added cheminformatics blog post

8 files changed, 346 insertions, 2 deletions

diff --git a/Content/posts/2021-06-26-Cheminformatics-On-The-Web-2021.md b/Content/posts/2021-06-26-Cheminformatics-On-The-Web-2021.md
new file mode 100644
index 0000000..49a5e04
--- /dev/null
+++ b/Content/posts/2021-06-26-Cheminformatics-On-The-Web-2021.md
@@ -0,0 +1,86 @@
+---
+date: 2021-06-26 13:04
+description: Summarising Cheminformatics on the web in 2021.
+tags: Cheminformatics, JavaScript
+---
+
+# Cheminformatics on the Web (2021)
+
+Here, I have compiled a list of some libraries and possible ideas.
+I, personally, like static websites which don't require a server side application and can be hosted on platforms like GitHub Pages.
+Or, just by opening the HTML file and running it in your browser. 
+WebAssembly (Wasm) has made running code written for other platforms on the web relatively easier.
+Combine Wasm with some pure JavaScript libraries, and you get a platform to quickly amp up your speed in some common tasks.
+
+## RDKit
+
+RDKit bundles a minimal JavaScript Wrapper in their core RDKit suite. 
+This is perfect for generating 2D Figures (HTML5 Canva/SVGs), Canonical SMILES, Descriptors e.t.c
+
+### Substructure Matching
+
+This can be used to flag undesirable functional groups in a given compound.
+Create a simple key:value pairs of name:SMARTS and use it to highlight substructure matches. 
+Thus, something like PostEra's Medicinal Chemistry Alert can be done with RDKit-JS alone.
+
+![PostEra Demo](/assets/posts/cheminformatics-web/postera-demo.png)
+
+### Computing Properties
+
+This is useful to calculate basic properties of a given compound.
+
+![RDKit-JS Demo](/assets/posts/cheminformatics-web/rdkit-demo.png)
+
+## Webina - Molecular Docking
+
+Webina is a JavaScript/Wasm library that runs AutoDock Vina, which can enable you to run Molecular Docking straight in the browser itself.
+
+![Webina Demo](/assets/posts/cheminformatics-web/webina-demo.png)
+
+Obviously, it takes a few hits in the time to complete the docking because the code is transpiled from C++ to Wasm.
+But, the only major drawback (for now) is that it uses SharedArrayBuffer.
+Due to Spectre, this feature was disabled on all browsers.
+Currently, only Chromium-based and Firefox browsers have reimplemented and enabled it. 
+Hopefully, soon, this will be again supported by all major browsers.
+
+## Machine Learning
+
+Frameworks have now evolved enough to allow exporting models to be able to run them through JavaScript/Wasm backend.
+An example task can be **NER** or Named-entity Recognition.
+It can be used to extract compounds or diseases from a large blob of text and then matched with external references.
+Another example is target-prediction right in the browser: [CHEMBL - Target Prediction in Browser](http://chembl.blogspot.com/2021/03/target-predictions-in-browser-with.html)
+
+CHEMBL Group is first training the model using PyTorch (A Python ML Library), then converting it to the ONNX runtime.
+A model like this can be directly implemented in TensorFlow, and then exported to be able to run with TensorFlow.js
+
+## Cheminfo-to-web
+
+The project aims to port cheminformatics libraries into JavaScript via Emscripten.
+They have ported InChI, Indigo, OpenBabel, and OpenMD
+
+### Kekule.js
+
+It is written by @partridgejiang, who is behind the Cheminfo-to-web project
+
+> It is molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.
+
+## Browser Extensions
+
+The previous machine learning examples can be packaged as browser-extensions to perform tasks on the article you are reading. 
+With iOS 15 bringing WebExtensions to iOS/iPadOS, the same browser extension source code can be now used on Desktop and Mobile Phones.
+You can quickly create an extension to convert PDB codes into links to RCSB, highlight SMILES, highlight output of NER models, e.t.c
+
+
+## Conclusion
+
+I have not even touched all the bases of cheminformatics for the web here.
