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9<a href=/index.xml target=_blank class=hob>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
10it through your personal DNA sequencer and get data like music, videos or
11computer programs from it. Well, this is all possible now. It was not done on a
12large scale because it is quite expensive to create DNA strands but it's
13possible.<p>Encoding data into DNA sequence is relatively simple process once you understand
14the relationship between binary data and nucleotides and scientists have been
15making large leaps in this field in order to provide viable long-term storage
16solution for our data that would potentially survive our specie if case of
17global disaster. We could imprint all the world's knowledge into plants and
18ensure the survival of our knowledge.<p>More optimistic usage for this technology would be easier storage of ever
19growing data we produce every day. Once machines for sequencing DNA become fast
20enough and cheaper this could mean the next evolution of storing data and
21abandoning classical hard and solid state drives in data warehouses.<p>As we currently stand this is still not viable but it is quite an amazing and
22cool technology.<p>My interests in this field are purely in encoding processes and experimental
23testing mainly because I don't have the access to this expensive machines. My
24initial goal was to create a toolkit that can be used by everybody to encode
25their data into a proper DNA sequence.<h2 id=glossary>Glossary</h2><p><strong>deoxyribose</strong> A five-carbon sugar molecule with a hydrogen atom rather than a
26hydroxyl group in the 2′ position; the sugar component of DNA nucleotides.<p><strong>double helix</strong> The molecular shape of DNA in which two strands of nucleotides
27wind around each other in a spiral shape.<p><strong>nitrogenous base</strong> A nitrogen-containing molecule that acts as a base; often
28referring to one of the purine or pyrimidine components of nucleic acids.<p><strong>phosphate group</strong> A molecular group consisting of a central phosphorus atom
29bound to four oxygen atoms.<p><strong>RGB</strong> The RGB color model is an additive color model in which red, green and
30blue light are added together in various ways to reproduce a broad array of
31colors.<p><strong>GCC</strong> The GNU Compiler Collection is a compiler system produced by the GNU
32Project supporting various programming languages.<h2 id=data-encoding>Data encoding</h2><p><strong>TL;DR:</strong> Encoding involves the use of a code to change original data into a
33form that can be used by an external process.<p>Encoding is the process of converting data into a format required for a number
34of information processing needs, including:<ul><li>Program compiling and execution<li>Data transmission, storage and compression/decompression<li>Application data processing, such as file conversion</ul><p>Encoding can have two meanings:<ul><li>In computer technology, encoding is the process of applying a specific code,
35such as letters, symbols and numbers, to data for conversion into an
36equivalent cipher.<li>In electronics, encoding refers to analog to digital conversion.</ul><h2 id=quick-history-of-dna>Quick history of DNA</h2><ul><li><strong>1869</strong> - Friedrich Miescher identifies "nuclein".<li><strong>1900s</strong> - The Eugenics Movement.<li><strong>1900</strong> – Mendel's theories are rediscovered by researchers.<li><strong>1944</strong> - Oswald Avery identifies DNA as the 'transforming principle'.<li><strong>1952</strong> - Rosalind Franklin photographs crystallized DNA fibres.<li><strong>1953</strong> - James Watson and Francis Crick discover the double helix structure of DNA.<li><strong>1965</strong> - Marshall Nirenberg is the first person to sequence the bases in each codon.<li><strong>1983</strong> - Huntington's disease is the first mapped genetic disease.<li><strong>1990</strong> - The Human Genome Project begins.<li><strong>1995</strong> - Haemophilus Influenzae is the first bacterium genome sequenced.<li><strong>1996</strong> - Dolly the sheep is cloned.<li><strong>1999</strong> - First human chromosome is decoded.<li><strong>2000</strong> – Genetic code of the fruit fly is decoded.<li><strong>2002</strong> – Mouse is the first mammal to have its genome decoded.<li><strong>2003</strong> – The Human Genome Project is completed.<li><strong>2013</strong> – DNA Worldwide and Eurofins Forensic discover identical twins have differences in their genetic makeup.</ul><h2 id=what-is-dna>What is DNA?</h2><p>Deoxyribonucleic acid, a self-replicating material which is <strong>present in nearly
37all living organisms</strong> as the main constituent of chromosomes. It is the
38<strong>carrier of genetic information</strong>.<blockquote><p>The nitrogen in our DNA, the calcium in our teeth, the iron in our blood,
39the carbon in our apple pies were made in the interiors of collapsing stars.
40We are made of starstuff.
