroscience
 * Open science advocates
 
-## Application
+## Registration
 
 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).
+[//]: # (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
 
@@ -53,10 +49,14 @@ If you are interested in **presenting** your dandiset(s), register as a presente
 | Introduction to the virtual data showcase | Organizers        | 9:00-9:20am   |
 | Virtual poster session                    | Data Contributors | 9:20-10:30am  |
 
-<!--
 ## 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)
 
 ## Organizing Committee
 

HCK21_2024_Janelia_NDRH/README.md

@@ -6,14 +6,16 @@
 [//]: # (* [Report](#report))
 * [Dates and Location](#dates-and-location)
 * [Objective](#objective)
-* [Eligibility](#eligibility)
-* [Application](#application)
 * [Logistics](#logistics)
 * [Organizing Committee](#organizing-committee)
 * [Resources](#resources)
 * [What to bring?](#what-to-bring)
+* [Schedule](#schedule)
 * [Disclaimer](#disclaimer)
 
+[//]: # (* [Eligibility](#eligibility))
+[//]: # (* [Application](#application))
+
 
 ## Dates and Location
 
@@ -50,6 +52,7 @@ awards $50,000 (USD) of funding to continue data reanalysis projects that come o
 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.
 
+<!-- 
 ## Eligibility
 
 This course is intended for PhD students, postdoctoral researchers, principal investigators, or similar.
@@ -63,6 +66,8 @@ Space for the event is limited. Apply to attend NeuroDataReHack 2024 [here](http
 * Application deadline: March 10
 * Notification of admission decisions: April 1
 
+-->
+
 ## Logistics
 
 Thanks to the generous sponsorship of The Janelia Research Campus, this event will be free to participants:
@@ -96,14 +101,12 @@ instructions on how to install PyNWB, see
 on how to install MatNWB, see
 [the MatNWB documentation](https://github.com/NeurodataWithoutBorders/matnwb/blob/master/README.md)
 
-<!--
 ## Schedule
 Tentative schedule:
 
 <img align="center" alt="Agenda NeuroDataReHack 2023" src="AgendaNeuroDataReHack2024.png" width="870">
 
 [PDF](AgendaNeuroDataReHack2024.pdf)
--->
 
 ## Disclaimer
 

README.md

@@ -3,13 +3,13 @@
 ## Hackathon Events
 
 ### Upcoming Events
-- [NWB Data Conversion Workshop: June 2024](HCK19_2024_Remote/README.md) - **June 12 - 14, 2024** (virtual)
-- [NWB and DANDI Workshop: June 2024](Workshop_2024_JHU/README.md) - **June 20 - 21, 2024** at Kavli Neuroscience Discovery Institute at Johns Hopkins University, Baltimore, MD, USA
-- [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**.
 - [NWB and DANDI Workshop INCF: September 2024](Workshop_2024_INCF/README.md) -  **September 26-27, 2024** in Austin, Texas, USA.
 
 ### Past Events
+- [Open Neurodata Showcase: Virtual, July, 2024](HCK20_2024_OpenNeurodataShowcase/README.md): **July 2, 2024** (virtual)
+- [NWB and DANDI Workshop: June 2024](Workshop_2024_JHU/README.md) - **June 20 - 21, 2024** at Kavli Neuroscience Discovery Institute at Johns Hopkins University, Baltimore, MD, USA
+- [NWB Data Conversion Workshop: June 2024](HCK19_2024_Remote/README.md) - **June 12 - 14, 2024** (virtual)
 - [NWB Developer Hackathon: April 2024](HCK18_2024_Dev_Hackathon_DataJoint/README.md): **April 17 - 19, 2024** 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
 - [Cosyne: February 2024](Cosyne_2024/README.md) - A tutorial session on NWB and DANDI was held during the

Workshop_2024_JHU/README.md

@@ -6,15 +6,15 @@
 
 **Dates:** June 20-21, 2024
 
-**Tentative Location:** [Clark Hall, Johns Hopkins University, Baltimore, MD, USA](https://maps.app.goo.gl/SUbwXYKHWnRGoRF97)
+**Locations:** Shaffer Hall and Clark Hall, Johns Hopkins University, Baltimore, MD, USA
 
 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.
 
 ## Agenda
 
-**Day 1: June 20, Lectures and Tutorials**
+**Day 1: June 20, Lectures and Tutorials** - Location: Shaffer 3
 
 * **10:30 - 11:30:** Introduction to NWB and DANDI
   * Intro to Neurodata Without Borders (NWB)
@@ -24,54 +24,62 @@ Representatives from the NWB and DANDI teams, Ben Dichter, Ryan Ly, and Stephani
   * OpenScope DataBook
   * Other NWB Events
   * Download the GUIDE
-* **11:30 - 12:** 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 - 1:** Networking lunch
-* **1 - 2:** Walk-through of NeuroConv, PyNWB and MatNWB. These software libraries
+* **11:30 - 12:15:** 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** Networking lunch
+* **1:30 - 2:30:** 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.
-* **2:00 – 2:30:** Interactive DANDI Demo. Explore the features of DANDI, including how to
+* **2:30 – 3:00:** Interactive DANDI Demo. Explore the features of DANDI, including how to
   find and analyze datasets. Topics include:
   * Navigating DANDI
   * Neurosift
   * Search
   * DANDI Hub
-* **2:30 - 2:45:** Break
-* **2:45 – 3:30:** Interactive demos for analyzing data on DANDI Hub.
+* **3:00 - 3:15:** Break
+* **3:15 – 4:00:** 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
-* **3:30 - 4:** Interactive demo of Dendro. Follow this self-paced tutorial to learn how to
+* **4:00 - 4:30:** 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 - 5:** BYOD (Bring Your Own Data) Hacking. Developers will be available for 1-1
+* **4:30 - 5:00:** BYOD (Bring Your Own Data) Hacking. Developers will be available for 1-1
   support.
 
-**Day 2: June 21, Hackathon**
+**Day 2: June 21, Hackathon** - Location: Clark Hall 316
 
-**10 AM - 4 PM:** BYOD (Bring Your Own Data) Hacking. Developers will be available
+**10 AM - 4 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, or 
   * advanced data storage.
 
 
+## Additional session
+
 On Day 1, we will also host a separate event for early-stage trainees.
 
-**Day 1, Thursday, June 20**
+**Day 1, Thursday, June 20** - Location: Clark Hall 110
 
-6 - 6:45 PM: Intro to Open Neurophysiology with NWB and DANDI.
+**6 - 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 re-using public NWB data in your
-research projects. **Pizza will be served.** Others are welcome to join but note that the
+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 PM: Q+A and Discussion
+**6:45 - 7 PM**: Q+A and Discussion
+
+## Registration
 
-<!-- ## Registration
+The event is free and open to all through the Kavli Neuroscience Discovery Institute.
+Please email [email protected] with any questions.
 
-The event is free and open to all, but registration is required for security purposes. -->
+## Flyer
 
-<!-- ## Flyer
+Download the event flyer [here](KavliNDI NWB Workshop_Flyer.pdf) and agenda [here](NWB Workshop_Agenda.pdf).
 
-Download the event flyer [here](images/nwb_dandi_bcm_2024_flyer.pdf). -->