Basic updates for the site

.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

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)_
 

_config.yaml

@@ -1,18 +1,15 @@
 # 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
 footer: images/background.jpg
 
 # site social media and other links
 links:
-  email: [email protected]
-  orcid: 0000-0001-8713-9213
-  google-scholar: ETJoidYAAAAJ
+  email: [email protected]
+  google-scholar: VI4vH9UAAAAJ
   github: asu-idi
-  twitter: asu-idi
-  youtube: asu-idi
 
 ### jekyll settings
 

_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
+[]

_includes/card-excerpt.html

@@ -0,0 +1,35 @@
+{% assign post = site.project_posts
+  | where_exp: "post", "post.slug == include.lookup"
+  | first
+  | default: include
+%}
+
+<div class="card-excerpt">
+  {% assign url = post.url %}
+  {% assign title = post.title %}
+  <a href="{{ url | relative_url }}">{{ title }}</a>
+
+  {%
+    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: "<!-- excerpt start -->(.*)<!-- excerpt end -->", true
+    | default: post.excerpt
+    | default: ""
+    | strip_html
+  %}
+  {% assign search = post.content
+    | strip_html 
+    | strip_newlines
+    | regex_strip
+  %}
+  <p data-search="{{ search }}">
+    {{ excerpt }}
+  </p>
+</div>

_includes/footer.html

@@ -28,7 +28,7 @@
     {{ site.title }}
       |   Built with
     <a href="https://github.com/greenelab/lab-website-template">
-      Lab Website Template
+      LWT
     </a>
   </div>
 

_includes/header.html

@@ -47,12 +47,14 @@
     %}
     {% for page in pages %}
       {% if page.nav %}
-        <a
-          href="{{ page.dir | relative_url }}"
-          data-tooltip="{{ page.nav.tooltip }}"
-        >
-          {{ page.title }}
-        </a>
+        {% if page.nav.display %}
+          <a
+            href="{{ page.dir | relative_url }}"
+            data-tooltip="{{ page.nav.tooltip }}"
+          >
+            {{ page.title }}
+          </a>
+        {% endif %}
       {% endif %}
     {% endfor %}
   </nav>

_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 %}
 
-<p class="center">
+<!-- <p class="center">
   <a href="{{ search | relative_url }}">
-    Search for {{ page.name | default: page.title }}'s papers on the Research page
+    Search for {{ page.name | default: page.title }}'s papers on the Publications page
   </a>
-</p>
+</p> -->
 
 {% capture search -%}
   blog/?search={{ page.name }}

_members/john-doe.md → _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.

_members/sarah-johnson.md → _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: [email protected]
-  twitter: sarahjohnson
+  email: [email protected]
+  github: veedata
 ---
 
 Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.

_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.

_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.

_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.

_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.