diff --git a/.github/DISCUSSION_TEMPLATE/general.yaml b/.github/DISCUSSION_TEMPLATE/general.yaml deleted file mode 100644 index 66b2c499f0..0000000000 --- a/.github/DISCUSSION_TEMPLATE/general.yaml +++ /dev/null @@ -1,35 +0,0 @@ -body: - - type: checkboxes - attributes: - label: Checks - options: - - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first. - required: true - - - type: input - id: repo - attributes: - label: Link to your website repo - description: "In almost all cases, **we cannot help you if you don't provide this**." - placeholder: ex. https://github.com/greenelab/greenelab.com - validations: - required: true - - - type: input - id: version - attributes: - label: Version of Lab Website Template you are using - description: See your `CITATION.cff` file. - placeholder: ex. 1.0.0 - validations: - required: true - - - type: textarea - id: description - attributes: - label: Description - description: | - Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in? - placeholder: Description - validations: - required: true diff --git a/.github/DISCUSSION_TEMPLATE/q-a.yaml b/.github/DISCUSSION_TEMPLATE/q-a.yaml deleted file mode 100644 index 66b2c499f0..0000000000 --- a/.github/DISCUSSION_TEMPLATE/q-a.yaml +++ /dev/null @@ -1,35 +0,0 @@ -body: - - type: checkboxes - attributes: - label: Checks - options: - - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first. - required: true - - - type: input - id: repo - attributes: - label: Link to your website repo - description: "In almost all cases, **we cannot help you if you don't provide this**." - placeholder: ex. https://github.com/greenelab/greenelab.com - validations: - required: true - - - type: input - id: version - attributes: - label: Version of Lab Website Template you are using - description: See your `CITATION.cff` file. - placeholder: ex. 1.0.0 - validations: - required: true - - - type: textarea - id: description - attributes: - label: Description - description: | - Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in? - placeholder: Description - validations: - required: true diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml deleted file mode 100644 index 7d0b7de5f8..0000000000 --- a/.github/ISSUE_TEMPLATE/config.yml +++ /dev/null @@ -1,8 +0,0 @@ -blank_issues_enabled: true -contact_links: - - name: π¬ Start a discussion - url: https://github.com/greenelab/lab-website-template/discussions - about: I need help, I have a question, or other discussion. - - name: π Docs issue - url: https://github.com/greenelab/lab-website-template-docs/issues - about: I have a question or issue related to the template documentation. diff --git a/.github/ISSUE_TEMPLATE/issue.yaml b/.github/ISSUE_TEMPLATE/issue.yaml deleted file mode 100644 index d812555039..0000000000 --- a/.github/ISSUE_TEMPLATE/issue.yaml +++ /dev/null @@ -1,38 +0,0 @@ -name: π Create an issue -description: I think I've discovered a bug, I want to request a feature/change, or other issue. - -body: - - type: checkboxes - attributes: - label: Checks - options: - - label: I have searched **[the docs](https://greene-lab.gitbook.io/lab-website-template-docs)**, [existing issues](https://github.com/greenelab/lab-website-template/issues), and [existing discussions](https://github.com/greenelab/lab-website-template/discussions) for answers first. - required: true - - - type: input - id: repo - attributes: - label: Link to your website repo - description: "In almost all cases, **we cannot help you if you don't provide this**." - placeholder: ex. https://github.com/greenelab/greenelab.com - validations: - required: true - - - type: input - id: version - attributes: - label: Version of Lab Website Template you are using - description: See your `CITATION.cff` file. - placeholder: ex. 1.0.0 - validations: - required: true - - - type: textarea - id: description - attributes: - label: Description - description: | - Describe your issue in as much detail as possible. For example: What happened? What did you expect to happen? How can we reproduce the problem? What browser are you seeing the problem in? - placeholder: Description - validations: - required: true diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index 6aaf76bdc2..00a0e7117c 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,13 +1,4 @@ -STOP!!! +This website is based on the Lab Website Template. +See its documentation for working with this site: -You are about to open this pull request against THE TEMPLATE ITSELF. You probably meant to open it against your own website repo. - ---- - -FOR THE TEMPLATE MAINTAINER(S) - -New template version checklist: - -- [ ] I have updated CITATION and CHANGELOG as appropriate. -- [ ] I have updated lab-website-template-docs as appropriate. -- [ ] I have checked the testbed as appropriate. +https://greene-lab.gitbook.io/lab-website-template-docs