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authorMitja Felicijan <m@mitjafelicijan.com>2023-07-08 23:26:39 +0200
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1<!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>What would DNA sound if synthesized to an audio file</title><meta name=description content="IntroductionLately, I have been thinking a lot about the nature of life, what are thefoundation blocks of life and things like that."><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:times new roman,Times,serif;line-height:1.35rem}hr{margin-block-start:1.5rem}h1,h2,h3{line-height:initial}footer{margin-block-start:3rem}table{max-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}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;margin-block-start:1.5rem;margin-block-end:1.5rem;padding:.5rem 0;border-top:1px solid #000;border-bottom:1px solid #000}pre code{line-height:1.3em}pre,code,pre *,code *{font-family:monospace;font-size:initial!important}img,video,audio{max-width:100%}header{display:flex;flex-direction:row;gap:3rem}nav{display:flex;gap:.75rem}.pstatus-orange{background:gold}.pstatus-green{background:#9acd32}.pstatus-red{background:#cd5c5c}@media only screen and (max-width:600px){header{flex-direction:column;gap:1rem}a{word-wrap:break-word}}</style><header><nav class=main><a href=/>Home</a>
2<a href=https://git.mitjafelicijan.com/ target=_blank>Git</a>
3<a href=https://files.mitjafelicijan.com/ target=_blank>Files</a>
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5<a href=/curriculum-vitae.html>CV</a>
6<a href=/index.xml target=_blank>RSS</a></nav></header><main><div><h1>What would DNA sound if synthesized to an audio file</h1><p>Jul 5, 2022<div><h2 id=introduction>Introduction</h2><p>Lately, I have been thinking a lot about the nature of life, what are the
7foundation blocks of life and things like that. It's remarkable how complex and
8on the other hand simple the creation is when you look at it. The miracle of
9life keeps us grounded when our imagination goes wild. If the DNA are the blocks
10of life, you could consider them to be an API nature provided us to better
11understand all of this chaos masquerading as order.<p>I have been reading a lot about superintelligence and our somehow misguided path
12to create general artificial intelligence. What would the building blocks or our
13creation look like? Is the compression really the ultimate storage of
14information? Will our creation also ponder this questions when creating new
15worlds for themselves, or will we just disappear into the vastness of
16possibilities? It is a little offensive that we are playing God whilst being
17completely ignorant of our own reality. Who knows! Like many other
18breakthroughs, this one will also come at a cost not known to us when it finally
19happens.<p>To keep things a bit lighter, I decided to convert some popular DNA sequences
20into an audio files for us to listen to. I am not the first one, nor I will be
21the last one to do this. But it is an interesting exercise in better
22understanding the relationship between art and science. Maybe listening to DNA
23instead of parsing it will find a way into better understanding, or at least
24enjoying 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
25<a href=/encoding-binary-data-into-dna-sequence.html>Encoding binary data into DNA
26sequence</a> where I have been
27converting all sorts of data into DNA sequences.<p>This will be a similar exercise but instead of converting to DNA, I will be
28generating 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
29Hz</a>. For this tuning, we also
30choose <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
31a bit. This is a famous quote I also used for the encoding tests, and it goes
32like this.<blockquote><p>How wonderful that we have met with a paradox. Now we have some hope of
33making progress.