+There is still a lot more to unpack.
+Hopefully, this encourages you to explore the world of cheminformatics on the web.
+
+## Further Reading
+
+[Blueobelisk Userscripts](https://blueobelisk.github.io/greasemonkey.html)
+
+[JavaScript for Cheminformatics](https://depth-first.com/articles/2019/05/01/javascript-for-cheminformatics-part-2/)
+
+[Getting Started with RDKit-JS](https://unpkg.com/@rdkit/rdkit@2021.3.3/Code/MinimalLib/dist/GettingStartedInJS.html)
diff --git a/docs/assets/posts/cheminformatics-web/postera-demo.png b/docs/assets/posts/cheminformatics-web/postera-demo.png
new file mode 100644
index 0000000..bc0268f
--- /dev/null
+++ b/docs/assets/posts/cheminformatics-web/postera-demo.png
diff --git a/docs/assets/posts/cheminformatics-web/rdkit-demo.png b/docs/assets/posts/cheminformatics-web/rdkit-demo.png
new file mode 100644
index 0000000..a23881c
--- /dev/null
+++ b/docs/assets/posts/cheminformatics-web/rdkit-demo.png
diff --git a/docs/assets/posts/cheminformatics-web/webina-demo.png b/docs/assets/posts/cheminformatics-web/webina-demo.png
new file mode 100644
index 0000000..4bfea04
--- /dev/null
+++ b/docs/assets/posts/cheminformatics-web/webina-demo.png
diff --git a/docs/feed.rss b/docs/feed.rss
index e959592..06f953c 100644
--- a/docs/feed.rss
+++ b/docs/feed.rss
@@ -4,8 +4,8 @@
 		<title>Navan's Archive</title>
 		<description>Rare Tips, Tricks and Posts</description>
 		<link>https://web.navan.dev/</link><language>en</language>
-		<lastBuildDate>Fri, 25 Jun 2021 17:37:47 -0000</lastBuildDate>
-		<pubDate>Fri, 25 Jun 2021 17:37:47 -0000</pubDate>
+		<lastBuildDate>Sat, 26 Jun 2021 18:27:33 -0000</lastBuildDate>
+		<pubDate>Sat, 26 Jun 2021 18:27:33 -0000</pubDate>
 		<ttl>250</ttl>
 		<atom:link href="https://web.navan.dev/feed.rss" rel="self" type="application/rss+xml"/>
 		
@@ -3330,6 +3330,105 @@ new Dics({
 		
 		<item>
 			<guid isPermaLink="true">
+				https://web.navan.dev/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html
+			</guid>
+			<title>
+				Cheminformatics on the Web (2021)
+			</title>
+			<description>
+				Summarising Cheminformatics on the web in 2021.
+			</description>
+			<link>https://web.navan.dev/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html</link>
+			<pubDate>Sat, 26 Jun 2021 13:04:00 -0000</pubDate>
+			<content:encoded><![CDATA[<h1>Cheminformatics on the Web (2021)</h1>
+
+<p>Here, I have compiled a list of some tools and possible solutions.
+The web is a nice platform, it is available anywhere and just requires an internet connection.
+I, personally like static websites which don't require a server side application and can be hosted on platforms like GitHub Pages.
+Or, just open the HTML file and run it in your browser. 
+No data is required to be sent to any server and your device's computational power is used.
+Even our phones have a lot of computational power now, which allows the user to run tasks on the go without needing to worry about managing dependencies.
+WebAssembly (Wasm) has made running code written for other platfroms on the web relativevly easier.
+Combine Wasm with some pure JavaScript libraries, and you get a platform to quickly amp up your speed in some common tasks.</p>
+
+<h2>RDKit</h2>
+
+<p>RDKit bundles a minimal JavaScript Wrapper in their core RDKit suite. 
+This is perfect for generating 2D Figures (HTML5 Canva/SVGs), Cannonical SMILES, Descriptors e.t.c</p>
+
+<h3>Substructure Matching</h3>
+
+<p>This can be used to flag undesirable functional groups in a given compound.
