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-rw-r--r--_includes/webring.html4
-rw-r--r--_layouts/base.html5
-rw-r--r--_posts/2019-01-03-encoding-binary-data-into-dna-sequence.md6
-rw-r--r--_posts/2022-06-30-trying-out-helix-editor.md3
-rw-r--r--index.html2
5 files changed, 14 insertions, 6 deletions
diff --git a/_includes/webring.html b/_includes/webring.html
index f68299d..071d7ef 100644
--- a/_includes/webring.html
+++ b/_includes/webring.html
@@ -32,8 +32,8 @@
32 <div>When a service fails to start up enough times in a row, systemd gives up on it. On servers, this isn’t what I want — in general it’s helpful for automated recovery if daemons are restarted indefinitely. As long as you don’t have circular dependencies between services, all your services will eventually come up after tra...</div> 32 <div>When a service fails to start up enough times in a row, systemd gives up on it. On servers, this isn’t what I want — in general it’s helpful for automated recovery if daemons are restarted indefinitely. As long as you don’t have circular dependencies between services, all your services will eventually come up after tra...</div>
33 </li> 33 </li>
34 <li> 34 <li>
35 <div><a href="https://utcc.utoronto.ca/~cks/space/blog/sysadmin/TrackingMachineImportance" target="_blank" rel="noopener">We might want to regularly keep track of how important each server is</a> — Chris&#39;s Wiki :: blog</div> 35 <div><a href="https://utcc.utoronto.ca/~cks/space/blog/linux/MyMachineDesires2024" target="_blank" rel="noopener">What I&#39;d like in a hypothetical new desktop machine in 2024</a> — Chris&#39;s Wiki :: blog</div>
36 <div>Today we had a significant machine room air conditioning failure in our main machine room, one that certainly couldn't be fixed on the spot ('glycol all over the roof' is not a phrase you really want to hear about your AC's chiller). To keep the machine room's temperature down, we had to power off as many machines as p...</div> 36 <div>My current work desktop and home desktop are getting somewhat long in the tooth, which has caused me to periodically think about what I'd want in new hardware for them. Sometimes I even look at potential hardware choices for such a replacement desktop (which can lead to grumbling). Today I want to write down my ideal b...</div>
37 </li> 37 </li>
38 <li> 38 <li>
39 <div><a href="https://szymonkaliski.com/newsletter/2024-01-01-q4-2023/" target="_blank" rel="noopener">Q4 2023 — Improving Replit's Console and a Database-y Creative Coding Environment</a> — Szymon Kaliski</div> 39 <div><a href="https://szymonkaliski.com/newsletter/2024-01-01-q4-2023/" target="_blank" rel="noopener">Q4 2023 — Improving Replit's Console and a Database-y Creative Coding Environment</a> — Szymon Kaliski</div>
diff --git a/_layouts/base.html b/_layouts/base.html
index e39acf4..aa4be41 100644
--- a/_layouts/base.html
+++ b/_layouts/base.html
@@ -110,6 +110,7 @@
110 overflow-x: auto; 110 overflow-x: auto;
111 padding: 1em; 111 padding: 1em;
112 border: var(--border-size) var(--border-style) var(--border-color); 112 border: var(--border-size) var(--border-style) var(--border-color);
113 border-radius: 3px;
113 } 114 }
114 115
115 code { 116 code {
@@ -121,6 +122,7 @@
121 122
122 pre code { 123 pre code {
123 background: transparent; 124 background: transparent;
125 padding: initial;
124 } 126 }
125 127
126 figure { 128 figure {
@@ -142,6 +144,7 @@
142 img, video, audio { 144 img, video, audio {
143 width: 800px; 145 width: 800px;
144 max-width: 100%; 146 max-width: 100%;
147 border-radius: 3px;
145 } 148 }
146 149
147 header nav { 150 header nav {
@@ -154,7 +157,7 @@
154 } 157 }
155 158
156 audio::-webkit-media-controls-enclosure { 159 audio::-webkit-media-controls-enclosure {
157 border-radius: 0; 160 border-radius: 3px;
158 } 161 }
159 162
160 .highlight .hll { background-color: #ffffcc } 163 .highlight .hll { background-color: #ffffcc }
diff --git a/_posts/2019-01-03-encoding-binary-data-into-dna-sequence.md b/_posts/2019-01-03-encoding-binary-data-into-dna-sequence.md
index 1de83af..6980ed1 100644
--- a/_posts/2019-01-03-encoding-binary-data-into-dna-sequence.md
+++ b/_posts/2019-01-03-encoding-binary-data-into-dna-sequence.md
@@ -111,6 +111,7 @@ Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine
111bases. The sugar and the base together are called a nucleoside. 111bases. The sugar and the base together are called a nucleoside.
