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@@ -1449,32 +1449,31 @@ however.</p>
1449</span></span><span style="display:flex;"><span>gnuplot audio.gpi 1449</span></span><span style="display:flex;"><span>gnuplot audio.gpi
1450</span></span></code></pre><p>And input file <code>audio.gpi</code> that would be passed to gnuplot looks something like 1450</span></span></code></pre><p>And input file <code>audio.gpi</code> that would be passed to gnuplot looks something like
1451this.</p> 1451this.</p>
1452<pre><code># set output format and size 1452<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span># set output format and size
1453set term png size 1000,280 1453</span></span><span style="display:flex;"><span>set term png size 1000,280
1454 1454</span></span><span style="display:flex;"><span>
1455# set output file 1455</span></span><span style="display:flex;"><span># set output file
1456set output "audio.png" 1456</span></span><span style="display:flex;"><span>set output "audio.png"
1457 1457</span></span><span style="display:flex;"><span>
1458# set y range 1458</span></span><span style="display:flex;"><span># set y range
1459set yr [-1:1] 1459</span></span><span style="display:flex;"><span>set yr [-1:1]
1460 1460</span></span><span style="display:flex;"><span>
1461# we want just the data 1461</span></span><span style="display:flex;"><span># we want just the data
1462unset key 1462</span></span><span style="display:flex;"><span>unset key
1463unset tics 1463</span></span><span style="display:flex;"><span>unset tics
1464unset border 1464</span></span><span style="display:flex;"><span>unset border
1465set lmargin 0 1465</span></span><span style="display:flex;"><span>set lmargin 0
1466set rmargin 0 1466</span></span><span style="display:flex;"><span>set rmargin 0
1467set tmargin 0 1467</span></span><span style="display:flex;"><span>set tmargin 0
1468set bmargin 0 1468</span></span><span style="display:flex;"><span>set bmargin 0
1469 1469</span></span><span style="display:flex;"><span>
1470# draw rectangle to change background color 1470</span></span><span style="display:flex;"><span># draw rectangle to change background color
1471set obj 1 rectangle behind from screen 0,0 to screen 1,1 1471</span></span><span style="display:flex;"><span>set obj 1 rectangle behind from screen 0,0 to screen 1,1
1472set obj 1 fillstyle solid 1.0 fillcolor rgbcolor "#ffffff" 1472</span></span><span style="display:flex;"><span>set obj 1 fillstyle solid 1.0 fillcolor rgbcolor "#ffffff"
1473 1473</span></span><span style="display:flex;"><span>
1474# draw data with foreground color 1474</span></span><span style="display:flex;"><span># draw data with foreground color
1475plot "audio_only.dat" with lines lt rgb 'red' 1475</span></span><span style="display:flex;"><span>plot "audio_only.dat" with lines lt rgb 'red'
1476</code></pre> 1476</span></span></code></pre><h2 id="pre-generated-sequences">Pre-generated sequences</h2>
1477<h2 id="pre-generated-sequences">Pre-generated sequences</h2>
1478<p>What I did was take interesting parts from an animal's genome and feed it to a 1477<p>What I did was take interesting parts from an animal's genome and feed it to a
1479tone generator script. This then generated a WAV file and I converted those to 1478tone generator script. This then generated a WAV file and I converted those to
1480MP3, so they can be played in a browser. The last step was creating a 1479MP3, so they can be played in a browser. The last step was creating a
@@ -1926,13 +1925,12 @@ Lets create a folder <code>bin/</code> in the root of our project wi
1926<p>At this point we can copy <code>bzImage</code> to <code>bin/</code> folder with 1925<p>At this point we can copy <code>bzImage</code> to <code>bin/</code> folder with
1927<code>cp linux-5.15.7/arch/x86_64/boot/bzImage bin/bzImage</code>.</p> 1926<code>cp linux-5.15.7/arch/x86_64/boot/bzImage bin/bzImage</code>.</p>
1928<p>The folder structure of this experiment should look like this.</p> 1927<p>The folder structure of this experiment should look like this.</p>
1929<pre><code>pid1/ 1928<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>pid1/
1930 bin/ 1929</span></span><span style="display:flex;"><span> bin/
1931 bzImage 1930</span></span><span style="display:flex;"><span> bzImage
1932 linux-5.15.7/ 1931</span></span><span style="display:flex;"><span> linux-5.15.7/
1933 linux-5.15.7.tar.xz 1932</span></span><span style="display:flex;"><span> linux-5.15.7.tar.xz
1934</code></pre> 1933</span></span></code></pre><h2 id="preparing-pid-1-application-in-golang">Preparing PID 1 application in Golang</h2>
1935<h2 id="preparing-pid-1-application-in-golang">Preparing PID 1 application in Golang</h2>
1936<p>This step is relatively easy. The only thing we must have in mind that we will 1934<p>This step is relatively easy. The only thing we must have in mind that we will
1937need to compile the binary as a static one.</p> 1935need to compile the binary as a static one.</p>
1938<p>Let's create <code>init.go</code> file in the root of the project.</p> 1936<p>Let's create <code>init.go</code> file in the root of the project.</p>
@@ -1968,15 +1966,14 @@ during the Linux startup process).</p>
1968<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>$ echo init | cpio -o --format=newc > initramfs 1966<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>$ echo init | cpio -o --format=newc > initramfs
