diff --git a/docs/data annotation support/_category_.json b/docs/data annotation support/_category_.json index 2f86a57..206e82a 100644 --- a/docs/data annotation support/_category_.json +++ b/docs/data annotation support/_category_.json @@ -1,6 +1,6 @@ { "label": "Data Annotation Support", - "position": 3, + "position": 4, "collapsible": true, "collapsed": true, "link": { diff --git a/docs/faq.md b/docs/faq.md index 8216cc3..8e474d9 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -1,5 +1,5 @@ --- -sidebar_position: 4 +sidebar_position: 5 --- # Frequently Asked Questions diff --git a/docs/onboarding/data-analysis.md b/docs/onboarding/data-analysis.md index c347794..f4fe6fc 100644 --- a/docs/onboarding/data-analysis.md +++ b/docs/onboarding/data-analysis.md @@ -27,6 +27,7 @@ Below, we provide more details on analysis apps and which data types are targete #### External Viewers -- [cBioPortal](https://docs.cbioportal.org/) for Cancer Genomics was originally developed at Memorial Sloan Kettering Cancer Center (MSK) for sharing genomic data. We provide a custom instance for the Gray Foundation. +- [cBioPortal](https://docs.cbioportal.org/) for Cancer Genomics was originally developed at Memorial Sloan Kettering Cancer Center (MSK) for sharing genomic data. We provide a custom instance for the Gray Foundation. +Sage and MSK teams will assist in the transfer of data to cBioportal. To learn more about the behind the scenes curation process [see here](https://github.com/cBioPortal/datahub/blob/master/docs/curation-process.md). - [CELLxGENE](https://github.com/chanzuckerberg/cellxgene) ("cell-by-gene") is an interactive data explorer specifically designed for analyzing single-cell datasets. diff --git a/docs/onboarding/onboarding-checklist.mdx b/docs/onboarding/onboarding-checklist.mdx index f6f204c..b2e2fb9 100644 --- a/docs/onboarding/onboarding-checklist.mdx +++ b/docs/onboarding/onboarding-checklist.mdx @@ -34,7 +34,7 @@ Here are the suggested responsibilites: | Confirm access permissions on the platform | ✓ | ✓ | ✓ | ✓ | | Review documentation | ✓ | ✓ | ✓ | ✓ | | Receive additional clinical data training | ✓ | | ✓ | | -| Attend Portal Design Working Group | ✓ | ✓ | ✓ | ✓ | +| [Attend Working Group Meetings](/docs/category/working-groups) | ✓ | ✓ | ✓ | ✓ | | Attend Gray Foundation Quarterly Updates | ✓ | ✓ | ✓ | ✓ | | Attend monthly meetings with DCC | | ✓ | ✓ | ✓ | | Designate data lead contacts | ✓ | | | | diff --git a/docs/working group meetings/_category_.json b/docs/working group meetings/_category_.json new file mode 100644 index 0000000..0f872f0 --- /dev/null +++ b/docs/working group meetings/_category_.json @@ -0,0 +1,9 @@ +{ + "label": "Working Groups", + "position": 4, + "collapsible": true, + "collapsed": true, + "link": { + "type": "generated-index" + } +} diff --git a/docs/working group meetings/clinical-data-standards.mdx b/docs/working group meetings/clinical-data-standards.mdx new file mode 100644 index 0000000..9546e38 --- /dev/null +++ b/docs/working group meetings/clinical-data-standards.mdx @@ -0,0 +1,13 @@ +import Tabs from '@theme/Tabs'; +import TabItem from '@theme/TabItem'; + +# Portal Design Working Group + +The focus of the Portal Design Working Group is to collaboratively brainstorm strategies for enhancing data discoverability, accessibility, interoperability, and reusability. Within this working group, our objectives include improving our existing portal and sharing valuable insights on how data can be effectively repurposed. This may include demonstrating methods for seamlessly transferring data to external analysis tools. +All persons affiliated the Gray Foundation atlas are encouraged to attend. + +#### Meeting Notes: + +- [Nov 2, 2023 Summary](https://docs.google.com/document/d/1KpUYz-yOqJ3Zrr6ZZSvg_HXsIL3oeV3_VwNeUUkzN78/edit#heading=h.wdrdbgqvrne) +- Dec 7, 2023 Summary +- Jan 4, 2024 Summary \ No newline at end of file diff --git a/docusaurus.config.js b/docusaurus.config.js index 1381e47..03ab6a8 100644 --- a/docusaurus.config.js +++ b/docusaurus.config.js @@ -73,6 +73,11 @@ const config = { label: 'Help', }, { to: '/blog', label: 'Blog', position: 'left' }, + { + href: 'https://join.slack.com/t/gfbrcaprecanceratlas/shared_invite/zt-254dbv304-F8ZjGMoFsHISGS1ouyp_Iw', + label: 'Join Slack Channel', + position: 'right', + }, { href: 'https://github.com/gf-dcc', label: 'GitHub', diff --git a/src/components/HomepageFeatures/index.js b/src/components/HomepageFeatures/index.js index 7e72360..81212fa 100644 --- a/src/components/HomepageFeatures/index.js +++ b/src/components/HomepageFeatures/index.js @@ -5,7 +5,7 @@ import styles from './styles.module.css'; const FeatureList = [ { title: 'Motivation', - Svg: require('@site/static/img/undraw_docusaurus_mountain.svg').default, + Svg: require('@site/static/img/launch.svg').default, description: ( <> The Gray Foundation is focused on accelerating cancer research to study BRCA-associated precancer and early cancerous lesions in order to develop new prevention, early detection, and interception approaches. @@ -15,16 +15,16 @@ const FeatureList = [ }, { title: 'Collaboration', - Svg: require('@site/static/img/undraw_docusaurus_tree.svg').default, + Svg: require('@site/static/img/group.svg').default, description: ( <> In BRCA-associated cancer, no one team can provide the entirety of the big picture. Teams are encouraged to share data and work together. - ), + ), }, { title: 'Data Coordination', - Svg: require('@site/static/img/undraw_docusaurus_react.svg').default, + Svg: require('@site/static/img/data.svg').default, description: ( <> The Gray Foundation Data Coordinating Center (GF-DCC) provide these documents to help researchers interact with the portal, data, metadata, and other resources. @@ -41,7 +41,7 @@ function Feature({Svg, title, description}) {
-