diff --git a/.github/user_pull_request_template.md b/.github/user_pull_request_template.md deleted file mode 100644 index 00a0e7117c..0000000000 --- a/.github/user_pull_request_template.md +++ /dev/null @@ -1,4 +0,0 @@ -This website is based on the Lab Website Template. -See its documentation for working with this site: - -https://greene-lab.gitbook.io/lab-website-template-docs diff --git a/.github/workflows/versioning.yaml b/.github/workflows/versioning.yaml deleted file mode 100644 index e148f366b7..0000000000 --- a/.github/workflows/versioning.yaml +++ /dev/null @@ -1,135 +0,0 @@ -name: versioning -run-name: versioning tasks - -on: - pull_request: - branches: - - main - push: - branches: - - main - -permissions: - contents: write - -jobs: - pull-request: - # only run on template itself, not user instance of template - if: | - github.repository == 'greenelab/lab-website-template' && - github.event_name == 'pull_request' - runs-on: ubuntu-latest - steps: - # for debugging - - uses: crazy-max/ghaction-dump-context@v2 - - if: runner.debug == '1' - uses: mxschmitt/action-tmate@v3 - - - name: Checkout base branch contents - uses: actions/checkout@v4 - with: - ref: main - path: base - - - name: Checkout pr branch contents - uses: actions/checkout@v4 - with: - path: pr - - - name: Install packages - run: npm install yaml semver - - - name: Check version, date, changelog - uses: actions/github-script@v7 - with: - script: | - const { readFileSync } = require("fs"); - const { lte, valid } = require("semver"); - const { parse } = require("yaml"); - - // load and parse file contents - const { version: oldVersion, "date-released": oldDate } = parse( - readFileSync("base/CITATION.cff").toString() - ); - const { version: newVersion, "date-released": newDate } = parse( - readFileSync("pr/CITATION.cff").toString() - ); - const changelog = readFileSync("pr/CHANGELOG.md") - .toString() - .split(/^## /m) - .map((section) => { - const [heading, ...body] = section.split("\n"); - return [heading.trim(), body.join("\n").trim()]; - }); - - // check version - if (!valid(newVersion)) throw Error("Version not valid"); - if (lte(newVersion, oldVersion)) throw Error("Version not updated"); - - // check date - if (new Date(newDate).toISOString().split("T")[0] !== newDate) - throw Error("Date not valid"); - if (new Date(newDate) <= new Date(oldDate)) throw Error("Date not updated"); - - // check changelog - const newSection = changelog.find( - ([heading, body]) => - heading.includes(newVersion) && heading.includes(newDate) && body - ); - if (!newSection) throw Error("Changelog not updated or not valid"); - - push: - # only run on template itself, not user instance of template - if: | - github.repository == 'greenelab/lab-website-template' && - github.event_name == 'push' - runs-on: ubuntu-latest - steps: - # for debugging - - uses: crazy-max/ghaction-dump-context@v2 - - - name: Checkout branch contents - uses: actions/checkout@v4 - - - name: Install packages - run: npm install yaml semver - - # for debugging - - if: runner.debug == '1' - uses: mxschmitt/action-tmate@v3 - - - name: Get version and body - id: version - uses: actions/github-script@v7 - with: - script: | - const { readFileSync } = require("fs"); - const { parse } = require("yaml"); - - // load and parse file contents - const { version, "date-released": date } = parse( - readFileSync("CITATION.cff").toString() - ); - const changelog = readFileSync("CHANGELOG.md") - .toString() - .split(/^## /m) - .map((section) => { - const [heading, ...body] = section.split("\n"); - return [heading.trim(), body.join("\n").trim()]; - }); - - // find changelog body for version - const [, body = ""] = - changelog.find( - ([heading]) => heading.includes(version) && heading.includes(date) - ) || []; - - return { version, body }; - - - name: Create GitHub release - uses: ncipollo/release-action@v1.14.0 - with: - commit: ${{ github.ref }} - tag: v${{ fromJson(steps.version.outputs.result).version }} - name: v${{ fromJson(steps.version.outputs.result).version }} - body: ${{ fromJson(steps.version.outputs.result).body }} diff --git a/CHANGELOG.md b/CHANGELOG.md deleted file mode 100644 index 35da88ea80..0000000000 --- a/CHANGELOG.md +++ /dev/null @@ -1,165 +0,0 @@ -# Changelog - -Reference: common-changelog.org - -## 1.2.2 - 2024-06-05 - -### Added - -- Add `affiliation` member portrait field. - -### Changed - -- Change order and type of preferred ids from ORCID API. -- Expand list of supported Manubot identifiers and thus keep ORCID API details less often. -- Simplify portrait component under-the-hood. -- Make tag component de-duplication consistent with search plugin de-duplication. - -## 1.2.1 - 2024-04-01 - -### Changed - -- Minor bug fixes in cite process and sitemap generation. - -## 1.2.0 - 2024-03-08 - -### Changed - -- Update all GitHub Actions