2023 update of the website

baymlab · May 9, 2023 · 90a20d8 · 90a20d8
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diff --git a/.gitignore b/.gitignore
@@ -1,4 +1,5 @@
 .DS_Store
 .jekyll-cache
 docs/_site/*
-docs/_config.yml
+docs/_config.yml
+docs/Gemfile*
diff --git a/docs/_config.yml b/docs/_config.yml
@@ -1,15 +1,15 @@
 # GENERAL
-title: HMS Phages
+title: Community Phages
 email: nquinones@g.harvard.edu
 description: >-
-  Online manual for the 2022 Summer Phage Discovery Program
+  Online manual for the 2023 Summer Phage Discovery Program
   at Harvard Medical School
 icon: "https://emojipedia-us.s3.dualstack.us-west-1.amazonaws.com/thumbs/240/apple/237/water-wave_1f30a.png"
 
 
 # JEKYLL STUFF
-remote_theme: just-the-docs/just-the-docs
-#theme: "just-the-docs"
+#remote_theme: just-the-docs/just-the-docs
+theme: "just-the-docs"
 color_scheme: nqo
 ga_tracking: G-W5S9LXVCCG
 logo: "/assets/images/logo.png"

diff --git a/docs/_includes/css/custom.scss.liquid b/docs/_includes/css/custom.scss.liquid
@@ -13,30 +13,30 @@
     font-weight: 800;
     color: black;
     text-align:  center;
-}  
+}
 
 .flex-child.magenta {
     flex: 1;
     justify-content: center;
     align-items: center;
-    background-color: $green-300;
+    background-color: $blue-300;
     color: $white;
     border-radius: 30px
-}  
+}
 
 .flex-child.magenta:hover {
-    background-color: $green-200;
-}  
+    background-color: $blue-200;
+}
 
 .flex-child.green {
     flex: 1;
-    background-color: $green-300;
+    background-color: $blue-300;
     color: $white;
-}  
+}
 
 .flex-child:first-child {
     margin-right: 20px;
-} 
+}
 
 
 strong {
@@ -127,7 +127,7 @@ mark {
   display: block;
   width: 100%;
   height: auto;
-  
+
 }
 
 
@@ -154,7 +154,7 @@ mark {
     display: flex;
     flex-wrap: wrap;
   }
-  
+
   .li-img,
   .li-text,
   .list li {
@@ -165,7 +165,7 @@ mark {
   .li-img {
     align-self: center; /* to match the middle alignment of the original */
   }
-  
+
   .inner {
     display: flex;
   }
@@ -177,7 +177,7 @@ mark {
     display: grid;
     grid-template-columns: repeat(auto-fill, minmax(400px, 1fr));
   }
-  
+
   .list li {
     width: auto; /* this overrides the media queries */
   }
@@ -187,9 +187,9 @@ mark {
 
 /** SLIDE EMBEDDING **/
 
-.responsive-wrap iframe { 
+.responsive-wrap iframe {
   max-width: 100%;
-} 
+}
 
 /** SLIDE EMBEDDING  END **/
 
@@ -218,9 +218,9 @@ mark {
 blockquote{
     font-style: italic;
     font-size: $font-size-4;
-    color: $green-300;
+    color: $blue-300;
     background: #f9f9f9;
-    border-left: 10px solid $green-300;
+    border-left: 10px solid $blue-300;
     margin: 1.5em 10px;
     padding: 0.2em 10px;
-}
+}
diff --git a/docs/_includes/flowchart.html b/docs/_includes/flowchart.html
diff --git a/docs/_includes/people-list.html → docs/_includes/people-list-2022.html b/docs/_includes/people-list.html → docs/_includes/people-list-2022.html
@@ -1,6 +1,6 @@
 <div class='div-list-people'>
   <ul class="list-people img-list">
-    {% for i in site.categories.people %}
+    {% for i in site.categories.people2022 %}
     <li>
       <div class="inner">
         <div class="li-img">
@@ -29,4 +29,3 @@ <h3 class="li-head">{{i.title}}</h3>
 
