diff --git a/.github/workflows/first-time-setup.yaml b/.github/workflows/first-time-setup.yaml index bf227f7..507d831 100644 --- a/.github/workflows/first-time-setup.yaml +++ b/.github/workflows/first-time-setup.yaml @@ -76,7 +76,7 @@ jobs: Visit **[website url](#)** 🚀 - _Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_ + _Built with [LWT](https://greene-lab.gitbook.io/lab-website-template-docs)_ " > README.md - name: Personalize Jekyll config for user diff --git a/README.md b/README.md index dad0d7b..334bcc4 100644 --- a/README.md +++ b/README.md @@ -3,5 +3,5 @@ Visit **[website url](#)** 🚀 -_Built with [Lab Website Template](https://greene-lab.gitbook.io/lab-website-template-docs)_ +_Built with [LWT](https://greene-lab.gitbook.io/lab-website-template-docs)_ diff --git a/_cite/.cache/cache.db b/_cite/.cache/cache.db index 4bbcc12..f0df437 100644 Binary files a/_cite/.cache/cache.db and b/_cite/.cache/cache.db differ diff --git a/_config.yaml b/_config.yaml index 5c860f5..e00a8f6 100644 --- a/_config.yaml +++ b/_config.yaml @@ -1,5 +1,5 @@ # site properties and page defaults -title: asu-idi +title: ASU-IDI subtitle: description: An engaging 1-3 sentence description of your lab. header: images/background.jpg @@ -7,12 +7,9 @@ footer: images/background.jpg # site social media and other links links: - email: contact@asu-idi.com - orcid: 0000-0001-8713-9213 - google-scholar: ETJoidYAAAAJ + email: zhichao.cao@asu.edu + google-scholar: VI4vH9UAAAAJ github: asu-idi - twitter: asu-idi - youtube: asu-idi ### jekyll settings diff --git a/_data/citations.yaml b/_data/citations.yaml index 0cc985a..275a699 100644 --- a/_data/citations.yaml +++ b/_data/citations.yaml @@ -1,155 +1,3 @@ # DO NOT EDIT, GENERATED AUTOMATICALLY -- 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:10.1186/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 - 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:10.1101/573782 - 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 - 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 - plugin: sources.py - file: sources.yaml +[] diff --git a/_data/orcid.yaml b/_data/orcid.yaml deleted file mode 100644 index 005d380..0000000 --- a/_data/orcid.yaml +++ /dev/null @@ -1 +0,0 @@ -- orcid: 0000-0002-4655-3773 diff --git a/_data/sources.yaml b/_data/sources.yaml deleted file mode 100644 index 62cd922..0000000 --- a/_data/sources.yaml +++ /dev/null @@ -1,23 +0,0 @@ -- 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:10.1016/j.csbj.2020.05.017 - image: https://ars.els-cdn.com/content/image/1-s2.0-S2001037020302804-gr1.jpg - -- 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/_includes/card-excerpt.html b/_includes/card-excerpt.html new file mode 100644 index 0000000..f97315f --- /dev/null +++ b/_includes/card-excerpt.html @@ -0,0 +1,35 @@ +{% assign post = site.project_posts + | where_exp: "post", "post.slug == include.lookup" + | first + | default: include +%} + +
+ {% assign url = post.url %} + {% assign title = post.title %} + {{ title }} + + {% + include post-info.html + author=post.author + published=post.date + updated=post.last_modified_at + tags=post.tags + %} + + {% assign excerpt = post.content + | default: "" + | regex_scan: "(.*)", true + | default: post.excerpt + | default: "" + | strip_html + %} + {% assign search = post.content + | strip_html + | strip_newlines + | regex_strip + %} +

+ {{ excerpt }} +

+
diff --git a/_includes/footer.html b/_includes/footer.html index 8230d53..fd36f76 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -28,7 +28,7 @@ {{ site.title }}   |   Built with - Lab Website Template + LWT diff --git a/_includes/header.html b/_includes/header.html index 967078c..2e79730 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -47,12 +47,14 @@ %} {% for page in pages %} {% if page.nav %} - - {{ page.title }} - + {% if page.nav.display %} + + {{ page.title }} + + {% endif %} {% endif %} {% endfor %} diff --git a/_layouts/member.html b/_layouts/member.html index 034b5d0..6337f20 100644 --- a/_layouts/member.html +++ b/_layouts/member.html @@ -29,14 +29,14 @@ %} {% capture search -%} - research/?search={% for alias in aliases %}"{{ alias }}" {% endfor %} + publications/?search={% for alias in aliases %}"{{ alias }}" {% endfor %} {%- endcapture %} -