to fix "Node v16 deprecated" warnings. -- Sources that Manubot doesn't know how to cite (e.g. wosuid:12345) are now ignored by default if they're from metasources. -- Fix bug where passing tags to tags component manually doesn't work. -- Fix bug in citation (and other) components when `lookup` is blank. -- Fix nested tables bug. -- Dark mode tweaks. -- Various CSS tweaks and fixes. - -### Added - -- Add `image` param to support blog post thumbnails. -- Add `html-proofer` plugin that checks for broken images/links/etc. -- Add `remove` flag to remove a source from a metasource. - -## 1.1.6 - 2023-10-06 - -### Changed - -- Use latest minor versions of Python packages in auto-cite script. - -## 1.1.5 - 2023-05-19 - -### Changed - -- Fix ORCID plugin bug and other cite process tweaks. - -## 1.1.4 - 2023-04-28 - -### Changed - -- Fix ORCID plugin and other cite process bugs. - -## 1.1.3 - 2023-04-20 - -### Changed - -- Fix first-time-setup mv bug. -- Fix citation, float, and portrait component CSS. -- Filter and trim citation info fields. - -## 1.1.2 - 2023-04-11 - -### Changed - -- Fix first-time-setup rm bug. - -## 1.1.1 - 2023-04-06 - -### Changed - -- Change member profile page from col layout to float. -- Fix first time setup. Preserve config formatting and comments. -- Improve Docker cite process behavior. -- Fix post excerpt component start/end markers and special search attr chars. -- Fix misc CSS. - -### Added - -- Add show-title and show-subtitle site config options. -- Include site subtitle in description meta tag. -- Add user pull request template. -- Add title and link fallbacks to citation component. - -## 1.1.0 - 2023-03-17 - -Add alert component, Docker support, accessibility fixes. - -### Changed - -- Fix Lighthouse accessibility issues. -- De-href components when link isn't provided (no hand cursor icon on hover or nav on click). -- In search script, limit highlights by total count instead of char length. -- Grid and link style tweaks. -- Take ORCID icon from Font Awesome. -- Misc bug fixes in tags script, float component. - -### Added - -- Add Docker configuration and scripts for local previewing. -- Add alert component and types. -- Role icon in portrait component hoisted to top left. - -## 1.0.0 - 2023-02-28 - -First official release. - -High-level comparison with pre-releases: - -- Simpler configuration. -- More automation, less setup. -- More customization and flexibility. -- Redesigned components. -- New docs. -- Complete rewrite. -- Culmination of years of feedback. - -### Changed - -- Template is no longer limited to GitHub Pages white-listed Jekyll plugins. Any plugins possible. -- Pull request previews happen right within GitHub instead of needing Netlify. -- Better versioning. `CITATION.cff` file now source of truth for version, and tags/releases enforced. -- Citation-related files in `/_data` must now be named prefixed with the cite plugin they are to be run with, e.g. `sources-2020.yaml` or `orcid-students.yaml`. -- Folder renames for clarity and for better separation of template and user content: `/auto-cite` β `/_cite`, `/css` β `/_styles`, `/js` β `/_scripts`. -- Rename "Tools" page to "Projects" to be more clear and general purpose. -- Rename `extra-links` to `buttons` in `sources.yaml` files. -- Rename `theme.scss` to `-theme.scss`. -- Rename/repurpose components: link β button, two-col β cols, gallery β grid. -- Combine "link" and "role" data lists into single `types.yaml` map. -- Redesign components, change parameters and behavior. -- Update Font Awesome icon names from v5 to v6. -- Change placeholder text, images, and other images. -- Use CSS variables instead of Sass variables. -- Simplify caching method in cite process. -- Simplify Liquid code by including custom Ruby plugins. -- Simplify styles and scripts. - -### Added - -- New docs at greene-lab.gitbook.io/lab-website-template-docs. -- Add automations for first time setup and URL change. -- Write PubMed and Google Scholar automatic citation plugins. -- Automatic citations through GitHub Actions should now work from (most) forks. -- Add optional description and type params for citations. -- Add periodic cite process run that opens a pull request. -- List component filters can now accept arbitrary regex. -- Add light/dark mode toggle. -- Pre-install selection of useful Jekyll plugins, namely Jekyll Spaceship. -- Add author portrait and updated date for blog posts. -- Add richer metadata for SEO. -- Google Fonts link determined automatically from theme file. - -### Removed - -- Remove options from `_config.yaml` to simplify configuration: `baseurl`, `auto-cite`, `logo`. -- Remove `/favicons` folder, hardcode files for logo, icon, and share in `/images`. -- Remove `palettes.scss` and `mixins.scss`. -- Remove banner component (same thing can be achieved with full width section and figure components). -- Remove role component. Combine with portrait component. diff --git a/README.md b/README.md index 29bf9a24af..6e9db184e1 100644 --- a/README.md +++ b/README.md @@ -1,30 +1,6 @@ -
