NeurodataWithoutBorders · rly · May 15, 2025 · May 2, 2025 · May 2, 2025 · May 2, 2025
diff --git a/content/events/cosyne-2019.md b/content/events/cosyne-2019.md
@@ -16,9 +16,9 @@ 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"
+  "Python jupyter notebook": "http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/Cosyne_2019/cosyne_NWB_tutorial_2019_python.html"
+  "MATLAB code": "http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/Cosyne_2019/cosyne_NWB_tutorial_2019_matlab.html"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/Cosyne_2019"
 ---
 
 ## Dates and Location
@@ -29,9 +29,9 @@ resources:
 
 ## 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 [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://pynwb.readthedocs.io) and [MatNWB](https://neurodatawithoutborders.github.io/matnwb) 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 [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/about-nwb/) 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.
 

diff --git a/content/events/docuthon-2022-september.md b/content/events/docuthon-2022-september.md
@@ -15,7 +15,7 @@ organizers:
   - "Matthew Avaylon"
 registration: "Registration is now closed."
 resources:
-  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/Docuthon_2022_09"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/Docuthon_2022_09"
 ---
 
 ## Dates and Location

diff --git a/content/events/docuthon-2022-spring.md b/content/events/docuthon-2022-spring.md
@@ -15,7 +15,7 @@ organizers:
   - "Matthew Avaylon"
 registration: "Registration is now closed."
 resources:
-  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/Docuthon_2022"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/Docuthon_2022"
   "NWB Documentation Survey": "https://forms.gle/TadZBRKJpwEWeErv8"
 ---
 

diff --git a/content/events/hck04-2018-seattle.md b/content/events/hck04-2018-seattle.md
@@ -15,7 +15,7 @@ organizers:
   - "Justin Kiggins"
 registration: "Registration is now closed."
 resources:
-  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/master/HCK04_2018_Seattle"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK04_2018_Seattle"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck05-2018-berkeley.md b/content/events/hck05-2018-berkeley.md
@@ -14,8 +14,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK05_2018_Berkeley/report/report-5th-nwbn-hackathon-at-lbnl.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK05_2018_Berkeley"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck06-2019-janelia.md b/content/events/hck06-2019-janelia.md
@@ -15,8 +15,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK06_2019_Janelia/report/Report___6th_NWB_N_Hackathon.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK06_2019_Janelia"
   "Slides": "https://drive.google.com/drive/folders/18oG1rRJpluXQJJQaH4xbz6u58LXPiZbI?usp=sharing"
 ---
 
@@ -45,8 +45,8 @@ The slides for the talks presented during the User Days are available [here.](ht
 
 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)
+* [python jupyter notebook](http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK06_2019_Janelia/NWB_tutorial_2019_python.html)
+* [matlab code](http://htmlpreview.github.io/?https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK06_2019_Janelia/NWB_tutorial_2019_matlab.html)
 
 Tom Davidson's 'early adopter experiences' talk (Day 1):
 

diff --git a/content/events/hck07-2020-seattle.md b/content/events/hck07-2020-seattle.md
@@ -13,7 +13,7 @@ organizers:
   - "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"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK07_2020_Seattle"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck08-2020-remote.md b/content/events/hck08-2020-remote.md
@@ -16,8 +16,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK08_2020_Remote/report/Report___8th_NWB_Hackathon.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK08_2020_Remote"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck09-2020-remote.md b/content/events/hck09-2020-remote.md
@@ -16,8 +16,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK09_2020_Remote/report/Report___9th_NWB_Hackathon.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK09_2020_Remote"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck10-2021-remote.md b/content/events/hck10-2021-remote.md
@@ -14,8 +14,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK10_2021_Remote/report/Report___10th_NWB_and_DANDI_Hackathon.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK10_2021_Remote"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck11-2021-remote.md b/content/events/hck11-2021-remote.md
@@ -16,8 +16,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK11_2021_Remote/report/Report___11th_NWB_User_Days_at_INCF.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK11_2021_Remote"
   "INCF Event Page": "https://www.incf.org/neurodata-without-borders-nwb-user-training-workshop"
 ---
 

diff --git a/content/events/hck12-2022-remote.md b/content/events/hck12-2022-remote.md
@@ -14,8 +14,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK12_2022_Remote/report/Report___12th_NWB_and_DANDI_Hackathon.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK12_2022_Remote"
 ---
 
