From ea1b20f2e465de8f409f6bc3fc6d319448165ce1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E2=80=9CWill?= <wwh22@uw.edu>
Date: Sun, 11 Aug 2024 18:40:31 -0700
Subject: [PATCH] Move assets to public

---
 .vitepress/theme/Home.vue                     |  71 ++++++++++++------
 README.md                                     |   5 +-
 package-lock.json                             |   1 -
 posts/h5-dms.md                               |  14 ++--
 .../assets}/papers/2013_ashenberg.jpg         | Bin
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 119 files changed, 55 insertions(+), 36 deletions(-)
 rename {assets => public/assets}/papers/2013_ashenberg.jpg (100%)
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diff --git a/.vitepress/theme/Home.vue b/.vitepress/theme/Home.vue
index b8c62fa..43a0c5b 100644
--- a/.vitepress/theme/Home.vue
+++ b/.vitepress/theme/Home.vue
@@ -61,7 +61,7 @@ export default {
                     <transition name="fade" mode="out-in">
                         <span :key="currentVirus" class="italic"
                             :style="{ color: currentColor, backgroundColor: getBackgroundWithOpacity(currentColor) }">{{
-                            currentVirus }}</span>
+                                currentVirus }}</span>
                     </transition>
                 </p>
                 <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-4 md:mt-6 lg:mt-12">
@@ -73,9 +73,12 @@ export default {
 
                     <br><br>
                     Our lab is part of the
-                    <a href="https://www.fredhutch.org/en/research/divisions/basic-sciences-division.html">Basic Sciences Divison</a>
+                    <a href="https://www.fredhutch.org/en/research/divisions/basic-sciences-division.html">Basic
+                        Sciences Divison</a>
                     and the
-                    <a href="https://www.fredhutch.org/en/research/divisions/public-health-sciences-division/research/computational-biology.html">Computational Biology Program</a>
+                    <a
+                        href="https://www.fredhutch.org/en/research/divisions/public-health-sciences-division/research/computational-biology.html">Computational
+                        Biology Program</a>
                     at the Fred Hutch. We are also affiliated with the
                     <a href="https://www.gs.washington.edu/">Genome Sciences</a>
                     and <a href="https://microbiology.washington.edu/uw-microbiology-home">Microbiology</a>
@@ -108,33 +111,39 @@ export default {
                 </h2>
                 <div class="description">
                     <div class="">
-                        <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-12"> 
+                        <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-12">
                             Our lab uses deep mutational scanning to
                             experimentally measure how tens-of-thousands of mutations to viral proteins
                             affect key properties including function, immune escape, and receptor binding.
                         </p>
-                        <img src="../../assets/research/dms.png" alt="Example of deep mutational scanning"
+                        <img src="/assets/research/dms.png" alt="Example of deep mutational scanning"
                             class="float-left mr-4 my-4 w-107 h-64">
                         <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-8">
                             We primarily perform these experiments using a
-                            <a href="https://www.sciencedirect.com/science/article/pii/S0092867423001034">pseudovirus system</a>
+                            <a href="https://www.sciencedirect.com/science/article/pii/S0092867423001034">pseudovirus
+                                system</a>
                             that allows us to safely characterize mutants of entry proteins from a wide range
                             of viruses, including
                             <a href="https://www.nature.com/articles/s41586-024-07636-1">SARS-CoV-2 spike</a>,
                             <a href="https://doi.org/10.1101/2024.05.23.595634">influenza hemagglutinin</a>,
-                            <a href="https://www.sciencedirect.com/science/article/pii/S1074761324003194">Lassa virus GPC</a>,
-                            <a href="https://www.sciencedirect.com/science/article/pii/S1931312823002184">HIV envelope</a>, and
+                            <a href="https://www.sciencedirect.com/science/article/pii/S1074761324003194">Lassa virus
+                                GPC</a>,
+                            <a href="https://www.sciencedirect.com/science/article/pii/S1931312823002184">HIV
+                                envelope</a>, and
                             <a href="https://doi.org/10.1101/2024.04.17.589977">Nipah virus RBP</a>.
                         </p>
                         <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-8">
                             Deep mutational scanning can inform efforts to
-                            <a href="https://www.nature.com/articles/s41586-024-07636-1">forecast the evolution of human seasonal viruses</a>
+                            <a href="https://www.nature.com/articles/s41586-024-07636-1">forecast the evolution of human
+                                seasonal viruses</a>
                             and
-                            <a href="https://doi.org/10.1101/2024.05.23.595634">surveil the evolution of potential pandemic viruses</a>.
+                            <a href="https://doi.org/10.1101/2024.05.23.595634">surveil the evolution of potential
+                                pandemic viruses</a>.
                             To facilitate the use of deep mutational scanning for these important goals,
                             we develop <a href="https://dms-viz.github.io/">interactive visualization tools</a>
                             and <a href="https://github.com/dms-vep/dms-vep-pipeline-3">data analysis pipelines</a>.
-                            See <a href="https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/">here</a>
+                            See <a
+                                href="https://dms-vep.org/Flu_H5_American-Wigeon_South-Carolina_2021-H5N1_DMS/">here</a>
                             for an example of how we analyze and visualize large datasets to
                             inform the study of viral evolution.