+ {% capture search -%} blog/?search={{ page.name }} diff --git a/_members/john-doe.md b/_members/chang-guo.md similarity index 79% rename from _members/john-doe.md rename to _members/chang-guo.md index 0e441c6..d6dcb7a 100644 --- a/_members/john-doe.md +++ b/_members/chang-guo.md @@ -1,10 +1,9 @@ --- -name: John Doe +name: Chang Guo image: images/photo.jpg role: phd -group: alum links: - github: john-doe + github: change72 --- Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/_members/jane-smith.md b/_members/jane-smith.md deleted file mode 100644 index f4cae89..0000000 --- a/_members/jane-smith.md +++ /dev/null @@ -1,19 +0,0 @@ ---- -name: Jane Smith -image: images/photo.jpg -role: pi -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/sarah-johnson.md b/_members/viraj-thakkar.md similarity index 57% rename from _members/sarah-johnson.md rename to _members/viraj-thakkar.md index b0d97b4..48080f8 100644 --- a/_members/sarah-johnson.md +++ b/_members/viraj-thakkar.md @@ -1,11 +1,10 @@ --- -name: Sarah Johnson +name: Viraj Thakkar image: images/photo.jpg -description: Lead Programmer -role: programmer +role: phd links: - email: sarah.johnson@gmail.com - twitter: sarahjohnson + email: viraj.online@asu.edu + github: veedata --- Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/_members/zhichao-cao.md b/_members/zhichao-cao.md new file mode 100644 index 0000000..ffba0c6 --- /dev/null +++ b/_members/zhichao-cao.md @@ -0,0 +1,12 @@ +--- +name: Zhichao Cao +image: images/photo.jpg +role: pi +links: + home-page: https://search.asu.edu/profile/4082902 + orcid: 0000-0001-6950-1776 +--- + +Zhichao Cao is an assistant professor in the School of Computing and Augmented Intelligence at Arizona State University. He leads the Intelligent Data Infrastructure (IDI) research lab, where he conducts research in the areas of database systems (e.g., key-value stores, graph databases, and timeseries databases), storage systems (e.g., file systems, cloud storage, and deduplication systems), and next-generation data infrastructure (e.g., disaggregated infrastructure, computing-in-X, and wireless datacenter). His research interests also lie in the design and development of data management systems for new memory and storage technologies, such as SMR, IMR, NVM, CXL, RDMA, ZNS, and DNA. Moreover, Prof. Cao's research also encompasses big data systems, with a focus on the development of query engines for large-scale scientific computing in HPC and storage solutions for AI/ML platforms. + +Prior to joining ASU, Prof. Cao worked as a research scientist at Facebook, where he contributed to storage and database research from 2018 to 2021. He earned his bachelor's degree in Automation from Tsinghua University in 2013 and his doctoral degree in Computer Science from the University of Minnesota, Twin Cities, in 2020. diff --git a/_project_posts/2019-01-07-example-post-1.md b/_project_posts/2019-01-07-example-post-1.md new file mode 100644 index 0000000..d586270 --- /dev/null +++ b/_project_posts/2019-01-07-example-post-1.md @@ -0,0 +1,10 @@ +--- +title: Example post 1 +author: sarah-johnson +tags: + - biology + - medicine + - big data +--- + +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/_project_posts/2021-09-30-example-post-2.md b/_project_posts/2021-09-30-example-post-2.md new file mode 100644 index 0000000..889c897 --- /dev/null +++ b/_project_posts/2021-09-30-example-post-2.md @@ -0,0 +1,6 @@ +--- +title: Example post 2 +author: jane-smith +--- + +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. diff --git a/_project_posts/2023-02-23-example-post-3.md b/_project_posts/2023-02-23-example-post-3.md new file mode 100644 index 0000000..c7b1038 --- /dev/null +++ b/_project_posts/2023-02-23-example-post-3.md @@ -0,0 +1,7 @@ +--- +title: Example post 3 +author: john-doe +tags: biology, medicine +--- + +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 b86f359..975b87f 100644 --- a/blog/index.md +++ b/blog/index.md @@ -3,6 +3,7 @@ title: Blog nav: order: 4 tooltip: Musings and miscellany + display: false --- # {% include icon.html icon="fa-solid fa-feather-pointed" %}Blog diff --git a/contact/index.md b/contact/index.md index d9b7e4b..86de52d 100644 --- a/contact/index.md +++ b/contact/index.md @@ -3,42 +3,33 @@ title: Contact nav: order: 5 tooltip: Email, address, and location + display: true --- # {% 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. +We are always working on exciting new ideas. If you are interested in +collaborating with us, or if you have any questions, we would love to hear. {% 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" -%} -{% - include button.html - type="address" - tooltip="Our location on Google Maps for easy navigation" - link="https://www.google.com/maps" + text="zhichao.cao@asu.edu" + link="zhichao.cao@asu.edu" %} {% include section.html %} {% capture col1 %} -{% - include figure.html - image="images/photo.jpg" - caption="Lorem ipsum" -%} +Brickyard Engineering is the home to the Intelligent Data Infrastructure Lab (IDI). You will often find one of our team members in the vicinity of the following address: + +**Street Address**
+699 S. Mill Ave.
+Tempe, AZ 85281 + +**Building Code**
+BYENG {% endcapture %} @@ -46,32 +37,10 @@ nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. {% include figure.html - image="images/photo.jpg" - caption="Lorem ipsum" + image="images/BrickyardASU.jpeg" + caption="Our Home @ ASU" %} {% 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/BrickyardASU.jpeg b/images/BrickyardASU.jpeg new file mode 100644 index 0000000..f0220f1 Binary files /dev/null and b/images/BrickyardASU.jpeg differ diff --git a/index.md b/index.md index 309a69a..50f5d8b 100644 --- a/index.md +++ b/index.md @@ -1,9 +1,9 @@ --- --- -# asu-idi's Website +