{title}

+

{title}

{description}

diff --git a/src/components/HomepageFeatures/styles.module.css b/src/components/HomepageFeatures/styles.module.css index b248eb2..41c4bb0 100644 --- a/src/components/HomepageFeatures/styles.module.css +++ b/src/components/HomepageFeatures/styles.module.css @@ -1,11 +1,12 @@ .features { display: flex; align-items: center; - padding: 2rem 0; + padding: 5rem 0; width: 100%; } .featureSvg { height: 200px; - width: 200px; + width: auto; } + diff --git a/static/img/data.svg b/static/img/data.svg new file mode 100644 index 0000000..66ff0ad --- /dev/null +++ b/static/img/data.svg @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/static/img/group.svg b/static/img/group.svg new file mode 100644 index 0000000..fa91b39 --- /dev/null +++ b/static/img/group.svg @@ -0,0 +1,82 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/static/img/launch.svg b/static/img/launch.svg new file mode 100644 index 0000000..1715fbb --- /dev/null +++ b/static/img/launch.svg @@ -0,0 +1,36 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/yarn.lock b/yarn.lock index 08e4a7b..f3caf79 100644 --- a/yarn.lock +++ b/yarn.lock @@ -6918,10 +6918,12 @@ node-releases@^2.0.13: resolved "https://registry.yarnpkg.com/node-releases/-/node-releases-2.0.13.tgz#d5ed1627c23e3461e819b02e57b75e4899b1c81d" integrity sha512-uYr7J37ae/ORWdZeQ1xxMJe3NtdmqMC/JZK+geofDrkLUApKRHPd18/TxtBOJ4A0/+uUIliorNrfYV6s1b02eQ== -node@^21.1.0: - version "21.1.0" - resolved "https://registry.yarnpkg.com/node/-/node-21.1.0.tgz#ddbc66eb3aa633d69cc13ed969ce9eb79e0a2e45" - integrity sha512-OQfrQdCuc+dAauWBA/QmmzGpIMzQz1RAj7f0AcWOXl/Tc9W5kv6JEJcR/cHH4ewj8rNWMbrcWAe5a0TIwDHuFw== + +node@^20.9.0: + version "20.9.0" + resolved "https://registry.yarnpkg.com/node/-/node-20.9.0.tgz#b183303786c736a2563e225b386693f618c793b2" + integrity sha512-5nZdun785z1iaF3zKby8SN4yHgQykqFHo15tMR2cXNmteciGrs3brPEIR7qnBic6kflEyldCGTey9kywANASzA== + dependencies: node-bin-setup "^1.0.0"