                         </p>
@@ -160,7 +169,8 @@ export default {
             class="carousel-item w-full h-full snap-always snap-start mx-auto max-w-4xl px-4 text-left flex flex-col justify-between">
             <div class="flex-grow">
                 <h2 class="text-2xl md:text-3xl lg:text-4xl text-gray-600 mt-2 lg:mt-4 font-normal select-none">
-                    <span class="underline decoration-indigo-500 font-semibold">Interplay of Immunity and Viral Evolution</span>
+                    <span class="underline decoration-indigo-500 font-semibold">Interplay of Immunity and Viral
+                        Evolution</span>
                 </h2>
                 <div class="description">
                     <div class="">
@@ -168,24 +178,30 @@ export default {
                             We study immunity and viral evolution at both the population and single-cell
                             levels.
                         </p>
-                        <img src="../../assets/research/seqneut.jpg" alt="Description"
+                        <img src="/assets/research/seqneut.jpg" alt="Description"
                             class="float-left mr-4 my-4 w-80 h-134">
                         <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-8">
-                            At the population level, differences in exposure history and immune imprinting lead 
+                            At the population level, differences in exposure history and immune imprinting lead
                             human individuals to make antibody responses that target different regions
                             of rapidly evolving viruses like influenza and SARS-CoV-2.
-                            This population heterogeneity has profound implications for viral evolution and disease susceptibility, as
+                            This population heterogeneity has profound implications for viral evolution and disease
+                            susceptibility, as
                             it causes viral mutations to impact the immunity of different individuals
                             differently. We are characterizing this population heterogeneity using both
-                            <a href="https://www.sciencedirect.com/science/article/pii/S1931312824002336">deep mutational scanning</a>
-                            and a <a href="https://doi.org/10.1101/2024.03.08.584176">sequencing based-neutralization assay</a>
-                            we developed that increases the throughput of traditional neutralization assays by several orders of magnitude (see schematic at left).
+                            <a href="https://www.sciencedirect.com/science/article/pii/S1931312824002336">deep
+                                mutational scanning</a>
+                            and a <a href="https://doi.org/10.1101/2024.03.08.584176">sequencing based-neutralization
+                                assay</a>
+                            we developed that increases the throughput of traditional neutralization assays by several
+                            orders of magnitude (see schematic at left).
 
                         </p>
                         <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-8">
                             At the single-cell level, we developed approaches to
-                            <a href="https://journals.asm.org/doi/10.1128/jvi.00500-19">sequence viruses in single cells</a>
-                            and <a href="https://elifesciences.org/articles/86852">quantify how many progeny each infected cell produces</a>.
+                            <a href="https://journals.asm.org/doi/10.1128/jvi.00500-19">sequence viruses in single
+                                cells</a>
+                            and <a href="https://elifesciences.org/articles/86852">quantify how many progeny each
+                                infected cell produces</a>.
                             We use these approaches to understand how viral variation impacts the
                             outcome of infection in individual cells.
                         </p>
@@ -224,19 +240,24 @@ export default {
                             (see <a href="https://academic.oup.com/ve/article/9/2/vead055/7265011">this paper</a>
                             and <a href="https://slides.com/jbloom/sars2-mut-fitness/">these slides</a>).
                             We've also created a platform to
-                            <a href="https://jbloomlab.github.io/SARS2-mut-fitness/">visualize the mutational effects</a>
+                            <a href="https://jbloomlab.github.io/SARS2-mut-fitness/">visualize the mutational
+                                effects</a>
                             to aid in interpretation of viral evolution.
                         </p>
                         <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-8">
                             We have also integrated thousands of deep mutational scanning measurements
-                            into an <a href="https://jbloomlab.github.io/SARS2-RBD-escape-calc/">antibody-escape calculator</a>
-                            that was <a href="https://slides.com/jbloom/sars2-rbd-escape-calc#/12">widely used</a> during the SARS-CoV-2 pandemic to understand
+                            into an <a href="https://jbloomlab.github.io/SARS2-RBD-escape-calc/">antibody-escape
+                                calculator</a>
+                            that was <a href="https://slides.com/jbloom/sars2-rbd-escape-calc#/12">widely used</a>
+                            during the SARS-CoV-2 pandemic to understand
                             the antigenic effects of viral mutations.
                         </p>
                         <p class="text-sm md:text-base lg:text-lg text-gray-500 mt-2 md:mt-4 lg:mt-8">
                             We also have projects that involve analyzing the evolution of viruses
-                            <a href="https://elifesciences.org/articles/26875">within individual infected humans</a>, and developing models
-                            to <a href="https://academic.oup.com/ve/article/8/2/veac110/6889254">understand epistasis among viral mutations</a>.
+                            <a href="https://elifesciences.org/articles/26875">within individual infected humans</a>,
+                            and developing models
+                            to <a href="https://academic.oup.com/ve/article/8/2/veac110/6889254">understand epistasis
+                                among viral mutations</a>.
