From 97b4808d2866841a3ff93e9c5ed7c6b7c5f4006f Mon Sep 17 00:00:00 2001
From: Mitja Felicijan <mitja.felicijan@gmail.com>
Date: Sun, 29 Oct 2023 16:18:09 +0100
Subject: Added vault

---
 public/encoding-binary-data-into-dna-sequence.html | 25 ++++++++++------------
 1 file changed, 11 insertions(+), 14 deletions(-)

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@@ -1,5 +1,5 @@
 <!doctype html><html lang=en-us><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><link href="data:image/x-icon;base64,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" rel=icon type=image/x-icon><title>Encoding binary data into DNA sequence</title><meta name=description content="Initial thoughtsImagine a world where you could go outside and take a leaf from a tree and putit through your personal DNA sequencer and get data like music, videos orcomputer programs from it."><link rel=alternate type=application/rss+xml title="Mitja Felicijan's posts" href=https://mitjafelicijan.com/index.xml><link rel=alternate type=application/rss+xml title="Mitja Felicijan's notes" href=https://mitjafelicijan.com/notes.xml><style>body{padding:1rem;max-width:760px;background:#fff;font-family:sans-serif;line-height:1.35rem;font-size:16px;margin:0 auto}hr{margin-block-start:1.5rem}h1,h2,h3{line-height:initial}h1{font-size:xx-large}footer{margin-block-start:2rem}cap{text-transform:capitalize}table{max-width:100%;width:100%;border-collapse:separate;border-spacing:2px;border:1px solid #000;border-left:1px solid #999;border-top:1px solid #999}blockquote{font-style:italic}table thead{background:#eee}ul.list li{padding:.2em 0}ul{line-height:1.4em}td,th{border:1px solid #000;padding:4px;border-right:1px solid #999;border-bottom:1px solid #999;text-align:left}pre{text-wrap:nowrap;overflow-x:auto;padding:0 1em;border:1px solid #dcdcdc}code{padding:0 3px;font-size:14px;border:0}pre code{line-height:1.3em}pre,code,pre *,code *{font-family:monospace}figure{margin-inline-start:0;margin-inline-end:0}figcaption{text-align:center}figcaption p{margin:.3em 0 0}img,video,audio{max-width:100%}header{display:flex;flex-direction:row;gap:3rem}nav{display:flex;gap:.75rem}nav.main{flex-grow:1}.pstatus-orange{background:gold}.pstatus-green{background:#9acd32}.pstatus-red{background:#cd5c5c}@media only screen and (max-width:600px){body{padding:15px}header{flex-direction:column;gap:1rem}a{word-wrap:break-word}}</style><header><nav class=main itemscope itemtype=http://schema.org/SiteNavigationElement role=toolbar><a href=/>Home</a>
-<a href=https://files.mitjafelicijan.com/ target=_blank>Files</a>
+<a href=/vault.html>Vault</a>
 <a href=/mitjafelicijan.pgp.pub.txt target=_blank>PGP</a>
 <a href=/curriculum-vitae.html>CV</a>
 <a href=/index.xml target=_blank>RSS</a></nav></header><main role=main><article itemtype=http://schema.org/Article><h1 itemtype=headline>Encoding binary data into DNA sequence</h1><p><cap>post</cap>, Jan 3, 2019 on <a href=https://mitjafelicijan.com>Mitja Felicijan's blog</a><div><h2 id=initial-thoughts>Initial thoughts</h2><p>Imagine a world where you could go outside and take a leaf from a tree and put
@@ -177,21 +177,18 @@ like</a>.<pre tabindex=0 style=background-color:#fff><code><span style=display:f
 data as intended).<figure><img src=/posts/dna-sequence/sample-binary-file.png alt="Sample binary file 1KB"></figure><p>We create following binary files:<ul><li>1KB.bin<li>10KB.bin<li>100KB.bin<li>1MB.bin<li>10MB.bin<li>100MB.bin</ul><p>After this we create FASTA files for all the binary files by encoding them
 into DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i 100MB.bin -o 100MB.fa
 </span></span></code></pre><p>Then we GZIP all the FASTA files to see how much the can be compressed.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>gzip -9 &lt; 10MB.fa &gt; 10MB.fa.gz