+Create a simple key:value pair of name:SMARTS and use it to highlight substructure matches. 
+Thus, something like PostEra's Medicinal Chemistry Alert can be done with RDKit-JS alone.</p>
+
+<p><img src="/assets/posts/cheminformatics-web/postera-demo.png" alt="PostEra Demo" /></p>
+
+<h3>Computing Properties</h3>
+
+<p>This is useful to calculate basic properties of a given compound.</p>
+
+<p><img src="/assets/posts/cheminformatics-web/rdkit-demo.png" alt="RDKit-JS Demo" /></p>
+
+<h2>Webina - Molecular Docking</h2>
+
+<p>Webina is a JavaScript/Wasm library that runs AutoDock Vina, which can enable you to run Molecular Docking straight in the browser itself.</p>
+
+<p><img src="/assets/posts/cheminformatics-web/webina-demo.png" alt="Webina Demo" /></p>
+
+<p>Obviously, it takes a few hits in the time to complete the docking because the code is transpiled from C++ to Wasm.
+But, the only major drawback (for now) is that it uses SharedArrayBuffer.
+Due to Spectre, this feature was disabled on all browsers.
+Currently, only Chromium-based and Firefox browsers have reimplemented and renabled it. 
+Hopefully, soon this will be again supported by all major browsers.</p>
+
+<h2>Machine Learning</h2>
+
+<p>Frameworks have now evolved enough to allow exporting models to be able to run them through JavaScript/Wasm backend.
+An example task can be <strong>NER</strong> or Named-entity Recognition.
+It can be used to extract compounds or diseases from a large blob of text and then matched with external refferences.
+Another example is target-prediction right in the browser: <a rel="noopener" target="_blank" href="http://chembl.blogspot.com/2021/03/target-predictions-in-browser-with.html">CHEMBL - Target Prediction in Browser</a></p>
+
+<p>CHEMBL Group is first training the model using PyTorch (A Python ML Library), then converting it to the ONNX runtime.
+A model like this can be directly implemented in Tensorflow, and then exported to be able to run with TensorFlow.js</p>
+
+<h2>Cheminfo-to-web</h2>
+
+<p>The project aims to port chemoinformatics libraries into JavaScript via Emscripten.
+They have ported InChI, Indigo, OpenBabel, and OpenMD</p>
+
+<h3>Kekule.js</h3>
+
+<p>It is written by @partridgejiang, who is behind the Cheminfo-to-web project</p>
+
+<blockquote>
+  <p>It is molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.</p>
+</blockquote>
+
+<h2>Browser Extensions</h2>
+
+<p>The previous machine learning examples can be packaged as browser-extensions to perform tasks on the article you are reading. 
+With iOS 15 bringing WebExtensions to iOS/iPadOS, the same browser extension source code can be now used on Desktop and Mobile Phones.
+You can quickly create an extenison to convert PDB codes into links to RCSB, highlight SMILES, highlight output of NER models, e.t.c</p>
+
+<h2>Conclusion</h2>
+
+<p>I have not even touched all the bases of cheminformatics for the web here.
+There is still a lot more to unpack.