Exploring frontiers in database, storage, and data infrastructure

-An engaging 1-3 sentence description of your lab. +The Intelligent Data Infrastructure (IDI) research lab delves into database systems, storage technologies, and next-generation data infrastructure. We tackle emerging challenges, designing cutting-edge solutions to advance data management and analysis in today's dynamic digital landscape. Our work spans a wide range of topics, including distributed systems, cloud computing, machine learning, and data analytics. We are passionate about pushing the boundaries of data infrastructure. {% include section.html %} @@ -15,7 +15,7 @@ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor i {% include button.html - link="research" + link="publications" text="See our publications" icon="fa-solid fa-arrow-right" flip=true @@ -27,8 +27,8 @@ Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor i {% include feature.html image="images/photo.jpg" - link="research" - title="Our Research" + link="publications" + title="Our Publications" text=text %} diff --git a/projects/index.md b/projects/index.md index 1d29a19..7dbc970 100644 --- a/projects/index.md +++ b/projects/index.md @@ -2,26 +2,18 @@ title: Projects nav: order: 2 - tooltip: Software, datasets, and more + tooltip: Software, databases, and more + display: true --- # {% include icon.html icon="fa-solid fa-wrench" %}Projects -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 tags.html tags="publication, resource, website" %} {% include search-info.html %} {% include section.html %} -## Featured - -{% include list.html component="card" data="projects" filters="group: featured" %} - -{% include section.html %} - -## More +## Current Projects -{% include list.html component="card" data="projects" filters="group: " style="small" %} +{% include list.html data="project_posts" component="post-excerpt" %} diff --git a/publications/index.md b/publications/index.md new file mode 100644 index 0000000..b212fb0 --- /dev/null +++ b/publications/index.md @@ -0,0 +1,17 @@ +--- +title: Publications +nav: + order: 1 + tooltip: Published works + display: false +--- + +# {% include icon.html icon="fa-solid fa-file-circle-check" %}Publications + +
+ +{% include search-box.html %} + +{% include search-info.html %} + +{% include list.html data="citations" component="citation" style="rich" %} diff --git a/research/index.md b/research/index.md deleted file mode 100644 index 0f700f4..0000000 --- a/research/index.md +++ /dev/null @@ -1,27 +0,0 @@ ---- -title: Research -nav: - order: 1 - tooltip: Published works ---- - -# {% include icon.html icon="fa-solid fa-microscope" %}Research - -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/team/index.md b/team/index.md index 08318c9..f80c5c1 100644 --- a/team/index.md +++ b/team/index.md @@ -3,33 +3,21 @@ title: Team nav: order: 3 tooltip: About our team + display: true --- -# {% include icon.html icon="fa-solid fa-users" %}Team - -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 %} - -{% include list.html data="members" component="portrait" filters="role: pi" %} -{% include list.html data="members" component="portrait" filters="role: ^(?!pi$)" %} - -{% include section.html background="images/background.jpg" dark=true %} - -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 icon.html icon="fa-solid fa-users" %}Team {% include section.html %} -{% capture content %} +## Current Members -{% include figure.html image="images/photo.jpg" %} -{% include figure.html image="images/photo.jpg" %} -{% include figure.html image="images/photo.jpg" %} +{% include list.html data="members" component="portrait" filters="role: pi" %} +{% include list.html data="members" component="portrait" filters="role: phd" %} +{% include list.html data="members" component="portrait" filters="role: ms" %} +{% include list.html data="members" component="portrait" filters="role: undergrad" %} -{% endcapture %} +## Alumni -{% include grid.html style="square" content=content %} +{% include list.html data="members" component="portrait" filters="role: alum" %}