From 0830148da22c99e38371046e2e41fede564bd858 Mon Sep 17 00:00:00 2001 From: WillHannon-MCB Date: Tue, 13 Feb 2024 22:35:12 +0000 Subject: [PATCH] deploy: dac1c84c4b05bc1e8566ad7363da4d4f0bceee9d --- 404.html | 4 ++-- README.html | 6 +++--- about.html | 6 +++--- assets/{app.exlaMXtI.js => app.O7VmKeu-.js} | 2 +- assets/chunks/{theme.uEQ0umWR.js => theme.HBrFSuTc.js} | 2 +- contributing.html | 6 +++--- experiments/h5n1/index.html | 6 +++--- experiments/hiv/index.html | 6 +++--- experiments/lassa/index.html | 6 +++--- experiments/nipah/index.html | 6 +++--- experiments/sars2/index.html | 6 +++--- experiments/sars2/posts/BA.2_ACE2_binding.html | 6 +++--- .../posts/XBB.1.5_ACE2_binding_serum_escape_cell_entry.html | 6 +++--- hashmap.json | 2 +- index.html | 6 +++--- methodology.html | 6 +++--- 16 files changed, 41 insertions(+), 41 deletions(-) rename assets/{app.exlaMXtI.js => app.O7VmKeu-.js} (95%) rename assets/chunks/{theme.uEQ0umWR.js => theme.HBrFSuTc.js} (98%) diff --git a/404.html b/404.html index 473ae65..670f99c 100644 --- a/404.html +++ b/404.html @@ -8,7 +8,7 @@ - + @@ -17,7 +17,7 @@

Appearance

404

PAGE NOT FOUND

But if you don't change your direction, and if you keep looking, you may end up where you are heading.
Take me home

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

- + \ No newline at end of file diff --git a/README.html b/README.html index 6e05836..665acdc 100644 --- a/README.html +++ b/README.html @@ -8,10 +8,10 @@ - + - + @@ -21,7 +21,7 @@

Appearance

dms-vep.org ​

Developing ​

First, clone the repository locally:

bash
git clone git@github.com:dms-vep/dms-vep.github.io.git
 cd dms-vep.github.io

To see a live preview of dms-vep.github.io, you must have node and npm installed on your machine. If you are missing one or both, follow the instructions here to install them.

This website is created using the static site generator VitePress. To spin up a local development server that provides a live preview of the site locally in your browser, simply run:

bash
npm run docs:dev

The dev server should now be running at http://localhost:5173. Visit this URL in your browser to see a preview of the site.

Deploying ​

The website is hosted on GitHub pages via a specific gh-pages branch and builds are automated using GitHub Actions via the deployment script /.github/workflows/deploy.yml. The website will build on pull requests and pushes to the main branch.

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

- + \ No newline at end of file diff --git a/about.html b/about.html index 52724f7..d826889 100644 --- a/about.html +++ b/about.html @@ -8,10 +8,10 @@ - + - + @@ -20,7 +20,7 @@

Appearance

About ​

dms-vep.github.io serves as a repository for deep mutational scanning (DMS) studies with a focus on viral entry proteins (VEPs). These studies offer insights into the impacts of mutations on immune evasion, viral fitness, and more. Traditionally, sharing the substantial amount of data generated from these experiments has posed significant challenges. Conventional methods of publication restrict the level of detail in which results can be conveyed, making it impossible to share the full breadth of our findings. dms-vep.github.io addresses this issue by offering a detailed overview of findings from DMS experiments. This includes expert interpretation and direct access to the underlying raw data, facilitating a deeper understanding and broader application of these studies.

On dms-vep.github.io you'll find detailed write-ups for DMS of multiple viral proteins that focus on the methodology, objectives, and findings of these experiments. These write-ups include both interactive and static data visualizations that help explore these large datasets. Finally, you'll find links to the raw and processed data used in each study along with a detailed description of the data's structure and purpose.

If you have questions about the experiments described on this website, feel free to ask them on our GitHub Discussions page.