                         </p>
                     </div>
                 </div>
diff --git a/README.md b/README.md
index b763330..8aa9b28 100644
--- a/README.md
+++ b/README.md
@@ -72,8 +72,7 @@ The general file structure of this website is as follows:
 ├── posts/ # <-------------- blog posts
 ├── projects/ # <-------------- projects and software
 ├── index.md
-├── assets/ # <-------------- images
-├── public
+├── public/assets/ # <-------------- images (note that paths to this directory are simply /assets/)
 ├── .vitepress # <-------------- source code
 ├── tailwind.config.mjs
 ├── postcss.config.mjs
@@ -192,7 +191,7 @@ selected: true # <------- OPTIONAL, this will add the paper to a list of selecte
 ---
 ```
 
-Most fields are self-explanatory. The `keywords` field is automatically parsed by the website, allowing you to quickly filter all of our papers for the ones relevant to you. Please reference this for existing keywords that pertain to your paper. Select a representative image from your paper and add it to the `assets/papers` directory using the same base name as for the markdown file.
+Most fields are self-explanatory. The `keywords` field is automatically parsed by the website, allowing you to quickly filter all of our papers for the ones relevant to you. Please reference this for existing keywords that pertain to your paper. Select a representative image from your paper and add it to the `/public/assets/papers` directory using the same base name as for the markdown file.
 
 There is an optional key called `selected:` that if added and set to `true` will add the paper to a list of selected paper at the top of the page.
 
diff --git a/package-lock.json b/package-lock.json
index 75fb7b1..8ee8940 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -4,7 +4,6 @@
   "requires": true,
   "packages": {
     "": {
-      "name": "jbloomlab.github.io",
       "dependencies": {
         "@primevue/themes": "^4.0.0-rc.2",
         "primevue": "^4.0.0-rc.2"
diff --git a/posts/h5-dms.md b/posts/h5-dms.md
index 08e39d0..995375c 100644
--- a/posts/h5-dms.md
+++ b/posts/h5-dms.md
@@ -18,34 +18,34 @@ From prior work, several molecular phenotypes of HA are known to contribute to p
 
 In [a new study led by Bernadeta Dadonaite](https://doi.org/10.1101/2024.05.23.595634), we used deep mutational scanning to measure how all HA amino-acid mutations affected key molecular phenotypes.
 
-![molecular phenotypes measured](../assets/research/h5-dms/phenotypes.jpg)
+![molecular phenotypes measured](/assets/research/h5-dms/phenotypes.jpg)
 
 To make these measurements safely, we used a previously described [pseudovirus deep mutational scanning system](https://www.sciencedirect.com/science/article/pii/S0092867423001034) that allows us to characterize the effects of mutations to viral entry proteins using single-cycle replicative lentiviral particles that can be safely studied at biosafety-level 2.
 Using this system, we made libraries that covered all amino-acid mutations to the current candidate vaccine strain HA for clade 2.3.4.4b H5 influenza.
 
-![pseudovirus schematic](../assets/research/h5-dms/schematic.jpg)
+![pseudovirus schematic](/assets/research/h5-dms/schematic.jpg)
 
 First we measured how all mutations affected the ability of HA to mediate cell entry.
 These results can be visualized either using a heatmap or by projecting functional constraint onto the HA protein structure, as show below.
 Overall, these measurements identify functionally constrained regions of HA that are unlikely to mutate, and so form good targets for antibodies and other therapeutics.
 
-![cell entry heatmap](../assets/research/h5-dms/cell_entry_heatmap.jpg)
-![cell entry structure](../assets/research/h5-dms/cell_entry_structure.jpg)
+![cell entry heatmap](/assets/research/h5-dms/cell_entry_heatmap.jpg)
+![cell entry structure](/assets/research/h5-dms/cell_entry_structure.jpg)
 
 Next we measured how mutations affect HA's ability to mediate entry into 293T cells that express a2-6 versus a2-3 linked sialic acids, which is important because human transmissible viruses use a2-6.
 Below are mutations that increase a2-6 usage:
 
-![a2-6 usage](../assets/research/h5-dms/a2-6.jpg)
+![a2-6 usage](/assets/research/h5-dms/a2-6.jpg)
 
 We also measured how mutations affect HA stability, which is important as increased HA stability is associated with increased airborne transmissibility.
 Below is a map of stability enhancing mutations, which tend to be located in helices in the fusion machinery and interfaces between the head and stalk domains:
 
-![stability](../assets/research/h5-dms/stability.jpg)
+![stability](/assets/research/h5-dms/stability.jpg)
 
 Finally, we measured how all the mutations affect neutralization by mouse and ferret sera.
 The key sites of neutralization escape are on the top of the HA head mostly in classically defined antigenic regions, although sites of escape differ a bit between mouse and ferret sera:
 
-![escape](../assets/research/h5-dms/escape.jpg)
+![escape](/assets/research/h5-dms/escape.jpg)
 
 To aid in using these data in surveillance, our collaborators (Jordan Ort and Louise Moncla) have integrated them into nextstrain (see [here](https://nextstrain.org/groups/moncla-lab/h5nx/h5-dms/clade-2344b) to color a phylogenetic tree by the measured phenotypes).
 
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