+Hopefully, this encourages you to explore the world of cheminformatics on the web.</p>
+
+<h2>Further Reading</h2>
+
+<p><a rel="noopener" target="_blank" href="https://blueobelisk.github.io/greasemonkey.html">Blueobelisk Userscripts</a></p>
+
+<p><a rel="noopener" target="_blank" href="https://depth-first.com/articles/2019/05/01/javascript-for-cheminformatics-part-2/">JavaScript for Cheminformatics</a></p>
+
+<p><a rel="noopener" target="_blank" href="https://unpkg.com/@rdkit/rdkit@2021.3.3/Code/MinimalLib/dist/GettingStartedInJS.html">Getting Started with RDKit-JS</a></p>
+]]></content:encoded>
+		</item>
+		
+		<item>
+			<guid isPermaLink="true">
 				https://web.navan.dev/posts/2020-06-01-Speeding-Up-Molecular-Docking-Workflow-AutoDock-Vina-and-PyMOL.html
 			</guid>
 			<title>
diff --git a/docs/index.html b/docs/index.html
index 50ce9c9..c220d2f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -45,6 +45,19 @@
 
 <ul>
 
+	<li><a href="/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html">Cheminformatics on the Web (2021)</a></li>
+	<ul>
+		<li>Summarising Cheminformatics on the web in 2021.</li>
+		<li>Published On: 2021-06-26 13:04</li>
+		<li>Tags: 
+			
+			Cheminformatics,
+			
+			JavaScript,
+			
+	</ul>
+
+
 	<li><a href="/posts/2021-06-25-NFC-Music-Cards-Basic-iOS.html">Basic NFC Music Cards for iOS</a></li>
 	<ul>
 		<li>Basic NFC Music Cards on iOS with Shortcuts</li>
diff --git a/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html
new file mode 100644
index 0000000..885c7b5
--- /dev/null
+++ b/docs/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html
@@ -0,0 +1,133 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    
+    <link rel="stylesheet" href="/assets/main.css" />
+    <link rel="stylesheet" href="/assets/sakura.css" />
+    <meta charset="utf-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Hey - Post</title>
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+    <meta name="og:title" content="Hey" />
+    <meta name="description" content="Welcome to my personal fragment of the internet." />
+    <meta name="twitter:description" content="Welcome to my personal fragment of the internet. Majority of the posts should be complete." />
+    <meta name="og:description" content="Welcome to my personal fragment of the internet." />
+    <meta name="twitter:card" content="summary" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
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+    
+</head>
+<body>
+    <nav style="display: block;">
+|
+<a href="/">home</a> |
+<a href="/about/">about/links</a> |
+<a href="/posts/">posts</a> |
+<a href="/publications/">publications</a> |
+<a href="/repo/">iOS repo</a> |
+<a href="/feed.rss">RSS Feed</a> |
+</nav>
+    
+<main>
+	<h1>Cheminformatics on the Web (2021)</h1>
+
+<p>Here, I have compiled a list of some tools and possible solutions.
+The web is a nice platform, it is available anywhere and just requires an internet connection.
+I, personally like static websites which don't require a server side application and can be hosted on platforms like GitHub Pages.
+Or, just open the HTML file and run it in your browser. 
+No data is required to be sent to any server and your device's computational power is used.
+Even our phones have a lot of computational power now, which allows the user to run tasks on the go without needing to worry about managing dependencies.
+WebAssembly (Wasm) has made running code written for other platfroms on the web relativevly easier.
+Combine Wasm with some pure JavaScript libraries, and you get a platform to quickly amp up your speed in some common tasks.</p>
+
+<h2>RDKit</h2>
+
+<p>RDKit bundles a minimal JavaScript Wrapper in their core RDKit suite. 
+This is perfect for generating 2D Figures (HTML5 Canva/SVGs), Cannonical SMILES, Descriptors e.t.c</p>
+
+<h3>Substructure Matching</h3>
+
+<p>This can be used to flag undesirable functional groups in a given compound.
+Create a simple key:value pair of name:SMARTS and use it to highlight substructure matches. 
+Thus, something like PostEra's Medicinal Chemistry Alert can be done with RDKit-JS alone.</p>
+
+<p><img src="/assets/posts/cheminformatics-web/postera-demo.png" alt="PostEra Demo" /></p>
+
+<h3>Computing Properties</h3>
+
+<p>This is useful to calculate basic properties of a given compound.</p>
+
+<p><img src="/assets/posts/cheminformatics-web/rdkit-demo.png" alt="RDKit-JS Demo" /></p>
+
+<h2>Webina - Molecular Docking</h2>
+
+<p>Webina is a JavaScript/Wasm library that runs AutoDock Vina, which can enable you to run Molecular Docking straight in the browser itself.</p>
+
+<p><img src="/assets/posts/cheminformatics-web/webina-demo.png" alt="Webina Demo" /></p>
+
+<p>Obviously, it takes a few hits in the time to complete the docking because the code is transpiled from C++ to Wasm.