- -
-Lab Website Template (LWT) is an easy-to-use, flexible website template for labs. -Spend less time worrying about managing a website and citations, and more time running your lab. +# time-lab-anuDESCRIPTION=An engaging 1-3 sentence description of your lab.'s Website -ππ **Get Started** ππ +Visit **[time.anu.edu.au](https://time.anu.edu.au)** π -[**Documentation**](https://greene-lab.gitbook.io/lab-website-template-docs) - -## Key Features - -- π€ Based on Git, GitHub, and Jekyll. -- π Automatically generated citations from simple identifiers (DOI, PubMed, ORCID, and many more) using Manubot. E.g. `doi:1234/5678` -> `title`, `authors`, `publisher`, `date`, etc. -- 𧱠A comprehensive and flexible suite of pre-made components (building blocks) for structuring and styling your website: - - Formatted tables, code blocks, figures, and other basic elements. - - Citations with thumbnails and other rich details. - - List large sets of data with flexible filters and components. - - ...many more -- ποΈ Automatic pull request previews. -- βοΈ Easy and automated configuration. -- π₯ Team member pages with bios, roles, and social media links. -- ποΈ Blog posts with tags and rich content. -- π± Works and looks good on desktop and mobile. -- π€ Great documentation and support (if we do say so ourselves). -- ... and much more! - -![GitHub last commit](https://img.shields.io/github/last-commit/greenelab/lab-website-template) +_Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_ diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 96041e520e..2fc471d6ad 100644 Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ diff --git a/_config.yaml b/_config.yaml index 1c6b790bda..8c9a9503ae 100644 --- a/_config.yaml +++ b/_config.yaml @@ -1,19 +1,19 @@ # site properties and page defaults -title: Lab Website Template -subtitle: by the Greene Lab -description: An easy-to-use, flexible website template for labs, with automatic citations, GitHub tag imports, pre-built components, and more. +title: TIME Lab +subtitle: Temporal Intelligence and Motion Extraction Lab +description: header: images/background.jpg footer: images/background.jpg proofer: false # site social media and other links links: - email: contact@your-lab.com - orcid: 0000-0001-8713-9213 - google-scholar: ETJoidYAAAAJ - github: your-lab - twitter: YourLabHandle - youtube: YourLabChannel + email: lei.w@anu.edu.au + # orcid: 0000-0001-8713-9213 + # google-scholar: ETJoidYAAAAJ + # github: time-lab-anuDESCRIPTION=An engaging 1-3 sentence description of your lab. + # twitter: time-lab-anuDESCRIPTION=An engaging 1-3 sentence description of your lab. + # youtube: time-lab-anuDESCRIPTION=An engaging 1-3 sentence description of your lab. ### jekyll settings diff --git a/_data/citations.yaml b/_data/citations.yaml index 0e483e3a9d..1ec2310b69 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -1,247 +1,40 @@ # DO NOT EDIT, GENERATED AUTOMATICALLY -- id: doi:10.1093/nar/gkad1082 - title: "The Monarch Initiative in 2024: an analytic platform integrating phenotypes,\ - \ genes\_and diseases across species" - authors: - - Tim E Putman - - Kevin Schaper - - Nicolas Matentzoglu - - "Vincent\_P Rubinetti" - - "Faisal\_S Alquaddoomi" - - Corey Cox - - J Harry Caufield - - Glass Elsarboukh - - Sarah Gehrke - - Harshad Hegde - - "Justin\_T Reese" - - Ian Braun - - "Richard\_M Bruskiewich" - - Luca Cappelletti - - Seth Carbon - - "Anita\_R Caron" - - "Lauren\_E Chan" - - "Christopher\_G Chute" - - "Katherina\_G Cortes" - - "Vin\xEDcius De\_Souza" - - Tommaso Fontana - - "Nomi\_L Harris" - - "Emily\_L Hartley" - - Eric Hurwitz - - "Julius\_O B Jacobsen" - - Madan Krishnamurthy - - "Bryan\_J Laraway" - - "James\_A McLaughlin" - - "Julie\_A McMurry" - - "Sierra\_A T Moxon" - - "Kathleen\_R Mullen" - - "Shawn\_T O\u2019Neil" - - "Kent\_A Shefchek" - - Ray Stefancsik - - Sabrina Toro - - "Nicole\_A Vasilevsky" - - "Ramona\_L Walls" - - "Patricia\_L Whetzel" - - David Osumi-Sutherland - - Damian Smedley - - "Peter\_N Robinson" - - "Christopher\_J Mungall" - - "Melissa\_A Haendel" - - "Monica\_C Munoz-Torres" - publisher: Nucleic Acids Research - date: '2023-11-24' - link: https://doi.org/gs6kmr - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1101/2023.10.11.560955 - title: Integration of 168,000 samples reveals global patterns of the human gut microbiome - authors: - - Richard J. Abdill - - Samantha P. Graham - - Vincent Rubinetti - - Frank W. Albert - - Casey S. Greene - - Sean Davis - - Ran Blekhman - publisher: Cold Spring Harbor Laboratory - date: '2023-10-11' - link: https://doi.org/gsvf5z - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1093/nar/gkad289 - title: 'MyGeneset.info: an interactive and programmatic platform for community-curated - and user-created collections of genes' - authors: - - Ricardo Avila - - Vincent Rubinetti - - Xinghua Zhou - - Dongbo Hu - - Zhongchao Qian - - Marco Alvarado Cano - - Everaldo Rodolpho - - Ginger Tsueng - - Casey Greene - - Chunlei Wu - publisher: Nucleic Acids Research - date: '2023-04-18' - link: https://doi.org/gr5hb5 - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1101/2023.01.05.522941 - title: Hetnet connectivity search provides rapid insights into how two biomedical - entities are related - authors: - - Daniel S. Himmelstein - - Michael Zietz - - Vincent Rubinetti - - Kyle Kloster - - Benjamin J. Heil - - Faisal Alquaddoomi - - Dongbo Hu - - David N. Nicholson - - Yun Hao - - Blair D. Sullivan - - Michael W. Nagle - - Casey S. Greene - publisher: Cold Spring Harbor Laboratory - date: '2023-01-07' - link: https://doi.org/grmcb9 - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1093/gigascience/giad047 - title: Hetnet connectivity search provides rapid insights into how biomedical entities - are related - authors: - - Daniel S Himmelstein - - Michael Zietz - - Vincent Rubinetti - - Kyle Kloster - - Benjamin J Heil - - Faisal Alquaddoomi - - Dongbo Hu - - David N Nicholson - - Yun Hao - - Blair D Sullivan - - Michael W Nagle - - Casey S Greene - publisher: GigaScience - date: '2022-12-28' - link: https://doi.org/gsd85n - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1101/2022.02.18.461833 - title: 'MolEvolvR: A web-app for characterizing proteins using molecular evolution - and phylogeny' - authors: - - Jacob D Krol - - Joseph T Burke - - Samuel Z Chen - - Lo M Sosinski - - Faisal S Alquaddoomi - - Evan P Brenner - - Ethan P Wolfe - - Vincent P Rubinetti - - Shaddai Amolitos - - Kellen M Reason - - John B Johnston - - Janani Ravi - publisher: Cold Spring Harbor Laboratory - date: '2022-02-22' - link: https://doi.org/gstx7j - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1186/s13059-020-02021-3 - title: Compressing gene expression data using multiple latent space dimensionalities - learns complementary biological representations - authors: - - Gregory P. Way - - Michael Zietz - - Vincent Rubinetti - - Daniel S. Himmelstein - - Casey S. Greene - publisher: Genome Biology - date: '2020-05-11' - link: https://doi.org/gg2mjh - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1371/journal.pcbi.1007128 - title: Open collaborative writing with Manubot - authors: - - Daniel S. Himmelstein - - Vincent Rubinetti - - David R. Slochower - - Dongbo Hu - - Venkat S. Malladi - - Casey S. Greene - - Anthony Gitter - publisher: PLOS Computational Biology - date: '2020-12-04' - link: https://doi.org/c7np - orcid: 0000-0002-4655-3773 - plugin: sources.py - file: sources.yaml - type: paper - description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed - do eiusmod tempor incididunt ut labore et dolore magna aliqua. - image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2 +- id: doi:10.48550/arXiv.2402.04857 + title: 'Advancing Video Anomaly Detection: A Concise Review and a New Dataset' + authors: + - Liyun Zhu + - Lei Wang + - Arjun Raj + - Tom Gedeon + - Chen Chen + publisher: arXiv + date: '2024-01-01' + link: https://doi.org/gt3q3r + image: https://msad-dataset.github.io/resources/images/dataset_samples.png buttons: - - type: manubot - link: https://greenelab.github.io/meta-review/ - - type: source - text: Manuscript Source - link: https://github.com/greenelab/meta-review - type: website - link: http://manubot.org/ + link: http://msad-dataset.github.io/ tags: - - open science - - collaboration - repo: greenelab/meta-review -- id: doi:10.1101/573782 - title: Sequential compression of gene expression across dimensionalities and methods - reveals no single best method or dimensionality - authors: - - Gregory P. Way - - Michael Zietz - - Vincent Rubinetti - - Daniel S. Himmelstein - - Casey S. Greene - publisher: Cold Spring Harbor Laboratory - date: '2019-03-11' - link: https://doi.org/gfxjxf - orcid: 0000-0002-4655-3773 - plugin: orcid.py - file: orcid.yaml -- id: doi:10.1016/j.csbj.2020.05.017 - title: Constructing knowledge graphs and their biomedical applications - authors: - - David N. Nicholson - - Casey S. Greene - publisher: Computational and Structural Biotechnology Journal - date: '2020-01-01' - link: https://doi.org/gg7m48 - image: https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg + - anomaly detection + - dataset plugin: sources.py file: sources.yaml -- id: doi:10.7554/eLife.32822 - title: Sci-Hub provides access to nearly all scholarly literature - authors: - - Daniel S Himmelstein - - Ariel Rodriguez Romero - - Jacob G Levernier - - Thomas Anthony Munro - - Stephen Reid McLaughlin - - Bastian Greshake