41<strong>-- Carl Sagan, Cosmos</strong></blockquote><p>The nucleotide in DNA consists of a sugar (deoxyribose), one of four bases
42(cytosine (C), thymine (T), adenine (A), guanine (G)), and a phosphate.
43Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine
44bases. The sugar and the base together are called a nucleoside.<figure><img src=/posts/dna-sequence/dna-basics.jpg alt=DNA><figcaption><p><em>DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and
45cytosine pairs with guanine. (credit a: modification of work by Jerome Walker,
46Dennis Myts)</em></figcaption></figure><h2 id=encode-binary-data-into-dna-sequence>Encode binary data into DNA sequence</h2><p>As an input file you can use any file you want:<ul><li>ASCII files,<li>Compiled programs,<li>Multimedia files (MP3, MP4, MVK, etc),<li>Images,<li>Database files,<li>etc.</ul><p>Note: If you would copy all the bytes from RAM to file or pipe data to file you
47could encode also this data as long as you provide file pointer to the encoder.<h3 id=basic-encoding>Basic Encoding</h3><p>As already mentioned, the Basic Encoding is based on a simple mapping. Since DNA
48is composed of 4 nucleotides (Adenine, Cytosine, Guanine, Thymine; usually
49referred using the first letter). 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In this way, we are able to use the 4 bases that
50compose the DNA strand to encode each byte of data.<table><thead><tr><th>Two bits<th>Nucleotides<tbody><tr><td>00<td><strong>A</strong> (Adenine)<tr><td>10<td><strong>G</strong> (Guanine)<tr><td>01<td><strong>C</strong> (Cytosine)<tr><td>11<td><strong>T</strong> (Thymine)</table><p>With this in mind we can simply encode any data by using two-bit to Nucleotides
51conversion.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>{ Algorithm 1: Naive byte array to DNA encode }
52</span></span><span style=display:flex><span>procedure EncodeToDNASequence(f) string
53</span></span><span style=display:flex><span>begin
54</span></span><span style=display:flex><span> enc string
55</span></span><span style=display:flex><span> <span style=color:#00f>while</span> <span style=color:#00f>not</span> eof(f) do
56</span></span><span style=display:flex><span> c byte := buffer[0] { Read 1 byte <span style=color:#00f>from</span> buffer }
57</span></span><span style=display:flex><span> bin integer := sprintf(<span style=color:#a31515>&#39;08b&#39;</span>, c) { Convert to string binary }
58</span></span><span style=display:flex><span> <span style=color:#00f>for</span> e <span style=color:#00f>in</span> range[0, 2, 4, 6] do
59</span></span><span style=display:flex><span> <span style=color:#00f>if</span> e[0] == 48 <span style=color:#00f>and</span> e[1] == 48 then { 0x00 - A (Adenine) }
60</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;A&#39;</span>
61</span></span><span style=display:flex><span> <span style=color:#00f>else</span> <span style=color:#00f>if</span> e[0] == 48 <span style=color:#00f>and</span> e[1] == 49 then { 0x01 - G (Guanine) }
62</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;G&#39;</span>
63</span></span><span style=display:flex><span> <span style=color:#00f>else</span> <span style=color:#00f>if</span> e[0] == 49 <span style=color:#00f>and</span> e[1] == 48 then { 0x10 - C (Cytosine) }
64</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;C&#39;</span>
65</span></span><span style=display:flex><span> <span style=color:#00f>else</span> <span style=color:#00f>if</span> e[0] == 49 <span style=color:#00f>and</span> e[1] == 49 then { 0x11 - T (Thymine) }
66</span></span><span style=display:flex><span> enc += <span style=color:#a31515>&#39;T&#39;</span>
67</span></span><span style=display:flex><span> <span style=color:#00f>return</span> enc { Return DNA sequence }
68</span></span><span style=display:flex><span>end
69</span></span></code></pre><p>Another encoding would be <strong>Goldman encoding</strong>. Using this encoding helps with
70Nonsense mutation (amino acids replaced by a stop codon) that occurs and is the
71most problematic during translation because it leads to truncated amino acid
72sequences, which in turn results in truncated proteins.<p><a href="https://www.youtube.com/watch?v=a4PiGWNsIEU">Where to store big data? In DNA: Nick Goldman at TEDxPrague</a><h3 id=fasta-file-format>FASTA file format</h3><p>In bioinformatics, FASTA format is a text-based format for representing either
73nucleotide sequences or peptide sequences, in which nucleotides or amino acids
74are represented using single-letter codes. The format also allows for sequence
75names and comments to precede the sequences. The format originates from the
76FASTA software package, but has now become a standard in the field of
77bioinformatics.<p>The first line in a FASTA file started either with a ">" (greater-than) symbol