-</span></span></code></pre><figure><img src=/posts/dna-sequence/chart-speed.svg alt="Encode to FASTA"><figcaption><p>The speed increase that occurs when encoding to FASTA format.</figcaption></figure><figure><img src=/posts/dna-sequence/chart-size.svg alt="File sizes"><figcaption><p>Size of the out file after encoding.</figcaption></figure><p><a href=/posts/dna-sequence/benchmarks.csv>Download CSV file with benchmarks</a>.<h2 id=references>References</h2><ul><li><a href=https://www.techopedia.com/definition/948/encoding>https://www.techopedia.com/definition/948/encoding</a><li><a href=https://www.dna-worldwide.com/resource/160/history-dna-timeline>https://www.dna-worldwide.com/resource/160/history-dna-timeline</a><li><a href=https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/>https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/</a><li><a href=https://arxiv.org/abs/1801.04774>https://arxiv.org/abs/1801.04774</a><li><a href=https://en.wikipedia.org/wiki/FASTA_format>https://en.wikipedia.org/wiki/FASTA_format</a></ul></div></article></main><section><hr><h2>Posts from blogs I follow around the net</h2><ul><li><a href=https://chotrin.org/writing/2023-10-20.html target=_blank rel=noopener>OpenBSD upgrade and fall things.</a><div>Been AFK for a bit. It's autumn and I upgraded this server to OpenBSD 7.4! — <a href=https://chotrin.org>chötrin's wiki.</a><li><a href=https://mirzapandzo.com/next-image-url-parameter-is-valid-but-upstream-response-is-invalid target=_blank rel=noopener>Next/Image "url" parameter is valid but upstream response is invalid</a><div>Getting "url" parameter is valid but upstream response is invalid error with Next/Image on WSL2 — <a href=https://mirzapandzo.com/>Mirza Pandzo's Blog</a><li><a href=https://drewdevault.com/2023/10/13/Going-off-script.html target=_blank rel=noopener>Going off-script</a><div>There is a phenomenon in society which I find quite bizarre. Upon our entry to
+</span></span></code></pre><figure><img src=/posts/dna-sequence/chart-speed.svg alt="Encode to FASTA"><figcaption><p>The speed increase that occurs when encoding to FASTA format.</figcaption></figure><figure><img src=/posts/dna-sequence/chart-size.svg alt="File sizes"><figcaption><p>Size of the out file after encoding.</figcaption></figure><p><a href=/posts/dna-sequence/benchmarks.csv>Download CSV file with benchmarks</a>.<h2 id=references>References</h2><ul><li><a href=https://www.techopedia.com/definition/948/encoding>https://www.techopedia.com/definition/948/encoding</a><li><a href=https://www.dna-worldwide.com/resource/160/history-dna-timeline>https://www.dna-worldwide.com/resource/160/history-dna-timeline</a><li><a href=https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/>https://opentextbc.ca/biology/chapter/9-1-the-structure-of-dna/</a><li><a href=https://arxiv.org/abs/1801.04774>https://arxiv.org/abs/1801.04774</a><li><a href=https://en.wikipedia.org/wiki/FASTA_format>https://en.wikipedia.org/wiki/FASTA_format</a></ul></div></article></main><section><hr><h2>Posts from blogs I follow around the net</h2><ul><li><a href=https://chotrin.org/writing/2023-10-29.html target=_blank rel=noopener>even more bike things.</a><div>I wrote about all sorts of biking and not-biking things in my life this week. — <a href=https://chotrin.org>chötrin's wiki.</a><li><a href="http://offbeatpursuit.com:80/blog/?id=25" target=_blank rel=noopener>A fix by any other name</a><div>tags:
+i2c, plan9
+Another month, another file system.
+Well, if you can’t fix it in software, fix it in hardware (looking at
+you, bme680, we’re not
+done yet). The show mu… — <a href=http://offbeatpursuit.com:80/blog/>WLOG - blog</a><li><a href=https://mirzapandzo.com/next-image-url-parameter-is-valid-but-upstream-response-is-invalid target=_blank rel=noopener>Next/Image "url" parameter is valid but upstream response is invalid</a><div>Getting "url" parameter is valid but upstream response is invalid error with Next/Image on WSL2 — <a href=https://mirzapandzo.com/>Mirza Pandzo's Blog</a><li><a href=https://drewdevault.com/2023/10/13/Going-off-script.html target=_blank rel=noopener>Going off-script</a><div>There is a phenomenon in society which I find quite bizarre. Upon our entry to
 this mortal coil, we are endowed with self-awareness, agency, and free will.