1969</span></span><span style="display:flex;"><span>$ mv initramfs bin/initramfs 1967</span></span><span style="display:flex;"><span>$ mv initramfs bin/initramfs
1970</span></span></code></pre><p>The projects at this stage should look like this.</p> 1968</span></span></code></pre><p>The projects at this stage should look like this.</p>
1971<pre><code>pid1/ 1969<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>pid1/
1972 bin/ 1970</span></span><span style="display:flex;"><span> bin/
1973 bzImage 1971</span></span><span style="display:flex;"><span> bzImage
1974 initramfs 1972</span></span><span style="display:flex;"><span> initramfs
1975 linux-5.15.7/ 1973</span></span><span style="display:flex;"><span> linux-5.15.7/
1976 linux-5.15.7.tar.xz 1974</span></span><span style="display:flex;"><span> linux-5.15.7.tar.xz
1977 init.go 1975</span></span><span style="display:flex;"><span> init.go
1978</code></pre> 1976</span></span></code></pre><h2 id="running-all-of-it-with-qemu">Running all of it with QEMU</h2>
1979<h2 id="running-all-of-it-with-qemu">Running all of it with QEMU</h2>
1980<p><a href="https://www.qemu.org/">QEMU</a> is a free and open-source hypervisor. It emulates 1977<p><a href="https://www.qemu.org/">QEMU</a> is a free and open-source hypervisor. It emulates
1981the machine's processor through dynamic binary translation and provides a set 1978the machine's processor through dynamic binary translation and provides a set
1982of different hardware and device models for the machine, enabling it to run a 1979of different hardware and device models for the machine, enabling it to run a
@@ -2876,9 +2873,8 @@ going on.</p>
2876or Python's <code>.venv</code> and <code>.git</code> folders.</p> 2873or Python's <code>.venv</code> and <code>.git</code> folders.</p>
2877</blockquote> 2874</blockquote>
2878<p>You can use this script in a combination with <a href="https://en.wikipedia.org/wiki/Cron">Cron</a>.</p> 2875<p>You can use this script in a combination with <a href="https://en.wikipedia.org/wiki/Cron">Cron</a>.</p>
2879<pre><code>0 2 * * * sh ~/Vault/bin/vault-backup.sh 2876<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>0 2 * * * sh ~/Vault/bin/vault-backup.sh
2880</code></pre> 2877</span></span></code></pre><p>When you start syncing your local stuff with a remote server you can review your
2881<p>When you start syncing your local stuff with a remote server you can review your
2882items on DigitalOcean.</p> 2878items on DigitalOcean.</p>
2883<figure> 2879<figure>
2884<img src="/posts/dropbox-sync/dropbox-spaces.png" alt="Dropbox Spaces" /> 2880<img src="/posts/dropbox-sync/dropbox-spaces.png" alt="Dropbox Spaces" />
@@ -4272,9 +4268,7 @@ could encode also this data as long as you provide file pointer to the encoder.&
4272<p>As already mentioned, the Basic Encoding is based on a simple mapping. Since DNA 4268<p>As already mentioned, the Basic Encoding is based on a simple mapping. Since DNA
4273is composed of 4 nucleotides (Adenine, Cytosine, Guanine, Thymine; usually 4269is composed of 4 nucleotides (Adenine, Cytosine, Guanine, Thymine; usually
4274referred using the first letter). Using this technique we can encode</p> 4270referred using the first letter). Using this technique we can encode</p>
4275<center> 4271<p><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" viewBox="0 -907.9672135000189 11313.37788460873 1185.0382429179317" style="width: 26.259ex; height: 2.721ex; vertical-align: -0.68ex; margin: 1px 0px;"><g stroke="black" fill="black" stroke-width="0" transform="matrix(1 0 0 -1 0 0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMATHI-6C"/><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMATHI-6F" x="303" y="0"/><g transform="translate(793,0)"><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMATHI-67"/><use transform="scale(0.7071067811865476)" xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-32" x="681" y="-213"/></g><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-28" x="1732" y="0"/><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-34" x="2126" y="0"/><use xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="#MJMAIN-29" x="2631" 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4277</center>
4278<p>using a single nucleotide. In this way, we are able to use the 4 bases that 4272<p>using a single nucleotide. In this way, we are able to use the 4 bases that
4279compose the DNA strand to encode each byte of data.</p> 4273compose the DNA strand to encode each byte of data.</p>
4280<table> 4274<table>
@@ -4342,26 +4336,25 @@ used was the first, it quickly became used to hold a summary description of the
4342sequence, often starting with a unique library accession number, and with time 4336sequence, often starting with a unique library accession number, and with time
4343it has become commonplace to always use ">" for the first line and to not use 4337it has become commonplace to always use ">" for the first line and to not use
4344";" comments (which would otherwise be ignored).</p> 4338";" comments (which would otherwise be ignored).</p>
4345<pre><code>;LCBO - Prolactin precursor - Bovine 4339<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>;LCBO - Prolactin precursor - Bovine
4346; a sample sequence in FASTA format 4340</span></span><span style="display:flex;"><span>; a sample sequence in FASTA format
4347MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS 4341</span></span><span style="display:flex;"><span>MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