78or, less frequently, a ";" (semicolon) was taken as a comment. Subsequent lines
79starting with a semicolon would be ignored by software. Since the only comment
80used was the first, it quickly became used to hold a summary description of the
81sequence, often starting with a unique library accession number, and with time
82it has become commonplace to always use ">" for the first line and to not use
83";" comments (which would otherwise be ignored).<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>;LCBO - Prolactin precursor - Bovine
84</span></span><span style=display:flex><span>; a sample sequence in FASTA format
85</span></span><span style=display:flex><span>MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS
86</span></span><span style=display:flex><span>EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL
87</span></span><span style=display:flex><span>VTEVRGMKGAPDAILSRAIEIEEENKRLLEGMEMIFGQVIPGAKETEPYPVWSGLPSLQTKDED
88</span></span><span style=display:flex><span>ARYSAFYNLLHCLRRDSSKIDTYLKLLNCRIIYNNNC*
89</span></span><span style=display:flex><span>
90</span></span><span style=display:flex><span>&gt;MCHU - Calmodulin - Human, rabbit, bovine, rat, and chicken
91</span></span><span style=display:flex><span>ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTID
92</span></span><span style=display:flex><span>FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREA
93</span></span><span style=display:flex><span>DIDGDGQVNYEEFVQMMTAK*
94</span></span><span style=display:flex><span>
95</span></span><span style=display:flex><span>&gt;gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
96</span></span><span style=display:flex><span>LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
97</span></span><span style=display:flex><span>EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
98</span></span><span style=display:flex><span>LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
99</span></span><span style=display:flex><span>GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
100</span></span><span style=display:flex><span>IENY
101</span></span></code></pre><p>FASTA format was extended by <a href=https://en.wikipedia.org/wiki/FASTQ_format>FASTQ</a>
102format from the <a href=https://www.sanger.ac.uk/>Sanger Centre</a> in Cambridge.<h3 id=png-encoded-dna-sequence>PNG encoded DNA sequence</h3><table><thead><tr><th>Nucleotides<th>RGB<th>Color name<tbody><tr><td>A ➞ Adenine<td>(0,0,255)<td>Blue<tr><td>G ➞ Guanine<td>(0,100,0)<td>Green<tr><td>C ➞ Cytosine<td>(255,0,0)<td>Red<tr><td>T ➞ Thymine<td>(255,255,0)<td>Yellow</table><p>With this in mind we can create a simple algorithm to create PNG representation
103of a DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>{ Algorithm 2: Naive DNA to PNG encode <span style=color:#00f>from</span> FASTA file }
104</span></span><span style=display:flex><span>procedure EncodeDNASequenceToPNG(f)
105</span></span><span style=display:flex><span>begin
106</span></span><span style=display:flex><span> i image
107</span></span><span style=display:flex><span> <span style=color:#00f>while</span> <span style=color:#00f>not</span> eof(f) do
108</span></span><span style=display:flex><span> c char := buffer[0] { Read 1 char <span style=color:#00f>from</span> buffer }
109</span></span><span style=display:flex><span> case c of
110</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;A&#39;</span>: color := RGB(0, 0, 255) { Blue }
111</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;G&#39;</span>: color := RGB(0, 100, 0) { Green }
112</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;C&#39;</span>: color := RGB(255, 0, 0) { Red }
113</span></span><span style=display:flex><span> <span style=color:#a31515>&#39;T&#39;</span>: color := RGB(255, 255, 0) { Yellow }
114</span></span><span style=display:flex><span> drawRect(i, [x, y], color)
115</span></span><span style=display:flex><span> save(i) { Save PNG image }
116</span></span><span style=display:flex><span>end
117</span></span></code></pre><h2 id=encoding-text-file-in-practice>Encoding text file in practice</h2><p>In this example we will take a simple text file as our input stream for
118encoding. This file will have a quote from Niels Bohr and saved as txt file.<blockquote><p>How wonderful that we have met with a paradox. Now we have some hope of
119making progress.
120― Niels Bohr</blockquote><p>First we encode text file into FASTA file.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i quote.txt -o quote.fa
121</span></span><span style=display:flex><span>2019/01/10 00:38:29 Gathering input file stats
122</span></span><span style=display:flex><span>2019/01/10 00:38:29 Starting encoding ...
123</span></span><span style=display:flex><span> 106 B / 106 B [==================================] 100.00% 0s
124</span></span><span style=display:flex><span>2019/01/10 00:38:29 Saving to FASTA file ...