-Each of th… — <a href=https://drewdevault.com>Drew DeVault's blog</a><li><a href=https://solar.lowtechmagazine.com/2023/10/workshop-in-rotterdam-how-to-build-a-bike-generator/ target=_blank rel=noopener>Workshop in Rotterdam: How to Build a Bike Generator</a><div>Afbeelding: Low-tech Magazine workshop in Rotterdam, the Netherlands. Poster: Marie Verdeil. Image: Sara Vercauteren
-The workshop takes place on behalf of the “Hou… — <a href=https://solar.lowtechmagazine.com/posts/>LOW←TECH MAGAZINE English</a><li><a href="http://offbeatpursuit.com:80/blog/?id=24" target=_blank rel=noopener>Printf debugging</a><div>tags:
-plan9
-There’s no shame in that. Yes, there is documentation, code to be
-read, and debuggers to be used. But sometimes you just need to “see”
-what is happening.
-So… — <a href=http://offbeatpursuit.com:80/blog/>WLOG - blog</a><li><a href=https://neil.computer/notes/chart-of-accounts-for-startups-and-saas-companies/ target=_blank rel=noopener>Chart of Accounts for Startups and SaaS Companies</a><div>Accounting is fundamental to starting a business. You need to have a basic understanding of accounting principles and essential bookkeeping. I had to learn it. Ther… — <a href=https://neil.computer/>Neil Panchal</a><li><a href=https://journal.valeriansaliou.name/deploy-a-nomad-cluster-on-alpine-linux-with-vultr/ target=_blank rel=noopener>Deploy a Nomad Cluster on Alpine Linux with Vultr</a><div>After spending countless hours trying to understand how to deploy my apps on Kubernetes for the first time to host Mirage, an AI API service that I run, I ended up … — <a href=https://journal.valeriansaliou.name/>Valerian Saliou</a><li><a href=https://jcs.org/2023/10/17/wikipedia target=_blank rel=noopener>Wikipedia Reader 1.0 Released</a><div>Wikipedia Reader
+Each of th… — <a href=https://drewdevault.com>Drew DeVault's blog</a><li><a href=https://solar.lowtechmagazine.com/2023/10/thematic-book-series-how-to-downsize-a-transport-network/ target=_blank rel=noopener>Thematic Book Series: How to Downsize a Transport Network?</a><div>Image: Book cover. [How to downsize a transport network?](https://www.lulu.com/shop/kris-de-decker/how-to-downsize-a-transport-network/paperback/product-42n4p7.htm… — <a href=https://solar.lowtechmagazine.com/posts/>LOW←TECH MAGAZINE English</a><li><a href=https://neil.computer/notes/chart-of-accounts-for-startups-and-saas-companies/ target=_blank rel=noopener>Chart of Accounts for Startups and SaaS Companies</a><div>Accounting is fundamental to starting a business. You need to have a basic understanding of accounting principles and essential bookkeeping. I had to learn it. Ther… — <a href=https://neil.computer/>Neil Panchal</a><li><a href=https://journal.valeriansaliou.name/deploy-a-nomad-cluster-on-alpine-linux-with-vultr/ target=_blank rel=noopener>Deploy a Nomad Cluster on Alpine Linux with Vultr</a><div>After spending countless hours trying to understand how to deploy my apps on Kubernetes for the first time to host Mirage, an AI API service that I run, I ended up … — <a href=https://journal.valeriansaliou.name/>Valerian Saliou</a><li><a href=https://jcs.org/2023/10/25/wifi_da target=_blank rel=noopener>BlueSCSI Wi-Fi Desk Accessory 1.0 Released</a><div>BlueSCSI Wi-Fi Desk Accessory
 1.0 has been released:
-wikipedia-1.0.sit
-(StuffIt 3 archive, includes
-source code
-and THINK C 5 project file)
-SHA256: 360e12d064f6579695f1e627ce34cb2f0… — <a href=https://jcs.org/>joshua stein</a></ul><p><a href=https://git.sr.ht/~sircmpwn/openring>Generated with openring.</a></section><footer><hr><p><big><strong>Want to comment or have something to add?</strong></big><p>You can write me an email
+wifi_da-1.0.sit
+(StuffIt 3 archive)
+SHA256: ccfc9d27dd5da7412d10cef73b81119a1fec3848e4d1d88ff652a07ffdc6a69aSHA1:… — <a href=https://jcs.org/>joshua stein</a></ul><p><a href=https://git.sr.ht/~sircmpwn/openring>Generated with openring.</a></section><footer><hr><p><big><strong>Want to comment or have something to add?</strong></big><p>You can write me an email
 at <a href=mailto:mitja.felicijan@gmail.com>mitja.felicijan@gmail.com</a> or
 catch up with me <a href=https://telegram.me/mitjafelicijan target=_blank>on Telegram</a>.<hr><p>This website does not track you. Content is made available under
 the <a href=https://creativecommons.org/licenses/by/4.0/ target=_blank rel=noreferrer>CC BY 4.0 license</a> unless specified
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