diff --git a/config/_default/menus.yaml b/config/_default/menus.yaml index bc23a9b..3d9e7ca 100644 --- a/config/_default/menus.yaml +++ b/config/_default/menus.yaml @@ -50,20 +50,24 @@ main: weight: 2 url: "events/" parent: "Community" + - name: "Community Gallery" + weight: 3 + url: "community/gallery/" + parent: "Community" - name: "Organizing NWB Events" weight: 4 url: "organizing-nwb-events/" parent: "Community" - name: "Enhancement Proposals" - weight: 4 + weight: 5 url: "https://github.com/nwb-extensions/nwbep-review/" parent: "Community" - name: "Working Groups" - weight: 5 + weight: 6 url: "working-groups/" parent: "Community" - name: "Team" - weight: 6 + weight: 7 url: "team/" parent: "Community" @@ -124,17 +128,20 @@ community_links: - name: "Events" weight: 2 url: "/events" - - name: "About Events" + - name: "Community Gallery" weight: 3 - url: "/about-events" + url: "/community/gallery" - name: "Organizing NWB Events" weight: 4 url: "/organizing-nwb-events" - - name: "Working Groups" + - name: "Enhancement Proposals" weight: 5 + url: "https://github.com/nwb-extensions/nwbep-review/" + - name: "Working Groups" + weight: 6 url: "/working-groups" - name: "Contact Us" - weight: 6 + weight: 7 url: "/contact-us" resources: @@ -156,4 +163,4 @@ resources: - name: "FAQ" weight: 6 url: "/faq" - \ No newline at end of file + diff --git a/content/community/_index.md b/content/community/_index.md new file mode 100644 index 0000000..b4b53fa --- /dev/null +++ b/content/community/_index.md @@ -0,0 +1,4 @@ +--- +title: "Community" +weight: 5 +--- diff --git a/content/community/gallery.md b/content/community/gallery.md new file mode 100644 index 0000000..f7fec66 --- /dev/null +++ b/content/community/gallery.md @@ -0,0 +1,51 @@ +--- +title: "Community Gallery" +weight: 1 +gallery_section: + enable: true + title: "Data Conversion" + content: "Tools and resources for converting data to NWB format" + boxes: + - title: "NeuroConv Catalog" + content: "Real-world examples of labs using NeuroConv to convert their data to NWB files. Each project listed contains a description and a link to an open GitHub repository. Many of the projects listed use advanced customization features beyond what is demonstrated in the core NeuroConv conversion gallery." + image: "/images/community_gallery/neuroconv_gallery.png" + url: "https://neuroconv.readthedocs.io/en/main/catalogue/index.html" + - title: "Bristol Neuroscience Data Guide" + content: "The Bristol Neuroscience Data Guide includes tutorials for converting data to NWB for extracellular electrophysiology data and optical physiology data using both the PyNWB and MatNWB APIs for NWB." + image: "/images/community_gallery/bristol_neuroscience_data_guide.png" + url: "https://dervinism.github.io/bristol-neuroscience-data-guide/tutorials/Bristol%20GIN%20for%20Silicon%20Probe%20Data.html" + +analysis_section: + enable: true + title: "Data Analysis and Reuse" + content: "Examples and resources for analyzing and reusing NWB data" + boxes: + - title: "DANDI Example Notebooks" + content: "DANDI (Distributed Archives for Neurophysiology Data Integration) maintains a collection of example notebooks associated with datasets, conference tools, or more generally notebooks that illustrate the use of data on DANDI." + image: "/images/community_gallery/dandi_example_notebooks.png" + url: "https://github.com/dandi/example-notebooks" + - title: "OpenScope Databook" + content: "The OpenScope Databook provides scripts and documentation used for brain data analysis and visualization, primarily working with NWB files and the DANDI archive. Through Jupyter Book, this code is structured as a series of notebooks intended to explain and educate users on how to work with brain data." + image: "/images/community_gallery/openscope_databook.png" + url: "https://alleninstitute.github.io/openscope_databook/" + - title: "IBL Brain-wide Map" + content: "The International Brain Laboratory (IBL) released a Brainwide Map of neural activity during decision-making, consisting of 547 Neuropixel recordings of 32,784 neurons across 194 regions of the mouse brain. The IBL team provides tutorials on Using IBL data with NWB." + image: "/images/community_gallery/ibl_brainmap.png" + url: "https://colab.research.google.com/drive/1zr6lP_zzRgPZuHs3nB5oGnFtPKrduQ3L" + +publications_section: + enable: true + title: "Publications That Reuse NWB Data" + content: "The NWB team maintains a running database of publications that reuse publicly available NWB data, particularly from the DANDI Archive." + boxes: + - title: "NWB Data Reuse Publications" + content: "A collection of publications that reuse publicly available NWB data." + image: "/images/publications-citing.png" + url: "https://www.notion.so/rly1/8b1d1f08841e41b89fdd9ab21d486d31?v=99f8e0f855a5486b8fc521066b34d4b3" + +disclaimer: + enable: true + content: "**Disclaimer:** Reference herein to any specific product, process, or service by its trade name, trademark, manufacturer, or otherwise, does not constitute or imply its endorsement, recommendation, or favoring by the NWB development team, United States Government or any agency thereof, or The Regents of the University of California. Use of the NeurodataWithoutBorders name for endorsements is prohibited." +--- + +This page is a collection of community conversion and analysis projects cataloged here as a convenient reference for NWB users. This list is not comprehensive and many of the projects and resources are built and supported by other groups, and are in active development. diff --git a/layouts/community/list.html b/layouts/community/list.html new file mode 100644 index 0000000..4c6e11a --- /dev/null +++ b/layouts/community/list.html @@ -0,0 +1,35 @@ +{{ define "main" }} +{{/* Hero Section */}} +
+