125</span></span><span style=display:flex><span>2019/01/10 00:38:29 Output FASTA file length is 438 B
126</span></span><span style=display:flex><span>2019/01/10 00:38:29 Process took 987.263µs
127</span></span><span style=display:flex><span>2019/01/10 00:38:29 Done ...
128</span></span></code></pre><p>Output of <code>quote.fa</code> file contains the encoded DNA sequence in ASCII format.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>&gt;SEQ1
129</span></span><span style=display:flex><span>GACAGCTTGTGTACAAGTGTGCTTGCTCGCGAGCGGGTACGCGCGTGGGCTAACAAGTGA
130</span></span><span style=display:flex><span>GCCAGCAGGTGAACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGCTGGCGGGTGA
131</span></span><span style=display:flex><span>ACAAGTGTGCCGGTGAGCCAACAAGCAGACAAGTAAGCAGGTACGCAGGCGAGCTTGTCA
132</span></span><span style=display:flex><span>ACTCACAAGATCGCTTGTGTACAAGTGTGCGGACAAGCCAGCAGGTGCGCGGACAAGTAT
133</span></span><span style=display:flex><span>GCTTGCTGGCGGACAAGCCAGCTTGTAAGCGGACAAGCTTGCGCACAAGCTGGCAGGCCT
134</span></span><span style=display:flex><span>GCCGGCTCGCGTACAAATTCACAAGTAAGTACGCTTGCGTGTACGCGGGTATGTATACTC
135</span></span><span style=display:flex><span>AACCTCACCAAACGGGACAAGATCGCCGGCGGGCTAGTATACAAGAACGCTTGCCAGTAC
136</span></span><span style=display:flex><span>AACC
137</span></span></code></pre><p>Then we encode FASTA file from previous operation to encode this data into PNG.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-png -i quote.fa -o quote.png
138</span></span><span style=display:flex><span>2019/01/10 00:40:09 Gathering input file stats ...
139</span></span><span style=display:flex><span>2019/01/10 00:40:09 Deconstructing FASTA file ...
140</span></span><span style=display:flex><span>2019/01/10 00:40:09 Compositing image file ...
141</span></span><span style=display:flex><span> 424 / 424 [==================================] 100.00% 0s
142</span></span><span style=display:flex><span>2019/01/10 00:40:09 Saving output file ...
143</span></span><span style=display:flex><span>2019/01/10 00:40:09 Output image file length is 1.1 kB
144</span></span><span style=display:flex><span>2019/01/10 00:40:09 Process took 19.036117ms
145</span></span><span style=display:flex><span>2019/01/10 00:40:09 Done ...
146</span></span></code></pre><p>After encoding into PNG format this file looks like this.<figure><img src=/posts/dna-sequence/quote.png alt="Encoded Quote in PNG format"><figcaption><p>The larger the input stream is the larger the PNG file would be.</figcaption></figure><p>Compiled basic Hello World C program with
147<a href=https://www.gnu.org/software/gcc/>GCC</a> would <a href=/posts/dna-sequence/sample.png>look
148like</a>.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span><span style=color:green>// gcc -O3 -o sample sample.c
149</span></span></span><span style=display:flex><span><span style=color:green></span><span style=color:#00f>#include</span> <span style=color:#00f>&lt;stdio.h&gt;</span><span style=color:#00f>
150</span></span></span><span style=display:flex><span><span style=color:#00f></span>
151</span></span><span style=display:flex><span>main() {
152</span></span><span style=display:flex><span> printf(<span style=color:#a31515>&#34;Hello, world!</span><span style=color:#a31515>\n</span><span style=color:#a31515>&#34;</span>);
153</span></span><span style=display:flex><span> <span style=color:#00f>return</span> 0;
154</span></span><span style=display:flex><span>}
155</span></span></code></pre><h2 id=toolkit-for-encoding-data>Toolkit for encoding data</h2><p>I have created a toolkit with two main programs:<ul><li>dnae-encode (encodes file into FASTA file)<li>dnae-png (encodes FASTA file into PNG)</ul><p>Toolkit with full source code is available on
156<a href=https://github.com/mitjafelicijan/dna-encoding>github.com/mitjafelicijan/dna-encoding</a>.<h3 id=dnae-encode>dnae-encode</h3><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>&gt; ./dnae-encode --help
157</span></span><span style=display:flex><span>usage: dnae-encode --input=INPUT [&lt;flags&gt;]
158</span></span><span style=display:flex><span>
159</span></span><span style=display:flex><span>A command-line application that encodes file into DNA sequence.