   </ul>
 </div>
-
diff --git a/docs/_includes/people-list-2023.html b/docs/_includes/people-list-2023.html
@@ -0,0 +1,31 @@
+<div class='div-list-people'>
+  <ul class="list-people img-list">
+    {% for i in site.categories.people2023 %}
+    <li>
+      <div class="inner">
+        <div class="li-img">
+          <img src="{{i.img}}" />
+        </div>
+        <div class="li-text">
+         <h3 class="li-head">{{i.title}}</h3>
+          <div class="li-sub">
+            <p>{{i.subtitle}}</p>
+          </div>
+          <div class="li-desc">
+            <p>{{i.content}}</p>
+          </div>
+          <div class="li-links">
+            {% if i.email_unlinked%}
+            <p>Email: {{i.email}}</p>
+            {% else %}
+            <p>Email: <a href="mailto:{{i.email}}">{{i.email}}</a></p>
+            {% endif %}
+          </div>
+        </div>
+      </div>
+    </li>
+    <hr>
+    {% endfor %}
+
+  </ul>
+</div>
diff --git a/docs/_sass/color_schemes/nqo.scss b/docs/_sass/color_schemes/nqo.scss
@@ -1 +1 @@
-$link-color: $green-300;
+$link-color: $blue-300;
diff --git a/docs/about_the_program/01_2022-program.md b/docs/about_the_program/01_2022-program.md
@@ -0,0 +1,13 @@
+---
+layout: default
+title: 2022 Program
+parent: About the Program
+permalink: about/2022-program
+nav_order: 1
+---
+
+# Past Instructors - 2022 Program
+
+---
+
+{% include people-list-2022.html %}
diff --git a/docs/about.md → docs/about_the_program/index.md b/docs/about.md → docs/about_the_program/index.md
@@ -1,15 +1,17 @@
 ---
 layout: page
+toc: false
 title: About the Program
 permalink: /about/
 nav_order: 6
+has_children: true
 ---
 
 # The HMS Phages team
 
 ---
 
-{% include people-list.html %}
+{% include people-list-2023.html %}
 
 # Diversity and Equity Mission
 

diff --git a/docs/assets/ai/labprotocols_flowchart.ai b/docs/assets/ai/labprotocols_flowchart.ai
diff --git a/docs/assets/ai/labprotocols_flowchart.svg b/docs/assets/ai/labprotocols_flowchart.svg
diff --git a/docs/assets/images/banner.jpeg b/docs/assets/images/banner.jpeg
diff --git a/docs/assets/images/banner2.jpeg b/docs/assets/images/banner2.jpeg
diff --git a/docs/assets/images/hs/ajohnson.jpg b/docs/assets/images/hs/ajohnson.jpg
diff --git a/docs/assets/images/hs/bohara.jpg b/docs/assets/images/hs/bohara.jpg
diff --git a/docs/assets/images/hs/brussell.jpg b/docs/assets/images/hs/brussell.jpg
diff --git a/docs/assets/images/hs/igonzalez.jpg b/docs/assets/images/hs/igonzalez.jpg
diff --git a/docs/assets/images/hs/jmspencer.jpg b/docs/assets/images/hs/jmspencer.jpg
diff --git a/docs/assets/images/hs/khenry.jpg b/docs/assets/images/hs/khenry.jpg
diff --git a/docs/assets/images/hs/pkranzusch.jpg b/docs/assets/images/hs/pkranzusch.jpg
diff --git a/docs/assets/images/hs/shobbs.jpg b/docs/assets/images/hs/shobbs.jpg
diff --git a/docs/assets/images/logo.png b/docs/assets/images/logo.png
diff --git a/docs/bioinformatics/protocol02_assembly.md b/docs/bioinformatics/protocol02_assembly.md
@@ -45,7 +45,7 @@ We will learn the basics of how to use the terminal to give direct instructions
 ```
 bash
 ```
-1. Write 
+1. Write
 ```
 ls
 ```
@@ -63,7 +63,7 @@ mkdir myfolder
 cd myfolder
 ```
     - What changed in the terminal?
-    
+
 1. Write:
 ```
 ls
@@ -125,7 +125,7 @@ We will download your read files and learn how to look at your reads in the term
 {: .label .label-green }
 
 1. Download your read files from Google Drive
-    - Visit the [Google Drive](https://drive.google.com/drive/folders/1Y7e7k120TuLlCOhuekfsPJ7g2HjMwzu5?usp=sharing) and open the folder with your name
+    - Visit the [Google Drive](https://drive.google.com/drive/folders/14AFbHZkzES69j9jdyqCtLmkQAYv2cwao?usp=share_link) and open the folder with your name
     - Click on the three dots in the top right of the page
     - Click download. This will get saved in your `Downloads/` folder
     - Move the folder from your `Downloads/` to your `Desktop/`
@@ -141,7 +141,7 @@ cd <name of your folder>
 ```
     - **Here, replace `<name of your folder>` with the name of the folder you downloaded!!**
     - Instructions between angle brackets  **`< like this >`** mean that you have to write the name of the files YOU have.
-1. Write 
+1. Write
 ```
 ls
 ```
@@ -164,7 +164,7 @@ less reads_R1.fastq
 ```
 echo $(cat reads_R1.fastq|wc -l)/4|bc
 ```
-    - This is another "special command" to count the number of reads in our file. (You don't need to remember this one.) 
+    - This is another "special command" to count the number of reads in our file. (You don't need to remember this one.)
     - How many reads are in one of your read files?
 
 
@@ -197,8 +197,8 @@ unicycler -h
 1. Now we will run the assembly. Write in a single line:
 ```
 unicycler
--1 <name_of_your_reads>_R1.trim.fastq.gz 
--2 <name_of_your_reads>_R2.trim.fastq.gz 
+-1 <name_of_your_reads>_R1.trim.fastq.gz
+-2 <name_of_your_reads>_R2.trim.fastq.gz
 -o assembly
 ```
     - What are the options `-1` and `-2`?
@@ -235,7 +235,7 @@ cd assembly
 ls
 ```
     - There, you will find many files, but the one we care about is `assembly.fasta`
-1. The assembly might contain more than one large piece of DNA. Let's check how many it has: 
+1. The assembly might contain more than one large piece of DNA. Let's check how many it has:
 ```
 grep -c "^>" assembly.fasta
 ```