112 112
113![DNA](/assets/posts/dna-sequence/dna-basics.jpg){:loading="lazy"} 113![DNA](/assets/posts/dna-sequence/dna-basics.jpg){:loading="lazy"}
114
114*DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and 115*DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and
115cytosine pairs with guanine. (credit a: modification of work by Jerome Walker, 116cytosine pairs with guanine. (credit a: modification of work by Jerome Walker,
116Dennis Myts)* 117Dennis Myts)*
@@ -301,6 +302,7 @@ Then we encode FASTA file from previous operation to encode this data into PNG.
301After encoding into PNG format this file looks like this. 302After encoding into PNG format this file looks like this.
302 303
303![Encoded Quote in PNG format](/assets/posts/dna-sequence/quote.png){:loading="lazy"} 304![Encoded Quote in PNG format](/assets/posts/dna-sequence/quote.png){:loading="lazy"}
305
304The larger the input stream is the larger the PNG file would be. 306The larger the input stream is the larger the PNG file would be.
305 307
306Compiled basic Hello World C program with 308Compiled basic Hello World C program with
@@ -368,8 +370,8 @@ First we generate some binary sample data with dd.
368dd if=<(openssl enc -aes-256-ctr -pass pass:"$(dd if=/dev/urandom bs=128 count=1 2>/dev/null | base64)" -nosalt < /dev/zero) of=1KB.bin bs=1KB count=1 iflag=fullblock 370dd if=<(openssl enc -aes-256-ctr -pass pass:"$(dd if=/dev/urandom bs=128 count=1 2>/dev/null | base64)" -nosalt < /dev/zero) of=1KB.bin bs=1KB count=1 iflag=fullblock
369``` 371```
370 372
371
372![Sample binary file 1KB](/assets/posts/dna-sequence/sample-binary-file.png){:loading="lazy"} 373![Sample binary file 1KB](/assets/posts/dna-sequence/sample-binary-file.png){:loading="lazy"}
374
373Our freshly generated 1KB file looks something like this (its full of 375Our freshly generated 1KB file looks something like this (its full of
374garbage data as intended). 376garbage data as intended).
375 377
@@ -396,9 +398,11 @@ gzip -9 < 10MB.fa > 10MB.fa.gz
396``` 398```
397 399
398![Encode to FASTA](/assets/posts/dna-sequence/chart-speed.svg){:loading="lazy"} 400![Encode to FASTA](/assets/posts/dna-sequence/chart-speed.svg){:loading="lazy"}
401
399The speed increase that occurs when encoding to FASTA format. 402The speed increase that occurs when encoding to FASTA format.
400 403
401![File sizes](/assets/posts/dna-sequence/chart-size.svg){:loading="lazy"} 404![File sizes](/assets/posts/dna-sequence/chart-size.svg){:loading="lazy"}
405
402Size of the out file after encoding. 406Size of the out file after encoding.
403 407
404[Download CSV file with benchmarks](/assets/posts/dna-sequence/benchmarks.csv). 408[Download CSV file with benchmarks](/assets/posts/dna-sequence/benchmarks.csv).
diff --git a/_posts/2022-06-30-trying-out-helix-editor.md b/_posts/2022-06-30-trying-out-helix-editor.md
index 61f653a..be369a1 100644
--- a/_posts/2022-06-30-trying-out-helix-editor.md
+++ b/_posts/2022-06-30-trying-out-helix-editor.md
@@ -36,7 +36,8 @@ One thing to do before you are able to use autocompletion and make use Language
36Server support is to install the language server with NPM. 36Server support is to install the language server with NPM.
37 37
38```sh 38```sh
39npm install -g typescript typescript-language-server 39# For C development this installs C LSP.
40sudo dnf install clang-tools-extra
40``` 41```
41 42
42I am still getting used to the keyboard shortcuts and getting better. What Helix 43I am still getting used to the keyboard shortcuts and getting better. What Helix
diff --git a/index.html b/index.html
index 9edce32..08bb037 100644
--- a/index.html
+++ b/index.html
@@ -5,7 +5,7 @@ layout: index
5<p><i>You do not learn by relaxing. You learn by violently assaulting your problem 5<p><i>You do not learn by relaxing. You learn by violently assaulting your problem
6until it surrenders its mysteries to you.</i></p> 6until it surrenders its mysteries to you.</i></p>
7 7
8<a style="max-width:650px;display:inline-block;background:blue;color:white;padding:1em;" href="https://mitjafelicijan.github.io/binary-visualization/" target="_blank"> 8<a style="border-radius:3px;max-width:650px;display:inline-block;background:blue;color:white;padding:1em;" href="https://mitjafelicijan.github.io/binary-visualization/" target="_blank">
9 <strong>Latest experiment:</strong> Examine graphical representations of 9 <strong>Latest experiment:</strong> Examine graphical representations of
10 binary files using diagrams that illustrate connections between pairs of bytes 10 binary files using diagrams that illustrate connections between pairs of bytes
11 (digraphs) and triplets of bytes (trigraphs). 11 (digraphs) and triplets of bytes (trigraphs).