diff --git a/content/events/cosyne-2019.md b/content/events/cosyne-2019.md index 325fcd9..637ce18 100644 --- 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 index ce0b056..0e984c5 100644 --- 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 index 5937059..9c1ccf5 100644 --- 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 index b6fa3f5..d4dcd9d 100644 --- 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 index c92ece3..6c42764 100644 --- 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 index d8e946e..32a2fd5 100644 --- 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 index e1a171d..aa1037f 100644 --- 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 index 9184e52..443a33a 100644 --- 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 index 037a3f2..c9eebe0 100644 --- 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 index cd9613e..ac3bf31 100644 --- 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 index db4a0df..c29c850 100644 --- 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 index 06babbe..d70f4d3 100644 --- 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 index 302c32f..d66d9b9 100644 --- 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 index 1feb0fe..0be445c 100644 --- 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 index a2a3f24..d3fc3a3 100644 --- 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 index 7fe3839..0dea4f4 100644 --- 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 index d0b34d7..b469029 100644 --- 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 index c014447..cca385c 100644 --- 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)