Merge pull request #8 from dms-vep/HIV_update

adds HIV update with CD4bs ab/sera data

experiments/hiv/index.md

@@ -1,7 +1,28 @@
 ---
 layout: doc
+aside: false
+dir: 'hiv'
+title: HIV
+subtext: Below are deep mutational scanning experiments of the HIV Envelope protein. See the details below for the best datasets for different research questions.
+pins:
+  - title: HIV Envelope strain BF520 TZM-bl Cell Entry
+    link: /experiments/hiv/posts/BF520_CD4bs_antibodies_and_sera
+    details: Here is the best data to checkout if you're interested in effects of mutations on cell entry
+    linkText: Check it out!
+  - title: HIV Envelope strain BF520 Serum Escape
+    details: Here are results from mapping neutralizing activity of broad human anti-HIV sera
+    link: /experiments/hiv/posts/BF520_CD4bs_antibodies_and_sera
+    linkText: Check it out!
 ---
 
-# HIV
+<Header :title="$frontmatter.title" :description="$frontmatter.subtext" /> 
 
-In Progress...
+<PinnedExperiments />
+
+<!-- Edit below -->
+## HIV Envelope deep mutational scanning datasets
+
+The pinned posts above include the most up to date data on the effects of mutations on cell entry, antibody escape, and serum escape for HIV Envelope. For a list of all the studies using the lentiviral deep mutational scanning system for HIV Envelope, see the experiments section below.
+<!-- Stop editing -->
+
+<Experiments :currentDirectory="$frontmatter.dir" />

experiments/hiv/posts/BF520_CD4bs_antibodies_and_sera.md

@@ -0,0 +1,65 @@
+---
+title: 'Effects of mutations on escape from CD4-binding-site targeting antibodies and human sera'
+aside: false
+author: 
+    - Caelan Radford
+    - Jesse Bloom
+date: 2023-07-12
+github: https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera
+paper: sciencedirect.com/science/article/pii/S1931312823002184
+keywords:
+    - BF520
+    - HIV Envelope
+    - 1-18
+    - 3BNC117
+    - PGT151
+    - Lentiviral Pseudotyping
+    - cell entry
+    - serum escape
+---
+
+# {{ $frontmatter.title }}
+
+Study by {{ $frontmatter.author.join(', ') }}, et al. The study is available <a v-bind:href="$frontmatter.paper">here</a>.
+
+## Effects of mutations to BF520 HIV Envelope on entry into cells and escape from CD4-binding-site targeting antibodies and human sera
+
+Plot below shows how mutations to BF520 HIV Envelope affect cell entry, escape from CD4-binding-site targeting antibodies, and escape from CD4-binding-site targeting human sera. All experiments were performed using TZM-bl cells.   
+
+These are interactive charts. Mouseover points for details and measurements, and use the top zoom bar to zoom in on specific sites. The options at the bottom let you apply or alter a variety of filters and viewing options, such as choosing the site summary metric, only showing escape for sites with some minimal functional effect, or choosing whether to floor the functional effects or escape at zero. 
+
+The line plots at top of each plot show the effects of mutations at each site, and the heatmaps show the effects of individual mutations on cell entry or immune escape.  
+
+Analysis by Radford et al., Cell Host & Microbe, DOI [10.1016/j.chom.2023.05.025 (2023)](https://www.sciencedirect.com/science/article/pii/S1931312823002184).  
+
+See [https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera](https://github.com/dms-vep/HIV_Envelope_BF520_DMS_CD4bs_sera) for code/data.
+
+### Effects of mutations on cell entry in the BF520 strain
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/muteffects_observed_heatmap.html'"></Altair>
+
+### Antibody 1-18 escape plot  
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/1-18_escape_plot.html'"></Altair>
+
+### Antibody 3BNC117 escape plot  
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/3BNC117_escape_plot.html'"></Altair>
+
+### Serum IDC561 escape plot  
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/IDC561_escape_plot.html'"></Altair>
+
+### Serum IDC513 escape plot  
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/IDC513_escape_plot.html'"></Altair>
+
+### Serum IDC508 escape plot  
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/IDC508_escape_plot.html'"></Altair>
+
+### Serum IDF033 escape plot  
+
+<Altair :spec-url="'https://dms-vep.org/HIV_Envelope_BF520_DMS_CD4bs_sera/IDF033_escape_plot.html'"></Altair>
+
+