Tzovaras - - Casey S Greene - publisher: eLife - date: '2018-03-01' - link: https://doi.org/ckcj - image: https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp +- id: doi:10.48550/arXiv.2402.03019 + title: Taylor Videos for Action Recognition + authors: + - Lei Wang + - Xiuyuan Yuan + - Tom Gedeon + - Liang Zheng + publisher: arXiv + date: '2024-01-01' + link: https://doi.org/gt3q6q + image: images/paper/taylor-paper-thumb.png + buttons: + - type: source + link: https://github.com/LeiWangR/video-ar/tree/main + tags: + - A* plugin: sources.py file: sources.yaml diff --git a/_data/orcid.yaml b/_data/orcid.yaml index 005d3808fe..410901aa20 100644 --- a/_data/orcid.yaml +++ b/_data/orcid.yaml @@ -1 +1 @@ -- orcid: 0000-0002-4655-3773 +# - orcid: 0000-0002-4655-3773 diff --git a/_data/sources.yaml b/_data/sources.yaml index 62cd922079..55c522b4f6 100644 --- a/_data/sources.yaml +++ b/_data/sources.yaml @@ -1,23 +1,33 @@ -- id: doi:10.1371/journal.pcbi.1007128 - type: paper - description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. - date: 2020-12-4 - image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2 +# - id: doi:10.1371/journal.pcbi.1007128 +# type: paper +# description: Lorem ipsum _dolor_ **sit amet**, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. +# date: 2020-12-4 +# image: https://journals.plos.org/ploscompbiol/article/figure/image?size=inline&id=info:doi/10.1371/journal.pcbi.1007128.g001&rev=2 +# buttons: +# - type: manubot +# link: https://greenelab.github.io/meta-review/ +# - type: source +# text: Manuscript Source +# link: https://github.com/greenelab/meta-review +# - type: website +# link: http://manubot.org/ +# tags: +# - open science +# - collaboration +# repo: greenelab/meta-review +- id: doi:10.48550/arXiv.2402.04857 + image: https://msad-dataset.github.io/resources/images/dataset_samples.png buttons: - - type: manubot - link: https://greenelab.github.io/meta-review/ - - type: source - text: Manuscript Source - link: https://github.com/greenelab/meta-review - type: website - link: http://manubot.org/ + link: http://msad-dataset.github.io/ tags: - - open science - - collaboration - repo: greenelab/meta-review - -- id: doi:10.1016/j.csbj.2020.05.017 - image: https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg + - anomaly detection + - dataset +- id: doi:10.48550/arXiv.2402.03019 + image: images/paper/taylor-paper-thumb.png + buttons: + - type: source + link: https://github.com/LeiWangR/video-ar/tree/main + tags: + - A* -- id: doi:10.7554/eLife.32822 - image: https://iiif.elifesciences.org/lax:32822%2Felife-32822-fig8-v3.tif/full/863,/0/default.webp diff --git a/_members/dexuan-ding.md b/_members/dexuan-ding.md new file mode 100644 index 0000000000..9a9bc6af38 --- /dev/null +++ b/_members/dexuan-ding.md @@ -0,0 +1,11 @@ +--- +name: Dexuan Ding + +image: images/team/template.jpg +role: undergrad +affiliation: Australian National University +description: Student +links: +--- + +Working on robust human-centric anomaly detection project. \ No newline at end of file diff --git a/_members/huilin-chen.md b/_members/huilin-chen.md new file mode 100644 index 0000000000..9a560269f7 --- /dev/null +++ b/_members/huilin-chen.md @@ -0,0 +1,11 @@ +--- +name: Huilin Chen + +image: images/team/template.jpg +role: undergrad +affiliation: Australian National University +description: Student +links: +--- + +Working on Spatio-temporal video coding: an in-depth analysis and assessment project. \ No newline at end of file diff --git a/_members/jane-smith.md b/_members/jane-smith.md deleted file mode 100644 index c60188ecd7..0000000000 --- a/_members/jane-smith.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Jane Smith -image: images/photo.jpg -role: pi -affiliation: University of Colorado -aliases: - - J. Smith - - J Smith -links: - home-page: https://janesmith.com - orcid: 0000-0001-8713-9213 ---- - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Faucibus purus in massa tempor nec feugiat nisl pretium fusce. -Elit at imperdiet dui accumsan. -Duis tristique sollicitudin nibh sit amet commodo nulla facilisi. -Vitae elementum curabitur vitae nunc sed velit dignissim sodales. -Lacinia at quis risus sed vulputate odio ut. -Magna eget est lorem ipsum. diff --git a/_members/john-doe.md b/_members/john-doe.md deleted file mode 100644 index 0e441c6d9f..0000000000 --- a/_members/john-doe.