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<a href=/index.xml target=_blank class=hob>RSS</a></nav></header><main role=main><article itemtype=http://schema.org/Article><h1 itemtype=headline>What would DNA sound if synthesized to an audio file</h1><p><cap>post</cap>, Jul 5, 2022 on <a href=https://mitjafelicijan.com>Mitja Felicijan's blog</a><div><h2 id=introduction>Introduction</h2><p>Lately, I have been thinking a lot about the nature of life, what are the
foundation blocks of life and things like that. It's remarkable how complex and
on the other hand simple the creation is when you look at it. The miracle of
life keeps us grounded when our imagination goes wild. If the DNA are the blocks
of life, you could consider them to be an API nature provided us to better
understand all of this chaos masquerading as order.<p>I have been reading a lot about superintelligence and our somehow misguided path
to create general artificial intelligence. What would the building blocks or our
creation look like? Is the compression really the ultimate storage of
information? Will our creation also ponder this questions when creating new
worlds for themselves, or will we just disappear into the vastness of
possibilities? It is a little offensive that we are playing God whilst being
completely ignorant of our own reality. Who knows! Like many other
breakthroughs, this one will also come at a cost not known to us when it finally
happens.<p>To keep things a bit lighter, I decided to convert some popular DNA sequences
into an audio files for us to listen to. I am not the first one, nor I will be
the last one to do this. But it is an interesting exercise in better
understanding the relationship between art and science. Maybe listening to DNA
instead of parsing it will find a way into better understanding, or at least
enjoying the creation and cryptic nature of life.<h2 id=dna-encoding-and-primer-example>DNA encoding and primer example</h2><p>I have been exploring DNA in the past in my post from about 3 years ago in
<a href=/encoding-binary-data-into-dna-sequence.html>Encoding binary data into DNA
sequence</a> where I have been
converting all sorts of data into DNA sequences.<p>This will be a similar exercise but instead of converting to DNA, I will be
generating tones from Nucleotides.<table><thead><tr><th>Nucleotides<th>Note<th>Frequency<tbody><tr><td><strong>A</strong> (Adenine)<td>A<td>440 Hz<tr><td><strong>C</strong> (Cytosine)<td>C<td>783.99 Hz<tr><td><strong>G</strong> (Guanine)<td>G<td>523.25 Hz<tr><td><strong>T</strong> (Thymine)<td>D<td>587.33 Hz</table><p>Since we do not have T in equal-tempered scale, I choose D to represent T note.<p>You can check <a href=https://pages.mtu.edu/~suits/notefreqs.html>Frequencies for equal-tempered scale, A4 = 440
Hz</a>. For this tuning, we also
choose <code>Speed of Sound = 345 m/s = 1130 ft/s = 770 miles/hr</code>.<p>Now that we have this out of the way, we can also brush up on the DNA sequencing
a bit. This is a famous quote I also used for the encoding tests, and it goes
like this.<blockquote><p>How wonderful that we have met with a paradox. Now we have some hope of
making progress.