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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return});return(i,r)=>e.pins?(F(),N("div",gxe,[D("div",mxe,[D("div",yxe,[(F(!0),N(Le,null,mt(e.pins,s=>(F(),N("div",{key:s.title,class:Ke(["item",[n.value]])},[re(pxe,{icon:s.icon,title:s.title,details:s.details,link:s.link,"link-text":s.linkText,rel:s.rel,target:s.target},null,8,["icon","title","details","link","link-text","rel","target"])],2))),128))])])])):Z("",!0)}},bxe=oe(vxe,[["__scopeId","data-v-0342b00a"]]),xxe=D("h2",{class:"section-header"},"Key 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Which will result in a view of the URL provided to the src property of the iframe. The result looks like this:

You can simply copy this code and replace the URL with the URL to your website of choice.

Style Guide ​

In progress...

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

- + \ No newline at end of file diff --git a/experiments/h5n1/index.html b/experiments/h5n1/index.html index c08e08b..ff7c786 100644 --- a/experiments/h5n1/index.html +++ b/experiments/h5n1/index.html @@ -8,10 +8,10 @@ - + - + @@ -20,7 +20,7 @@

Appearance

Influenza H5N1 ​

In Progress...

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

- + \ No newline at end of file diff --git a/experiments/hiv/index.html b/experiments/hiv/index.html index b7b51a3..7047048 100644 --- a/experiments/hiv/index.html +++ b/experiments/hiv/index.html @@ -8,10 +8,10 @@ - + - + @@ -20,7 +20,7 @@

Appearance

HIV ​

In Progress...

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

- + \ No newline at end of file diff --git a/experiments/lassa/index.html b/experiments/lassa/index.html index 2662056..b9578d8 100644 --- a/experiments/lassa/index.html +++ b/experiments/lassa/index.html @@ -8,10 +8,10 @@ - + - + @@ -20,7 +20,7 @@

Appearance

Lassa ​

In Progress...

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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Nipah ​

In Progress...

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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SARS-CoV-2

Deep mutational scanning of the SARS-CoV-2 spike.

SARS-CoV-2 lentiviral deep mutational scanning datasets ​

The pinned posts above include the most up to date data on the effects of mutations on various SARS-CoV-2 spike phenotypes. For datasets related to other studies using lentiviral deep mutational scanning system for spike see experiments section below.

Explore all SARS-CoV-2 experiments

See below to explore all experiments for SARS-CoV-2. You can use the select box to filter the experiments by keyword.

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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Effects of mutations in BA.2 spike on ACE2 binding ​

Study by Bernadeta Dadonaite, Jesse Bloom, et al. The pre-print for this study is here.

Effects of mutations to BA.2 spike on ACE2 binding ​

Plot below shows how mutations to BA.2 spike affect monomeric ACE2 binding.

This is is an interactive chart. Mouseover points for details and use the top zoom bar to zoom in on specific sites.

Analysis by Dadonaite et al., bioRxiv, DOI 10.1101/2023.11.13.566961 (2023).

See https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS for code/data.

Data above was generated using lentiviral deep mutational scanning system described in Dadonaite et al., Cell, (2023).

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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Effects of mutations on ACE2 binding, serum escape and cell entry ​

Study by Bernadeta Dadonaite, Jesse Bloom, et al. The pre-print for this study is here.

Effects of mutations to XBB.1.5 spike on escape from serum antibodies, ACE2-mediated cell entry, and ACE2 binding ​

Plot below shows how mutations to XBB.1.5 spike affect ACE2 binding, XBB breakthrough sera escape, and ACE2-mediated cell entry. Serum escape data is and average escape of sera from 10 individual with who all had XBB* breakthrough infection. ACE2 binding experiments were done with monomeric ACE2. Cell entry experiments were performed using 293T cells overexpressing ACE2.

This is is an interactive chart. 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 only show escape for sites with some minimal functional effect, choose the site summary metric, or floor the escape at zero.

The line plots at top show the escape at each site across all sera and for individual sera, and the heatmaps show the effects of individual mutations on sera escape or functions of the protein.

Analysis by Dadonaite et al., bioRxiv, DOI 10.1101/2023.11.13.566961 (2023).

See https://github.com/dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS for code/data.

Data above was generated using lentiviral deep mutational scanning system described in Dadonaite et al., Cell, (2023).

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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DMS VEP

An archive of deep mutational scanning (DMS) experiments of viral entry proteins (VEPs)

SARS-CoV-2

Spike

HIV

Env

H5N1

HA

Lassa

GPC

Nipah

RBP

Contributors

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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Methodology ​

This page contains details on the methodologies used to generate the data in this website.

Released under the MIT License.

Copyright © 2024-present Jesse Bloom

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