diff --git a/docs/index.md b/docs/index.md
@@ -11,11 +11,11 @@ nav_order: 1
 </div>
 
 {: .fs-7}
-# Welcome to the HMS Phages 2022 program website!
+# Welcome to the Community Phages 2023 program website!
 
-HMS Phages is an 8-week summer research internship program where undergraduate students from neighboring Roxbury Community College will partner with researchers in the [Bernhardt](http://www.bernhardtlab.com) and [Baym](https://baymlab.hms.harvard.edu) laboratories at Harvard Medical School to isolate novel bacteriophages. The program is supported by the Howard Hughes Medical Institute. 
+Community Phages is an 8-week summer research internship program where undergraduate students from neighboring Roxbury Community College will partner with researchers in the [Bernhardt](http://www.bernhardtlab.com) and [Baym](https://baymlab.hms.harvard.edu) laboratories at Harvard Medical School to isolate novel bacteriophages. The program is supported by the Howard Hughes Medical Institute.
 
-This website serves as a centralized hub for our protocols and resources. Find out more about the HMS Phages 2022 program and organizers on the [About the Program](./about) page.
+This website serves as a centralized hub for our protocols and resources. Find out more about the Community Phages 2023 program and organizers on the [About the Program](./about) page.
 
 ---
 

diff --git a/docs/labprotocols/protocol_01-intro.md b/docs/labprotocols/protocol_01-intro.md
@@ -20,11 +20,6 @@ published: true
 
 ---
 
-## Team _Coryne_ phages
-
-Team Coryne
-{: .label .label-red }
-
 ### Project description
 {: .no_toc }
 
@@ -39,32 +34,3 @@ One common trait shared between humans and bacteria is that we are all infected
 | Temperature    | 30℃                 |
 | Media          | LB                  |
 | Doubling time  | 50 min              |
-
----
-
-## Team _plasmid-dependent_ phages
-
-Team plasmid-dependent
-{: .label .label-purple }
-
-### Project description
-{: .no_toc }
-
-Phages are usually very specific to the bacteria they infect, and they often infect by recognizing conserved structures found on the host's surface. However, there are certain phages that instead recognize structures expressed by plasmids. (That's why we call them **plasmid-dependent** phages!) Plasmids are small DNA molecules that live inside cells and can autonomously replicate and transfer between different bacteria. Because certain plasmids can live in a large variety of number of bacterial species, plasmid-dependent phages can also have a wide host range, which is special in the phage world!
-
-In this project, we will be working with **pRP4**, a broad-host plasmid that can go into both *E. coli* and *P. putida*, and will use these two strains to look for plasmid-dependent phages. By isolating these phages, we hope to explore questions like: _How do these phages manage to infect different hosts?_ and _How does phage predation affect the evolution of the plasmid?_
-
-
-### Hosts: _Escherichia coli_ (Eco) & _Pseudomonas putida_ (Ppu) with pRP4 plasmid.
-{: .no_toc }
-
-- _E. coli_ is perhaps the most famous bacterium used in labs! In nature, it is commonly part of the normal microbiota of animals, but some strains can cause disease in humans.
-- _P. putida_ is a bacterium that usually lives in soil. It has very interesting metabolic properties which have been used for bioremediation.
-- pRP4 is a broad-host, conjugative plasmid that confers resistance to the antibiotic trimethoprim. Most importantly for us, this plasmid makes its bacterial host susceptible to certain phages. pRP4 has been introduced to both _E. coli_ and _P. putida_, and we will be using both of these hosts in our plasmid-dependent phage hunting mission.
-
-
-| -------------- | ---------------------------- |
-| Temperature    | 30 ℃                         |
-| Media          | LB                           |
-| Doubling time  | 20 min (_Eco_) <br> 25 min (_Ppu_) |
-