― Niels Bohr</blockquote><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>>SEQ1
</span></span><span style=display:flex><span>GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA
</span></span><span style=display:flex><span>GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA
</span></span><span style=display:flex><span>ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA
</span></span><span style=display:flex><span>ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT
</span></span><span style=display:flex><span>GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT
</span></span><span style=display:flex><span>GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC
</span></span><span style=display:flex><span>AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC
</span></span><span style=display:flex><span>AACC
</span></span></code></pre><p>This is what we gonna work with to get things rolling forward, when creating
parser and waveform generator.<h2 id=parsing-dna-data>Parsing DNA data</h2><p>This step is rather simple one. All we need to do is parse input DNA sequence in
<a href=https://en.wikipedia.org/wiki/FASTA_format>FASTA format</a> well known in
<a href=https://en.wikipedia.org/wiki/Bioinformatics>Bioinformatics</a> to extract single
Nucleotides that will be converted into separate tones based on equal-tempered
scale explained above.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>nucleotide_tone_map = {
</span></span><span style=display:flex><span> <span style=color:#a31515>'A'</span>: 440,
</span></span><span style=display:flex><span> <span style=color:#a31515>'C'</span>: 523.25,
</span></span><span style=display:flex><span> <span style=color:#a31515>'G'</span>: 783.99,
</span></span><span style=display:flex><span> <span style=color:#a31515>'T'</span>: 587.33, <span style=color:green># converted to D</span>
</span></span><span style=display:flex><span>}
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>def</span> split(word):
</span></span><span style=display:flex><span> <span style=color:#00f>return</span> [char <span style=color:#00f>for</span> char <span style=color:#00f>in</span> word]
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>def</span> generate_from_dna_sequence(sequence):
</span></span><span style=display:flex><span> <span style=color:#00f>for</span> nucleotide <span style=color:#00f>in</span> split(sequence):
</span></span><span style=display:flex><span> print(nucleotide, nucleotide_tone_map[nucleotide])
</span></span></code></pre><h2 id=generating-sine-wave>Generating sine wave</h2><p>Because we are essentially creating a long stream of notes we will be appending
sine notes to a global array we will later use for creating a WAV file out of
it.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:#00f>import</span> math
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>def</span> append_sinewave(freq=440.0, duration_milliseconds=500, volume=1.0):
</span></span><span style=display:flex><span> <span style=color:#00f>global</span> audio
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span> num_samples = duration_milliseconds * (sample_rate / 1000.0)
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span> <span style=color:#00f>for</span> x <span style=color:#00f>in</span> range(int(num_samples)):
</span></span><span style=display:flex><span> audio.append(volume * math.sin(2 * math.pi * freq * (x / sample_rate)))
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span> <span style=color:#00f>return</span>
</span></span></code></pre><p>The sine wave generated here is the standard beep. If you want something more
aggressive, you could try a square or saw tooth waveform.<h2 id=generating-a-wav-file-from-accumulated-sine-waves>Generating a WAV file from accumulated sine waves</h2><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:#00f>import</span> wave
</span></span><span style=display:flex><span><span style=color:#00f>import</span> struct
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>def</span> save_wav(file_name):
</span></span><span style=display:flex><span> wav_file = wave.open(file_name, <span style=color:#a31515>'w'</span>)
</span></span><span style=display:flex><span> nchannels = 1
</span></span><span style=display:flex><span> sampwidth = 2
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span> nframes = len(audio)
</span></span><span style=display:flex><span> comptype = <span style=color:#a31515>'NONE'</span>
</span></span><span style=display:flex><span> compname = <span style=color:#a31515>'not compressed'</span>
</span></span><span style=display:flex><span> wav_file.setparams((nchannels, sampwidth, sample_rate, nframes, comptype, compname))
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span> <span style=color:#00f>for</span> sample <span style=color:#00f>in</span> audio:
</span></span><span style=display:flex><span> wav_file.writeframes(struct.pack(<span style=color:#a31515>'h'</span>, int(sample * 32767.0)))
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span> wav_file.close()
</span></span></code></pre><p>44100 is the industry standard sample rate - CD quality. If you need to save on
file size, you can adjust it downwards. The standard for low quality is, 8000 or
8kHz.<p>WAV files here are using short, 16 bit, signed integers for the sample size.