34― Niels Bohr</blockquote><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>&gt;SEQ1
35</span></span><span style=display:flex><span>GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA
36</span></span><span style=display:flex><span>GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA
37</span></span><span style=display:flex><span>ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA
38</span></span><span style=display:flex><span>ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT
39</span></span><span style=display:flex><span>GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT
40</span></span><span style=display:flex><span>GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC
41</span></span><span style=display:flex><span>AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC
42</span></span><span style=display:flex><span>AACC
43</span></span></code></pre><p>This is what we gonna work with to get things rolling forward, when creating
44parser 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
45<a href=https://en.wikipedia.org/wiki/FASTA_format>FASTA format</a> well known in
46<a href=https://en.wikipedia.org/wiki/Bioinformatics>Bioinformatics</a> to extract single
47Nucleotides that will be converted into separate tones based on equal-tempered
48scale explained above.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>nucleotide_tone_map = {
49</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;A&#39;</span>: 440,
50</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;C&#39;</span>: 523.25,
51</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;G&#39;</span>: 783.99,
52</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;T&#39;</span>: 587.33, <span style=color:green># converted to D</span>
53</span></span><span style=display:flex><span>}
54</span></span><span style=display:flex><span>
55</span></span><span style=display:flex><span><span style=color:#00f>def</span> split(word):
56</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]
57</span></span><span style=display:flex><span>
58</span></span><span style=display:flex><span><span style=color:#00f>def</span> generate_from_dna_sequence(sequence):
59</span></span><span style=display:flex><span> <span style=color:#00f>for</span> nucleotide <span style=color:#00f>in</span> split(sequence):
60</span></span><span style=display:flex><span> print(nucleotide, nucleotide_tone_map[nucleotide])
61</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
62sine notes to a global array we will later use for creating a WAV file out of
63it.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:#00f>import</span> math
64</span></span><span style=display:flex><span>
65</span></span><span style=display:flex><span><span style=color:#00f>def</span> append_sinewave(freq=440.0, duration_milliseconds=500, volume=1.0):
66</span></span><span style=display:flex><span> <span style=color:#00f>global</span> audio
67</span></span><span style=display:flex><span>
68</span></span><span style=display:flex><span> num_samples = duration_milliseconds * (sample_rate / 1000.0)
69</span></span><span style=display:flex><span>
70</span></span><span style=display:flex><span> <span style=color:#00f>for</span> x <span style=color:#00f>in</span> range(int(num_samples)):
71</span></span><span style=display:flex><span> audio.append(volume * math.sin(2 * math.pi * freq * (x / sample_rate)))
72</span></span><span style=display:flex><span>
73</span></span><span style=display:flex><span> <span style=color:#00f>return</span>
74</span></span></code></pre><p>The sine wave generated here is the standard beep. If you want something more
75aggressive, 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
76</span></span><span style=display:flex><span><span style=color:#00f>import</span> struct
77</span></span><span style=display:flex><span>
78</span></span><span style=display:flex><span><span style=color:#00f>def</span> save_wav(file_name):
79</span></span><span style=display:flex><span> wav_file = wave.open(file_name, <span style=color:#a31515>&#39;w&#39;</span>)
80</span></span><span style=display:flex><span> nchannels = 1
81</span></span><span style=display:flex><span> sampwidth = 2
82</span></span><span style=display:flex><span>
83</span></span><span style=display:flex><span> nframes = len(audio)
84</span></span><span style=display:flex><span> comptype = <span style=color:#a31515>&#39;NONE&#39;</span>
85</span></span><span style=display:flex><span> compname = <span style=color:#a31515>&#39;not compressed&#39;</span>
86</span></span><span style=display:flex><span> wav_file.setparams((nchannels, sampwidth, sample_rate, nframes, comptype, compname))
87</span></span><span style=display:flex><span>
88</span></span><span style=display:flex><span> <span style=color:#00f>for</span> sample <span style=color:#00f>in</span> audio:
89</span></span><span style=display:flex><span> wav_file.writeframes(struct.pack(<span style=color:#a31515>&#39;h&#39;</span>, int(sample * 32767.0)))
90</span></span><span style=display:flex><span>
91</span></span><span style=display:flex><span> wav_file.close()
92</span></span></code></pre><p>44100 is the industry standard sample rate - CD quality. If you need to save on
93file size, you can adjust it downwards. The standard for low quality is, 8000 or
948kHz.<p>WAV files here are using short, 16 bit, signed integers for the sample size.