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -name: John Doe -image: images/photo.jpg -role: phd -group: alum -links: - github: john-doe ---- - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/_members/jushang-qiu.md b/_members/jushang-qiu.md new file mode 100644 index 0000000000..8bded69fba --- /dev/null +++ b/_members/jushang-qiu.md @@ -0,0 +1,11 @@ +--- +name: Jushang Qiu + +image: images/team/template.jpg +role: undergrad +affiliation: Australian National University +description: Student +links: +--- + +Working on dynamics distillation for scalable models \ No newline at end of file diff --git a/_members/lei-wang.md b/_members/lei-wang.md new file mode 100644 index 0000000000..83430a5e32 --- /dev/null +++ b/_members/lei-wang.md @@ -0,0 +1,29 @@ +--- +name: Dr. Lei Wang +image: images/team/lei-wang-photo.jpg +role: pi +affiliation: ANU & Data61/CSIRO +description: Lab Lead +links: + home-page: https://leiwangr.github.io/ + email: lei.w@anu.edu.au + orcid: 0000-0002-8600-7099 + google-scholar: https://scholar.google.com/citations?user=VWCZLXgAAAAJ&hl=en + linkedin: https://www.linkedin.com/in/lei-l-wang/ +--- + +Lei Wang serves as a Research Fellow at the School of Computing, within the ANU College of Engineering, Computing, and Cybernetics. He is under the guidance of Assoc. Prof. Liang Zheng (ANU) and Prof. Tom Gedeon (Curtin University). + +Currently, he also holds the position of Computer Scientist at Active Intelligence Australia Pty Ltd in Perth. In this role, he leads research and development efforts in the field of commercial anomaly detection solutions. His project has successfully raised 1.2 million US dollars, and as a result, he was awarded the Incentive Unit Award. + +In addition to his academic and research responsibilities, Lei Wang also contributes to the field as a Visiting Scientist in the Machine Learning Research Group (MLRG) at Data61 (formerly NICTA), a division of The Commonwealth Scientific and Industrial Research Organisation (CSIRO). + +Since 2018, Lei has been dedicated to his work as a full-time Computer Vision Researcher with iCetana Pty Ltd in Perth. During this time, he also acted as a Visiting Researcher in MLRG at Data61/CSIRO and contributed as a Visiting Researcher with the Department of Computer Science and Software Engineering at The University of Western Australia (UWA). + +Prior to commencing his PhD at ANU and Data61/CSIRO, Lei received several competitive full PhD scholarships, including the ARC Industrial Transformation Training Centre Scholarship, UWA International Fee Scholarship, University Postgraduate Award, Data61 PhD Scholarship, Data61 Top-up Scholarship, and ANU HDR Fee Remission Merit Scholarship. + +Throughout his PhD candidature, Lei authored a significant number of first-author papers published in esteemed venues, such as CVPR, ICCV, ECCV, ACM MM, TPAMI, IJCV, and TIP. His research, conducted under the guidance of Dr. Piotr Koniusz (Data61/CSIRO & ANU), earned him the Sang Uk Lee Best Student Paper Award from ACCVβ22. + +Leiβs research interests encompass a wide range of topics, including action recognition in videos, anomaly detection, video image processing, one- and few-shot learning, deep learning, tensor learning, and domain adaptation. + +He is an active member of both IEEE and ACM as a Student Member. \ No newline at end of file diff --git a/_members/liwen-luo.md b/_members/liwen-luo.md new file mode 100644 index 0000000000..bfdb703764 --- /dev/null +++ b/_members/liwen-luo.md @@ -0,0 +1,11 @@ +--- +name: Liwen Luo + +image: images/team/template.jpg +role: undergrad +affiliation: Australian National University +description: Student +links: +--- + +Working on spatio-temporal motion prediction. \ No newline at end of file diff --git a/_members/liyun-zhu.md b/_members/liyun-zhu.md new file mode 100644 index 0000000000..9821ffe6b1 --- /dev/null +++ b/_members/liyun-zhu.md @@ -0,0 +1,12 @@ +--- +name: Liyun Zhu + +image: images/team/liyun-zhu-photo.jpg +role: undergrad +affiliation: Australian National University +description: Student +links: + email: liyun.zhu@anu.edu.au +--- + +Working on a comparative review of recent video-based anomaly detection algorithms (co-supervised with Prof. Chen Chen from the University of Central Florida) \ No newline at end of file diff --git a/_members/qixiang-chen.md b/_members/qixiang-chen.md new file mode 100644 index 0000000000..2cc26ecf7d --- /dev/null +++ b/_members/qixiang-chen.md @@ -0,0 +1,11 @@ +--- +name: Qixiang Chen + +image: images/team/template.jpg +role: undergrad +affiliation: Australian National University +description: Student +links: +--- + +Working on a closer look at fine-grained motions project (co-supervised with Prof. Chen Chen from the University of Central Florida). \ No newline at end of file diff --git a/_members/sarah-johnson.md b/_members/sarah-johnson.md deleted file mode 100644 index b0d97b441a..0000000000 --- a/_members/sarah-johnson.md +++ /dev/null @@ -1,11 +0,0 @@ ---- -name: Sarah Johnson -image: images/photo.jpg -description: Lead Programmer -role: programmer -links: - email: sarah.johnson@gmail.com - twitter: sarahjohnson ---- - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/blog/index.md b/blog/index.md index b86f3598a0..b1715cc94e 100644 --- a/blog/index.md +++ b/blog/index.md @@ -1,4 +1,4 @@ ---- + diff --git a/contact/index.md b/contact/index.md index d9b7e4bcaf..00338fa08b 100644 --- a/contact/index.md +++ b/contact/index.md @@ -7,71 +7,20 @@ nav: # {% include icon.html icon="fa-regular fa-envelope" %}Contact -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor -incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis -nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. +Please contact our lab's lead, Dr. Lei Wang, for any enquires. {% include button.html type="email" - text="jane@smith.com" - link="jane@smith.com" -%} -{% - include button.html - type="phone" - text="(555) 867-5309" - link="+1-555-867-5309" + text="lei.w@anu.edu.au" + link="lei.w@anu.edu.au" %} + + {% include button.html type="address" + text="B141 Desk 4" tooltip="Our location on Google Maps for easy navigation" - link="https://www.google.com/maps" -%} - -{% include section.html %} - -{% capture col1 %} - -{% - include figure.html - image="images/photo.jpg" - caption="Lorem ipsum" -%} - -{% endcapture %} - -{% capture col2 %} - -{% - include figure.html - image="images/photo.jpg" - caption="Lorem ipsum" + link="https://maps.app.goo.gl/T5MHmSzTYZ2CXUnD8" %} - -{% endcapture %} - -{% include cols.html col1=col1 col2=col2 %} - -{% include section.html dark=true %} - -{% capture col1 %} -Lorem ipsum dolor sit amet -consectetur adipiscing elit -sed do eiusmod tempor -{% endcapture %} - -{% capture col2 %} -Lorem ipsum dolor sit amet -consectetur adipiscing elit -sed do eiusmod tempor -{% endcapture %} - -{% capture col3 %} -Lorem ipsum dolor sit amet -consectetur adipiscing elit -sed do eiusmod tempor -{% endcapture %} - -{% include cols.html col1=col1 col2=col2 col3=col3 %} diff --git a/images/paper/taylor-paper-thumb.png b/images/paper/taylor-paper-thumb.png new file mode 100644 index 0000000000..74aedc4446 Binary files /dev/null and b/images/paper/taylor-paper-thumb.png differ diff --git a/images/team/lei-wang-photo.jpg b/images/team/lei-wang-photo.jpg new file mode 100644 index 0000000000..ea0dba646d Binary files /dev/null and b/images/team/lei-wang-photo.jpg differ diff --git a/images/team/liyun-zhu-photo.jpg b/images/team/liyun-zhu-photo.jpg new file mode 100644 index 0000000000..6ae6e7ec31 Binary files /dev/null and b/images/team/liyun-zhu-photo.jpg differ diff --git a/images/team/template.jpg b/images/team/template.jpg new file mode 100644 index 0000000000..691a9880a3 Binary files /dev/null and b/images/team/template.jpg differ diff --git a/index.md b/index.md index bea698059b..da22cffb90 100644 --- a/index.md +++ b/index.md @@ -1,22 +1,9 @@ --- --- -# Lab Website Template +# An engaging 1-3 sentence description of your lab's Website -[Lab Website Template](https://github.com/greenelab/lab-website-template) is an easy-to-use, flexible website template for [labs](https://www.greenelab.com/). -Spend less time worrying about managing a website and citations, and more time running your lab. -{% - include button.html - type="docs" - link="https://greene-lab.gitbook.io/lab-website-template-docs" -%} -{% - include button.html - type="github" - text="On GitHub" - link="greenelab/lab-website-template" -%} {% include section.html %} diff --git a/research/index.md b/research/index.md index 0f700f4f09..bb18426681 100644 --- a/research/index.md +++ b/research/index.md @@ -1,27 +1,17 @@ --- -title: Research +title: Publications nav: order: 1 tooltip: Published works --- -# {% include icon.html icon="fa-solid fa-microscope" %}Research +# {% include icon.html icon="fa-solid fa-microscope" %}Publications Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. {% include section.html %} -## Highlighted -{% include citation.html lookup="Open collaborative writing with Manubot" style="rich" %} - -{% include section.html %} - -## All - -{% include search-box.html %} - -{% include search-info.html %} {% include list.html data="citations" component="citation" style="rich" %} diff --git a/testbed.md b/testbed.md deleted file mode 100644 index 6b343a5eca..0000000000 --- a/testbed.md +++ /dev/null @@ -1,437 +0,0 @@ ---- -title: Testbed -header: https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg/1024px-Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg -footer: https://upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg/1024px-Van_Gogh_-_Starry_Night_-_Google_Art_Project.jpg -header-dark: false -footer-dark: false ---- - -# Testbed - -{% include section.html %} - -# Basic formatting - -Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. -Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. -Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. -Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum. - -[External link](https://some-website.org/) - -[Internal link](team) - -_italic text_ - -**bold text** - -~~strike-through text~~ - -