160</span></span><span style=display:flex><span>
161</span></span><span style=display:flex><span>Flags:
162</span></span><span style=display:flex><span> --help Show context-sensitive help (also try --help-long and --help-man).
163</span></span><span style=display:flex><span> -i, --input=INPUT Input file (ASCII or binary) which will be encoded into DNA sequence.
164</span></span><span style=display:flex><span> -o, --output=<span style=color:#a31515>&#34;out.fa&#34;</span> Output file which stores DNA sequence in FASTA format.
165</span></span><span style=display:flex><span> -s, --sequence=SEQ1 The description line (defline) or header/identifier line, gives a name and/or a unique identifier <span style=color:#00f>for</span> the sequence.
166</span></span><span style=display:flex><span> -c, --columns=60 Row characters length (no more than 120 characters). Devices preallocate fixed line sizes in software.
167</span></span><span style=display:flex><span> --version Show application version.
168</span></span></code></pre><h3 id=dnae-png>dnae-png</h3><pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>&gt; ./dnae-png --help
169</span></span><span style=display:flex><span>usage: dnae-png --input=INPUT [&lt;flags&gt;]
170</span></span><span style=display:flex><span>
171</span></span><span style=display:flex><span>A command-line application that encodes FASTA file into PNG image.
172</span></span><span style=display:flex><span>
173</span></span><span style=display:flex><span>Flags:
174</span></span><span style=display:flex><span> --help Show context-sensitive help (also try --help-long and --help-man).
175</span></span><span style=display:flex><span> -i, --input=INPUT Input FASTA file which will be encoded into PNG image.
176</span></span><span style=display:flex><span> -o, --output=<span style=color:#a31515>&#34;out.png&#34;</span> Output file in PNG format that represents DNA sequence in graphical way.
177</span></span><span style=display:flex><span> -s, --size=10 Size of pairings of DNA bases on image in pixels (lower resolution lower file size).
178</span></span><span style=display:flex><span> --version Show application version.
179</span></span></code></pre><h2 id=benchmarks>Benchmarks</h2><p>First we generate some binary sample data with dd.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>dd <span style=color:#00f>if</span>=&lt;(openssl enc -aes-256-ctr -pass pass:<span style=color:#a31515>&#34;</span><span style=color:#00f>$(</span>dd <span style=color:#00f>if</span>=/dev/urandom bs=128 count=1 2&gt;/dev/null | base64<span style=color:#00f>)</span><span style=color:#a31515>&#34;</span> -nosalt &lt; /dev/zero) of=1KB.bin bs=1KB count=1 iflag=fullblock
180</span></span></code></pre><figure><img src=/posts/dna-sequence/sample-binary-file.png alt="Sample binary file 1KB"><figcaption><p>Our freshly generated 1KB file looks something like this (its full of
181garbage data as intended).</figcaption></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
182into DNA sequence.<pre tabindex=0 style=background-color:#fff><code><span style=display:flex><span>./dnae-encode -i 100MB.bin -o 100MB.fa
183</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
184</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://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
185a lock on a Linux NFS server, which turned
186out to be specific to NFS v3 (which I really should have seen coming,
187since it involved NLM and lockd). Finding the NFS v4 client that
188owns 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
189and Bradley Kuhn, are interacting on the OSI's license-discuss
190list where the're doing
191bad computer history and insisting that a guy Larry Rosen
192coincidentally interviewed for a book years ago is clearly the origin of
193somethin…<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:
194i2c, plan9
195Another month, another file system.
196Well, if you can’t fix it in software, fix it in hardware (looking at
197you, bme680, we’re not
198done yet). The show must go on, as they say, and I would like my
199experiments to go on.
200So a “new” addition to the environmental sensor family connected to
201the 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
202this mortal coil, we are endowed with self-awareness, agency, and free will.
203Each of the 8 billion members of this human race represents a unique person, a
204unique 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.
205My 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
2061.0 has been released:
207wifi_da-1.0.sit
208(StuffIt 3 archive)
209SHA256: ccfc9d27dd5da7412d10cef73b81119a1fec3848e4d1d88ff652a07ffdc6a69aSHA1: ff124972f202ceda6d7fa4788110a67ccda6a13a
210This is the initial public release of my BlueSCSI Wi-Fi Desk Accessory for
211classic 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.
212In this article, I describe my goals, which hardware I picked for my new build (and why) and how I set it up.
213Design Goals
214I 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
215at <a href=mailto:mitja.felicijan@gmail.com>mitja.felicijan@gmail.com</a> or
216catch 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
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