95So, we multiply the floating-point data we have by 32767, the maximum value for
96a short integer.<blockquote><p>It is theoretically possible to use the floating point -1.0 to 1.0 data
97directly in a WAV file, but not obvious how to do that using the wave module
98in 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
99out to use the <a href=https://linux.die.net/man/1/sox>SoX - Sound eXchange, the Swiss Army knife of audio
100manipulation</a> one because it didn't require
101anything else.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>sox output.wav -n spectrogram -o spectrogram.png
102</span></span></code></pre><p>An example spectrogram of Ludwig van Beethoven Symphony No. 6 First movement.</p><audio controls><source src=/assets/dna-synthesized/symphony-no6-1st-movement.mp3 type=audio/mpeg></audio><p><img src=/assets/dna-synthesized/symphony-no6-1st-movement.png alt="Ludwig van Beethoven Symphony No. 6 First movement"><p>The other option could also be in combination with
103<a href=http://www.gnuplot.info/>gnuplot</a>. This would require an intermediary step,
104however.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>sox output.wav audio.dat
105</span></span><span style=display:flex><span>tail -n+3 audio.dat &gt; audio_only.dat
106</span></span><span style=display:flex><span>gnuplot audio.gpi
107</span></span></code></pre><p>And input file <code>audio.gpi</code> that would be passed to gnuplot looks something like
108this.<pre><code># set output format and size
109set term png size 1000,280
110
111# set output file
112set output &quot;audio.png&quot;
113
114# set y range
115set yr [-1:1]
116
117# we want just the data
118unset key
119unset tics
120unset border
121set lmargin 0
122set rmargin 0
123set tmargin 0
124set bmargin 0
125
126# draw rectangle to change background color
127set obj 1 rectangle behind from screen 0,0 to screen 1,1
128set obj 1 fillstyle solid 1.0 fillcolor rgbcolor &quot;#ffffff&quot;
129
130# draw data with foreground color
131plot &quot;audio_only.dat&quot; with lines lt rgb 'red'
132</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
133tone generator script. This then generated a WAV file and I converted those to
134MP3, so they can be played in a browser. The last step was creating a
135spectrogram based on a WAV file.<h3 id=niels-bohr-quote>Niels Bohr quote</h3><audio controls><source src=/assets/dna-synthesized/quote/out.mp3 type=audio/mpeg></audio><p><img src=/assets/dna-synthesized/quote/spectogram.png alt=Spectogram><h3 id=mouse>Mouse</h3><p>This is part of a mouse genome <code>Mus_musculus.GRCm39.dna.nonchromosomal</code>. You
136can get <a href=http://ftp.ensembl.org/pub/release-106/fasta/mus_musculus/dna/>genom data
137here</a>.</p><audio controls><source src=/assets/dna-synthesized/mouse/out.mp3 type=audio/mpeg></audio><p><img src=/assets/dna-synthesized/mouse/spectogram.png alt=Spectogram><h3 id=bison>Bison</h3><p>This is part of a bison genome <code>Bison_bison_bison.Bison_UMD1.0.cdna</code>. You can
138get <a href=http://ftp.ensembl.org/pub/release-106/fasta/bison_bison_bison/cdna/>genom data
139here</a>.</p><audio controls><source src=/assets/dna-synthesized/bison/out.mp3 type=audio/mpeg></audio><p><img src=/assets/dna-synthesized/bison/spectogram.png alt=Spectogram><h3 id=taurus>Taurus</h3><p>This is part of a taurus genome <code>Bos_taurus.ARS-UCD1.2.cdna</code>. You can get
140<a href=http://ftp.ensembl.org/pub/release-106/fasta/bos_taurus/cdna/>genom data
141here</a>.</p><audio controls><source src=/assets/dna-synthesized/taurus/out.mp3 type=audio/mpeg></audio><p><img src=/assets/dna-synthesized/taurus/spectogram.png alt=Spectogram><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
142<a href=https://www.elektron.se/en/model-samples>Elektron Model:Samples</a>. This is a
143really cool piece of equipment that supports MIDI in via USB and 3.5 mm audio
144jack.<p>Elektron is connected to my MacBook via USB cable and audio out is patched to a
145Sony Bluetooth speaker I have that supports 3.5 mm audio in. Elektron doesn't
146have internal speakers.<p><img src=/assets/dna-synthesized/elektron/IMG_0619.jpg alt><p><img src=/assets/dna-synthesized/elektron/IMG_0620.jpg alt><p><img src=/assets/dna-synthesized/elektron/IMG_0622.jpg alt><p>For communicating with Elektron, I choose <code>pygame</code> Python module that has MIDI
147built in. With this, it was rather simple to send notes to the device. All I did
148was map MIDI notes to the actual Nucleotides.<p>Before all of this I also checked Audio MIDI Setup app under MacOS and checked