4348EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL 4342</span></span><span style="display:flex;"><span>EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
4349VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED 4343</span></span><span style="display:flex;"><span>VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
4350ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC* 4344</span></span><span style="display:flex;"><span>ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
4351 4345</span></span><span style="display:flex;"><span>
4352>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken 4346</span></span><span style="display:flex;"><span>>MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
4353ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID 4347</span></span><span style="display:flex;"><span>ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
4354FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA 4348</span></span><span style="display:flex;"><span>FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
4355DIDGDGQVNYEEFVQMMTAK* 4349</span></span><span style="display:flex;"><span>DIDGDGQVNYEEFVQMMTAK*
4356 4350</span></span><span style="display:flex;"><span>
4357>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus] 4351</span></span><span style="display:flex;"><span>>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
4358LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV 4352</span></span><span style="display:flex;"><span>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
4359EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG 4353</span></span><span style="display:flex;"><span>EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
4360LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL 4354</span></span><span style="display:flex;"><span>LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
4361GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX 4355</span></span><span style="display:flex;"><span>GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
4362IENY 4356</span></span><span style="display:flex;"><span>IENY
4363</code></pre> 4357</span></span></code></pre><p>FASTA format was extended by <a href="https://en.wikipedia.org/wiki/FASTQ_format">FASTQ</a>
4364<p>FASTA format was extended by <a href="https://en.wikipedia.org/wiki/FASTQ_format">FASTQ</a>
4365format from the <a href="https://www.sanger.ac.uk/">Sanger Centre</a> in Cambridge.</p> 4358format from the <a href="https://www.sanger.ac.uk/">Sanger Centre</a> in Cambridge.</p>
4366<h3 id="png-encoded-dna-sequence">PNG encoded DNA sequence</h3> 4359<h3 id="png-encoded-dna-sequence">PNG encoded DNA sequence</h3>
4367<table> 4360<table>
@@ -4429,17 +4422,16 @@ making progress.
4429</span></span><span style="display:flex;"><span>2019/01/10 00:38:29 Process took 987.263µs 4422</span></span><span style="display:flex;"><span>2019/01/10 00:38:29 Process took 987.263µs
4430</span></span><span style="display:flex;"><span>2019/01/10 00:38:29 Done ... 4423</span></span><span style="display:flex;"><span>2019/01/10 00:38:29 Done ...
4431</span></span></code></pre><p>Output of <code>quote.fa</code> file contains the encoded DNA sequence in ASCII format.</p> 4424</span></span></code></pre><p>Output of <code>quote.fa</code> file contains the encoded DNA sequence in ASCII format.</p>
4432<pre><code>>SEQ1 4425<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>>SEQ1
4433GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA 4426</span></span><span style="display:flex;"><span>GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA
4434GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA 4427</span></span><span style="display:flex;"><span>GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA
4435ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA 4428</span></span><span style="display:flex;"><span>ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA
4436ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT 4429</span></span><span style="display:flex;"><span>ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT
4437GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT 4430</span></span><span style="display:flex;"><span>GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT
4438GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC 4431</span></span><span style="display:flex;"><span>GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC
4439AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC 4432</span></span><span style="display:flex;"><span>AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC
4440AACC 4433</span></span><span style="display:flex;"><span>AACC
4441</code></pre> 4434</span></span></code></pre><p>Then we encode FASTA file from previous operation to encode this data into PNG.</p>
4442<p>Then we encode FASTA file from previous operation to encode this data into PNG.</p>
4443<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>./dnae-png -i quote.fa -o quote.png 4435<pre tabindex="0" style="background-color:#fff;"><code><span style="display:flex;"><span>./dnae-png -i quote.fa -o quote.png
4444</span></span><span style="display:flex;"><span>2019/01/10 00:40:09 Gathering input file stats ... 4436</span></span><span style="display:flex;"><span>2019/01/10 00:40:09 Gathering input file stats ...
4445</span></span><span style="display:flex;"><span>2019/01/10 00:40:09 Deconstructing FASTA file ... 4437</span></span><span style="display:flex;"><span>2019/01/10 00:40:09 Deconstructing FASTA file ...