 ## Dates and Location

diff --git a/content/events/hck13-2022-janelia.md b/content/events/hck13-2022-janelia.md
@@ -13,9 +13,9 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK13_2022_Janelia/report/Report___13th_NWB_and_User_Days_at_HHMI_Janelia.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK13_2022_Janelia"
+  "Tutorial Materials": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK13_2022_Janelia/projects"
 ---
 
 ## Dates and Location
@@ -33,8 +33,8 @@ Note: This event was meant to foster community and collaboration around NWB, not
 
 ## 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)
+* [BEADL Tutorial](https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK13_2022_Janelia/projects/beadl_tutorial)
+* [NeuroConv Tutorial](https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK13_2022_Janelia/projects/neuroconv_tutorial)
 
 ## Resources
 
@@ -45,7 +45,7 @@ Recordings of talks were made available on the [NWB Youtube channel](https://www
 
 * 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)
+* Bring your laptop with appropriate software installed. For instructions on how to install PyNWB see [https://pynwb.readthedocs.io/en/latest/install_users.html](https://pynwb.readthedocs.io/en/latest/install_users.html)
 
 ## Additional Organizational Support
 

diff --git a/content/events/hck14-2022-seattle-rh.md b/content/events/hck14-2022-seattle-rh.md
@@ -16,8 +16,8 @@ organizers:
   - "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"
+  "Final Report (PDF)": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/blob/main/HCK14_2022_Seattle_RH/report/Report_Neurodata_Rehack_v2.pdf"
+  "GitHub Repository": "https://github.com/NeurodataWithoutBorders/nwb_hackathons/tree/main/HCK14_2022_Seattle_RH"
   "Allen Institute Event Page": "https://alleninstitute.org/what-we-do/brain-science/events-training/2022-neurodatarehack-hackathon/"
 ---
 
@@ -71,7 +71,7 @@ Recordings of talks were made available on the [NWB Youtube channel](https://www
 ## 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)
+* Bring your laptop with appropriate software installed. For instructions on how to install PyNWB, see [the PyNWB documentation](https://pynwb.readthedocs.io/en/latest/install_users.html). For instructions on how to install MatNWB, see [the MatNWB documentation](https://matnwb.readthedocs.io)
 
 ## Additional Organizational Support
 

diff --git a/content/events/hck21-2024-janelia-ndrh.md b/content/events/hck21-2024-janelia-ndrh.md
@@ -60,7 +60,7 @@ Resources to help participants prepare for the event:
 
 ## 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).
+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://matnwb.readthedocs.io/en/latest/).
 
 ## Past Events
 

diff --git a/content/events/hck24-2025-janelia-ndrh.md b/content/events/hck24-2025-janelia-ndrh.md
@@ -16,7 +16,7 @@ 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"
+  "MatNWB Documentation": "https://matnwb.readthedocs.io"
 aliases:
   - /nwb_hackathons/HCK24_2025_Janelia_NDRH
 ---
@@ -81,7 +81,7 @@ Bring a laptop with appropriate software installed. Python should be installed a
 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)
+[the MatNWB documentation](https://matnwb.readthedocs.io)
 
 ## Testimonials from NeuroDataReHack 2024
 

diff --git a/content/tools/analysis/extract.md b/content/tools/analysis/extract.md
@@ -23,5 +23,5 @@ EXTRACT (Tractable and Robust Automated Cell extraction Tool) is designed for ca
 ## Resources
 
 - [Source Code](https://github.com/schnitzer-lab/EXTRACT-public)
-- [NWB Tutorials](https://github.com/schnitzer-lab/EXTRACT-public/tree/master/Learning%20materials/NWB%20Tutorials)
+- [NWB Tutorials](https://github.com/schnitzer-lab/EXTRACT-public/tree/master/Learning-materials/Additional%20demos/NWB%20Demos)
 - [Publication](https://www.biorxiv.org/content/10.1101/2021.03.24.436279v2)
diff --git a/content/tools/analysis/pynapple.md b/content/tools/analysis/pynapple.md
@@ -31,6 +31,6 @@ Pynapple is a unified toolbox for integrated analysis of multiple data sources.
 ## Resources
 
 - [Documentation](https://pynapple-org.github.io/pynapple/)
-- [DANDI Demo](https://pynapple-org.github.io/pynapple/generated/gallery/tutorial_pynapple_dandi/)
+- [DANDI Demo](https://pynapple.org/examples/tutorial_pynapple_dandi.html)
 - [Source Code](https://github.com/pynapple-org/pynapple)
 - [Twitter](https://twitter.com/thepynapple)