149MIDI Studio by pressing ⌘-2.<p><img src=/assets/dna-synthesized/elektron/midi-studio.jpg alt><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
150</span></span><span style=display:flex><span><span style=color:#00f>import</span> time
151</span></span><span style=display:flex><span>
152</span></span><span style=display:flex><span>pygame.midi.init()
153</span></span><span style=display:flex><span>
154</span></span><span style=display:flex><span>print(pygame.midi.get_default_output_id())
155</span></span><span style=display:flex><span>print(pygame.midi.get_device_info(0))
156</span></span><span style=display:flex><span>
157</span></span><span style=display:flex><span>player = pygame.midi.Output(1)
158</span></span><span style=display:flex><span>player.set_instrument(2)
159</span></span><span style=display:flex><span>
160</span></span><span style=display:flex><span><span style=color:#00f>def</span> send_note(note, velocity):
161</span></span><span style=display:flex><span> <span style=color:#00f>global</span> player
162</span></span><span style=display:flex><span> player.note_on(note, velocity)
163</span></span><span style=display:flex><span> time.sleep(0.3)
164</span></span><span style=display:flex><span> player.note_off(note, velocity)
165</span></span><span style=display:flex><span>
166</span></span><span style=display:flex><span>
167</span></span><span style=display:flex><span>nucleotide_midi_map = {
168</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;A&#39;</span>: 60,
169</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;C&#39;</span>: 90,
170</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;G&#39;</span>: 160,
171</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;T&#39;</span>: 180, <span style=color:green># is D</span>
172</span></span><span style=display:flex><span>}
173</span></span><span style=display:flex><span>
174</span></span><span style=display:flex><span><span style=color:#00f>with</span> open(<span style=color:#a31515>&#34;quote.fa&#34;</span>) <span style=color:#00f>as</span> f:
175</span></span><span style=display:flex><span> sequence = f.read().replace(<span style=color:#a31515>&#39;</span><span style=color:#a31515>\n</span><span style=color:#a31515>&#39;</span>, <span style=color:#a31515>&#39;&#39;</span>)
176</span></span><span style=display:flex><span>
177</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]:
178</span></span><span style=display:flex><span> print(<span style=color:#a31515>&#34;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>&#34;</span>.format(
179</span></span><span style=display:flex><span> nucleotide, nucleotide_midi_map[nucleotide]))
180</span></span><span style=display:flex><span> send_note(nucleotide_midi_map[nucleotide], 127)
181</span></span><span style=display:flex><span>
182</span></span><span style=display:flex><span><span style=color:#00f>del</span> player
183</span></span><span style=display:flex><span>pygame.midi.quit()
184</span></span></code></pre><p><video src=/assets/dna-synthesized/elektron/elektron.mp4 controls></video><p>All of this could be made much more interesting if I choose different
185instruments for different Nucleotides, or doing more funky stuff with Elektron.
186But for now, this should be enough. It is just a proof of concept. Something to
187play 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
188to be expected because we are operating only with 4 notes essentially. What
189could make this more interesting is using something like
190<a href=https://supercollider.github.io/>Supercollider</a> to create more interesting
191sounds. By transposing notes or using effects based on repeated data in a
192sequence. Possibilities are endless.<p>It is really astonishing what can be achieved with a little bit of code and an
193idea. I could see this becoming an interesting background soundscape instrument
194if done properly. It could replace random note generator with something more
195intriguing, biological, natural.<p>I actually find the results fascinating. I took some time and listened to this
196music of nature. Even though it's quite the same, it's also quite different.
197The subtle differences on repeat kind of creates music on its own. Makes you
198wonder. It kind of puts Occam’s Razor in its place. Nature for sure loves to
199make things as energy efficient as possible.</div></div></main><footer><hr><div><h3>Want to comment or have something to add?</h3>You can write me an email at
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