+But, the only major drawback (for now) is that it uses SharedArrayBuffer.
+Due to Spectre, this feature was disabled on all browsers.
+Currently, only Chromium-based and Firefox browsers have reimplemented and renabled it. 
+Hopefully, soon this will be again supported by all major browsers.</p>
+
+<h2>Machine Learning</h2>
+
+<p>Frameworks have now evolved enough to allow exporting models to be able to run them through JavaScript/Wasm backend.
+An example task can be <strong>NER</strong> or Named-entity Recognition.
+It can be used to extract compounds or diseases from a large blob of text and then matched with external refferences.
+Another example is target-prediction right in the browser: <a rel="noopener" target="_blank" href="http://chembl.blogspot.com/2021/03/target-predictions-in-browser-with.html">CHEMBL - Target Prediction in Browser</a></p>
+
+<p>CHEMBL Group is first training the model using PyTorch (A Python ML Library), then converting it to the ONNX runtime.
+A model like this can be directly implemented in Tensorflow, and then exported to be able to run with TensorFlow.js</p>
+
+<h2>Cheminfo-to-web</h2>
+
+<p>The project aims to port chemoinformatics libraries into JavaScript via Emscripten.
+They have ported InChI, Indigo, OpenBabel, and OpenMD</p>
+
+<h3>Kekule.js</h3>
+
+<p>It is written by @partridgejiang, who is behind the Cheminfo-to-web project</p>
+
+<blockquote>
+  <p>It is molecule-centric, focusing on providing the ability to represent, draw, edit, compare and search molecule structures on web browsers.</p>
+</blockquote>
+
+<h2>Browser Extensions</h2>
+
+<p>The previous machine learning examples can be packaged as browser-extensions to perform tasks on the article you are reading. 
+With iOS 15 bringing WebExtensions to iOS/iPadOS, the same browser extension source code can be now used on Desktop and Mobile Phones.
+You can quickly create an extenison to convert PDB codes into links to RCSB, highlight SMILES, highlight output of NER models, e.t.c</p>
+
+<h2>Conclusion</h2>
+
+<p>I have not even touched all the bases of cheminformatics for the web here.
+There is still a lot more to unpack.
+Hopefully, this encourages you to explore the world of cheminformatics on the web.</p>
+
+<h2>Further Reading</h2>
+
+<p><a rel="noopener" target="_blank" href="https://blueobelisk.github.io/greasemonkey.html">Blueobelisk Userscripts</a></p>
+
+<p><a rel="noopener" target="_blank" href="https://depth-first.com/articles/2019/05/01/javascript-for-cheminformatics-part-2/">JavaScript for Cheminformatics</a></p>
+
+<p><a rel="noopener" target="_blank" href="https://unpkg.com/@rdkit/rdkit@2021.3.3/Code/MinimalLib/dist/GettingStartedInJS.html">Getting Started with RDKit-JS</a></p>
+
+</main>
+
+
+<script src="assets/manup.min.js"></script>
+<script src="/pwabuilder-sw-register.js"></script>    
+</body>
+</html>
\ No newline at end of file
diff --git a/docs/posts/index.html b/docs/posts/index.html
index 9288bb3..119b7e6 100644
--- a/docs/posts/index.html
+++ b/docs/posts/index.html
@@ -48,6 +48,19 @@
 
 <ul>
 
+	<li><a href="/posts/2021-06-26-Cheminformatics-On-The-Web-2021.html">Cheminformatics on the Web (2021)</a></li>
+	<ul>
+		<li>Summarising Cheminformatics on the web in 2021.</li>
+		<li>Published On: 2021-06-26 13:04</li>
+		<li>Tags: 
+			
+			Cheminformatics,
+			
+			JavaScript,
+			
+	</ul>
+
+
 	<li><a href="/posts/2021-06-25-NFC-Music-Cards-Basic-iOS.html">Basic NFC Music Cards for iOS</a></li>
 	<ul>
 		<li>Basic NFC Music Cards on iOS with Shortcuts</li>