So, we multiply the floating-point data we have by 32767, the maximum value for
a short integer.<blockquote><p>It is theoretically possible to use the floating point -1.0 to 1.0 data
directly in a WAV file, but not obvious how to do that using the wave module
in Python.</blockquote><h2 id=generating-spectograms>Generating Spectograms</h2><p>I have tried two methods of doing this and both were just fine. I however opted
out to use the <a href=https://linux.die.net/man/1/sox>SoX - Sound eXchange, the Swiss Army knife of audio
manipulation</a> one because it didn't require
anything else.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>sox output.wav -n spectrogram -o spectrogram.png
</span></span></code></pre><p>An example spectrogram of Ludwig van Beethoven Symphony No. 6 First movement.</p><audio controls><source src=/posts/dna-synthesized/symphony-no6-1st-movement.mp3 type=audio/mpeg></audio><figure><img loading="lazy" src=/posts/dna-synthesized/symphony-no6-1st-movement.png alt="Ludwig van Beethoven Symphony No. 6 First movement"></figure><p>The other option could also be in combination with
<a href=http://www.gnuplot.info/>gnuplot</a>. This would require an intermediary step,
however.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>sox output.wav audio.dat
</span></span><span style=display:flex><span>tail -n+3 audio.dat > audio_only.dat
</span></span><span style=display:flex><span>gnuplot audio.gpi
</span></span></code></pre><p>And input file <code>audio.gpi</code> that would be passed to gnuplot looks something like
this.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span># set output format and size
</span></span><span style=display:flex><span>set term png size 1000,280
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span># set output file
</span></span><span style=display:flex><span>set output "audio.png"
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span># set y range
</span></span><span style=display:flex><span>set yr [-1:1]
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span># we want just the data
</span></span><span style=display:flex><span>unset key
</span></span><span style=display:flex><span>unset tics
</span></span><span style=display:flex><span>unset border
</span></span><span style=display:flex><span>set lmargin 0
</span></span><span style=display:flex><span>set rmargin 0
</span></span><span style=display:flex><span>set tmargin 0
</span></span><span style=display:flex><span>set bmargin 0
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span># draw rectangle to change background color
</span></span><span style=display:flex><span>set obj 1 rectangle behind from screen 0,0 to screen 1,1
</span></span><span style=display:flex><span>set obj 1 fillstyle solid 1.0 fillcolor rgbcolor "#ffffff"
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span># draw data with foreground color
</span></span><span style=display:flex><span>plot "audio_only.dat" with lines lt rgb 'red'
</span></span></code></pre><h2 id=pre-generated-sequences>Pre-generated sequences</h2><p>What I did was take interesting parts from an animal's genome and feed it to a
tone generator script. This then generated a WAV file and I converted those to
MP3, so they can be played in a browser. The last step was creating a
spectrogram based on a WAV file.<h3 id=niels-bohr-quote>Niels Bohr quote</h3><audio controls><source src=/posts/dna-synthesized/quote/out.mp3 type=audio/mpeg></audio><figure><img loading="lazy" src=/posts/dna-synthesized/quote/spectogram.png alt=Spectogram></figure><h3 id=mouse>Mouse</h3><p>This is part of a mouse genome <code>Mus_musculus.GRCm39.dna.nonchromosomal</code>. You
can get <a href=http://ftp.ensembl.org/pub/release-106/fasta/mus_musculus/dna/>genom data
here</a>.</p><audio controls><source src=/posts/dna-synthesized/mouse/out.mp3 type=audio/mpeg></audio><figure><img loading="lazy" src=/posts/dna-synthesized/mouse/spectogram.png alt=Spectogram></figure><h3 id=bison>Bison</h3><p>This is part of a bison genome <code>Bison_bison_bison.Bison_UMD1.0.cdna</code>. You can
get <a href=http://ftp.ensembl.org/pub/release-106/fasta/bison_bison_bison/cdna/>genom data
here</a>.</p><audio controls><source src=/posts/dna-synthesized/bison/out.mp3 type=audio/mpeg></audio><figure><img loading="lazy" src=/posts/dna-synthesized/bison/spectogram.png alt=Spectogram></figure><h3 id=taurus>Taurus</h3><p>This is part of a taurus genome <code>Bos_taurus.ARS-UCD1.2.cdna</code>. You can get
<a href=http://ftp.ensembl.org/pub/release-106/fasta/bos_taurus/cdna/>genom data
here</a>.</p><audio controls><source src=/posts/dna-synthesized/taurus/out.mp3 type=audio/mpeg></audio><figure><img loading="lazy" src=/posts/dna-synthesized/taurus/spectogram.png alt=Spectogram></figure><h2 id=making-a-drummer-out-of-a-dna-sequence>Making a drummer out of a DNA sequence</h2><p>To make things even more interesting, I decided to send this data via MIDI to my
<a href=https://www.elektron.se/en/model-samples>Elektron Model:Samples</a>. This is a