{{ .Title | markdownify }}

+
+ +
+
+{{/* End Hero Section */}} + +
+
+
+
+ {{ .Content }} +
+
+
+ {{ range .Pages }} +
+ +
+

{{ .Title }}

+

{{ .Summary }}

+
+ +
+ {{ end }} +
+
+
+
+
+{{ end }} diff --git a/layouts/community/single.html b/layouts/community/single.html new file mode 100644 index 0000000..babe835 --- /dev/null +++ b/layouts/community/single.html @@ -0,0 +1,142 @@ +{{ define "main" }} +{{/* Hero Section */}} +
+

{{ .Title | markdownify }}

+
+ +
+
+{{/* End Hero Section */}} + +
+
+
+
+ {{ .Content }} +
+
+
+
+ +{{/* Data Conversion Section */}} +{{ with .Params.gallery_section }} +{{ if .enable }} +
+
+

{{ .title | markdownify }}

+

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+
+ {{ range .boxes }} +
+
+
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+ + {{ .title }} + +
+
+ +
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+ +

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+
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+
+
+ {{ end }} +
+
+
+{{ end }} +{{ end }} +{{/* End Data Conversion Section */}} + +{{/* Data Analysis Section */}} +{{ with .Params.analysis_section }} +{{ if .enable }} +
+
+

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+

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+
+ {{ range .boxes }} +
+
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+ + {{ .title }} + +
+
+ +
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+ +

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+
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+
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+ {{ end }} +
+
+
+{{ end }} +{{ end }} +{{/* End Data Analysis Section */}} + +{{/* Publications Section */}} +{{ with .Params.publications_section }} +{{ if .enable }} +
+
+

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+

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+
+ {{ range .boxes }} +
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+ + {{ .title }} + +
+
+ +
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+ +

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+
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+ {{ end }} +
+
+
+{{ end }} +{{ end }} +{{/* End Publications Section */}} + +{{/* Disclaimer Section */}} +{{ with .Params.disclaimer }} +{{ if .enable }} +
+
+
+
+
+

{{ .content | markdownify }}

+
+
+
+
+
+{{ end }} +{{ end }} +{{/* End Disclaimer Section */}} + +{{ end }} diff --git a/static/images/community_gallery/bristol_neuroscience_data_guide.png b/static/images/community_gallery/bristol_neuroscience_data_guide.png new file mode 100644 index 0000000..b0f36b6 Binary files /dev/null and b/static/images/community_gallery/bristol_neuroscience_data_guide.png differ diff --git a/static/images/community_gallery/dandi_example_notebooks.png b/static/images/community_gallery/dandi_example_notebooks.png new file mode 100644 index 0000000..84db7b2 Binary files /dev/null and b/static/images/community_gallery/dandi_example_notebooks.png differ diff --git a/static/images/community_gallery/ibl_brainmap.png b/static/images/community_gallery/ibl_brainmap.png new file mode 100644 index 0000000..d62c250 Binary files /dev/null and b/static/images/community_gallery/ibl_brainmap.png differ diff --git a/static/images/community_gallery/neuroconv_gallery.png b/static/images/community_gallery/neuroconv_gallery.png new file mode 100644 index 0000000..2f21101 Binary files /dev/null and b/static/images/community_gallery/neuroconv_gallery.png differ diff --git a/static/images/community_gallery/openscope_databook.png b/static/images/community_gallery/openscope_databook.png new file mode 100644 index 0000000..b2909db Binary files /dev/null and b/static/images/community_gallery/openscope_databook.png differ