really cool piece of equipment that supports MIDI in via USB and 3.5 mm audio
jack.<p>Elektron is connected to my MacBook via USB cable and audio out is patched to a
Sony Bluetooth speaker I have that supports 3.5 mm audio in. Elektron doesn't
have internal speakers.<figure><img loading="lazy" src=/posts/dna-synthesized/elektron/IMG_0619.jpg alt></figure><figure><img loading="lazy" src=/posts/dna-synthesized/elektron/IMG_0620.jpg alt></figure><figure><img loading="lazy" src=/posts/dna-synthesized/elektron/IMG_0622.jpg alt></figure><p>For communicating with Elektron, I choose <code>pygame</code> Python module that has MIDI
built in. With this, it was rather simple to send notes to the device. All I did
was map MIDI notes to the actual Nucleotides.<p>Before all of this I also checked Audio MIDI Setup app under MacOS and checked
MIDI Studio by pressing ⌘-2.<figure><img loading="lazy" src=/posts/dna-synthesized/elektron/midi-studio.jpg alt></figure><p>The whole script that parses and send notes to the Elektron looks like this.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:#00f>import</span> pygame.midi
</span></span><span style=display:flex><span><span style=color:#00f>import</span> time
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span>pygame.midi.init()
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span>print(pygame.midi.get_default_output_id())
</span></span><span style=display:flex><span>print(pygame.midi.get_device_info(0))
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span>player = pygame.midi.Output(1)
</span></span><span style=display:flex><span>player.set_instrument(2)
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>def</span> send_note(note, velocity):
</span></span><span style=display:flex><span> <span style=color:#00f>global</span> player
</span></span><span style=display:flex><span> player.note_on(note, velocity)
</span></span><span style=display:flex><span> time.sleep(0.3)
</span></span><span style=display:flex><span> player.note_off(note, velocity)
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span>nucleotide_midi_map = {
</span></span><span style=display:flex><span> <span style=color:#a31515>'A'</span>: 60,
</span></span><span style=display:flex><span> <span style=color:#a31515>'C'</span>: 90,
</span></span><span style=display:flex><span> <span style=color:#a31515>'G'</span>: 160,
</span></span><span style=display:flex><span> <span style=color:#a31515>'T'</span>: 180, <span style=color:green># is D</span>
</span></span><span style=display:flex><span>}
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>with</span> open(<span style=color:#a31515>"quote.fa"</span>) <span style=color:#00f>as</span> f:
</span></span><span style=display:flex><span> sequence = f.read().replace(<span style=color:#a31515>'</span><span style=color:#a31515>\n</span><span style=color:#a31515>'</span>, <span style=color:#a31515>''</span>)
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>for</span> nucleotide <span style=color:#00f>in</span> [char <span style=color:#00f>for</span> char <span style=color:#00f>in</span> sequence]:
</span></span><span style=display:flex><span> print(<span style=color:#a31515>"Playing nucleotide </span><span style=color:#a31515>{}</span><span style=color:#a31515> with MIDI note </span><span style=color:#a31515>{}</span><span style=color:#a31515>"</span>.format(
</span></span><span style=display:flex><span> nucleotide, nucleotide_midi_map[nucleotide]))
</span></span><span style=display:flex><span> send_note(nucleotide_midi_map[nucleotide], 127)
</span></span><span style=display:flex><span>
</span></span><span style=display:flex><span><span style=color:#00f>del</span> player
</span></span><span style=display:flex><span>pygame.midi.quit()
</span></span></code></pre><p><video src=/posts/dna-synthesized/elektron/elektron.mp4 controls></video><p>All of this could be made much more interesting if I choose different
instruments for different Nucleotides, or doing more funky stuff with Elektron.
But for now, this should be enough. It is just a proof of concept. Something to
play around with.<h2 id=going-even-further>Going even further</h2><p>As you probably notice, the end results are quite similar to each other. This is
to be expected because we are operating only with 4 notes essentially. What
could make this more interesting is using something like
<a href=https://supercollider.github.io/>Supercollider</a> to create more interesting
sounds. By transposing notes or using effects based on repeated data in a
sequence. Possibilities are endless.<p>It is really astonishing what can be achieved with a little bit of code and an
idea. I could see this becoming an interesting background soundscape instrument
if done properly. It could replace random note generator with something more
intriguing, biological, natural.<p>I actually find the results fascinating. I took some time and listened to this
music of nature. Even though it's quite the same, it's also quite different.
The subtle differences on repeat kind of creates music on its own. Makes you
wonder. It kind of puts Occam’s Razor in its place. Nature for sure loves to
make things as energy efficient as possible.</div></article></main><section><hr><h2>Posts from blogs I follow around the net</h2><ul><li><a href=https://utcc.utoronto.ca/~cks/space/blog/linux/NFSv4ServerLockClients target=_blank rel=noopener>Finding which NFSv4 client owns a lock on a Linux NFS(v4) server</a> — <a href=https://utcc.utoronto.ca/~cks/space/blog/>Chris's Wiki :: blog</a><div>A while back I wrote an entry about finding which NFS client owns
a lock on a Linux NFS server, which turned
out to be specific to NFS v3 (which I really should have seen coming,
since it involved NLM and lockd). Finding the NFS v4 client that
owns a lock is, depending on your perspective, either simpl…<li><a href=http://www.landley.net/notes-2023.html#28-10-2023 target=_blank rel=noopener>October 28, 2023</a> — <a href=http://www.landley.net/notes-2023.html>Rob Landley's Blog Thing for 2023</a><div>Oh good grief, two of my least favorite licensing people, Larry Rosen
and Bradley Kuhn, are interacting on the OSI's license-discuss
list where the're doing
bad computer history and insisting that a guy Larry Rosen
coincidentally interviewed for a book years ago is clearly the origin of
somethin…<li><a href="http://offbeatpursuit.com:80/blog/?id=25" target=_blank rel=noopener>A fix by any other name</a> — <a href=http://offbeatpursuit.com:80/blog/>WLOG - blog</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 must go on, as they say, and I would like my
experiments to go on.
So a “new” addition to the environmental sensor family connected to
the h…<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> — <a href=https://mirzapandzo.com/>Mirza Pandzo's Blog</a><div>Getting "url" parameter is valid but upstream response is invalid error with Next/Image on WSL2<li><a href=https://drewdevault.com/2023/10/13/Going-off-script.html target=_blank rel=noopener>Going off-script</a> — <a href=https://drewdevault.com>Drew DeVault's blog</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 the 8 billion members of this human race represents a unique person, a
unique worldview, and a unique agency. Yet, many of us have the sam…<li><a href=https://szymonkaliski.com/writing/2023-10-02-building-a-diy-pen-plotter/ target=_blank rel=noopener>Building a DIY Pen Plotter</a> — <a href=http://github.com/dylang/node-rss>Szymon Kaliski</a><div>This article documents my learnings from designing and building a DIY Pen Plotter during the summer of 2023.
My ultimate goal is to build my…<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> — <a href=https://neil.computer/>Neil Panchal</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. There was no choice. For filing taxes, your CPA is going to ask you for an Income Statement (also known as P/L statement). If<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> — <a href=https://journal.valeriansaliou.name/>Valerian Saliou</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 making myself a promise that the next app I work on would be using a more productive & simpler<li><a href=https://jcs.org/2023/10/25/wifi_da target=_blank rel=noopener>BlueSCSI Wi-Fi Desk Accessory 1.0 Released</a> — <a href=https://jcs.org/>joshua stein</a><div>BlueSCSI Wi-Fi Desk Accessory
1.0 has been released:
wifi_da-1.0.sit
(StuffIt 3 archive)
SHA256: ccfc9d27dd5da7412d10cef73b81119a1fec3848e4d1d88ff652a07ffdc6a69aSHA1: ff124972f202ceda6d7fa4788110a67ccda6a13a
This is the initial public release of my BlueSCSI Wi-Fi Desk Accessory for
classic MacOS.<li><a href=https://michael.stapelberg.ch/posts/2023-10-25-my-all-flash-zfs-network-storage-build/ target=_blank rel=noopener>My 2023 all-flash ZFS NAS (Network Storage) build</a> — <a href=https://michael.stapelberg.ch/>Michael Stapelbergs Website</a><div>For over 10 years now, I run two self-built NAS (Network Storage) devices which serve media (currently via Jellyfin) and run daily backups of all my PCs and servers.
In this article, I describe my goals, which hardware I picked for my new build (and why) and how I set it up.
Design Goals
I use my netw…</ul><p>Generated with <a href=https://git.sr.ht/~sircmpwn/openring target=_blank rel=noopener>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
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