Cleanup of posts

author: Mitja Felicijan <m@mitjafelicijan.com> 2023-08-05 13:41:36 +0200
committer: Mitja Felicijan <m@mitjafelicijan.com> 2023-08-05 13:41:36 +0200
commit: 057be23acf19acae0683c59b0a346b411a04880a (patch)
tree: 852fcf2ca92060b2e70401df446b572b7fd8d874
parent: 2f5ea5f4982d6276881c9a3342ed8847ebc7d326 (diff)
download: mitjafelicijan.com-057be23acf19acae0683c59b0a346b411a04880a.tar.gz
14 files changed, 3053 insertions, 9 deletions
diff --git a/content/notes/2023-08-01-make-b-w-svg-charts-with-matplotlib.md b/content/notes/2023-08-01-make-b-w-svg-charts-with-matplotlib.md
index 4a8f4f4..51e85ec 100644
--- a/content/notes/2023-08-01-make-b-w-svg-charts-with-matplotlib.md
+++ b/content/notes/2023-08-01-make-b-w-svg-charts-with-matplotlib.md
@@ -45,6 +45,7 @@ df = pd.read_csv("data.csv")
 # Settings
 plt.title("Connect median NLB vs ALB")
+plt.tight_layout(pad=2)
 fig = plt.gcf()
 fig.set_size_inches(10, 4)
diff --git a/content/posts/2019-01-03-encoding-binary-data-into-dna-sequence.md b/content/posts/2019-01-03-encoding-binary-data-into-dna-sequence.md
index f003fc3..0d44a40 100644
--- a/content/posts/2019-01-03-encoding-binary-data-into-dna-sequence.md
+++ b/content/posts/2019-01-03-encoding-binary-data-into-dna-sequence.md
@@ -110,7 +110,6 @@ Cytosine and thymine are pyrimidine bases, while adenine and guanine are purine
 bases. The sugar and the base together are called a nucleoside.
 ![DNA](/posts/dna-sequence/dna-basics.jpg)
 *DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and
 cytosine pairs with guanine. (credit a: modification of work by Jerome Walker,
 Dennis Myts)*
@@ -135,7 +134,9 @@ As already mentioned, the Basic Encoding is based on a simple mapping. Since DNA
 is composed of 4 nucleotides (Adenine, Cytosine, Guanine, Thymine; usually
 referred using the first letter). Using this technique we can encode
-$$ log_2(4) = log_2(2^2) = 2 bits $$
+<center>
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+</center>
 using a single nucleotide. In this way, we are able to use the 4 bases that
 compose the DNA strand to encode each byte of data.
@@ -301,7 +302,6 @@ Then we encode FASTA file from previous operation to encode this data into PNG.
 After encoding into PNG format this file looks like this.
 ![Encoded Quote in PNG format](/posts/dna-sequence/quote.png)
 The larger the input stream is the larger the PNG file would be.
 Compiled basic Hello World C program with
@@ -396,11 +396,13 @@ Then we GZIP all the FASTA files to see how much the can be compressed.
 gzip -9 < 10MB.fa > 10MB.fa.gz
 ```
-[Download ODS file with benchmarks](/dna-sequence/benchmarks.ods).
+![Encode to FASTA](/posts/dna-sequence/chart-speed.svg)
+The speed increase that occurs when encoding to FASTA format.
-![Sample binary file 1KB](/posts/dna-sequence/chart-1.png)
+![File sizes](/posts/dna-sequence/chart-size.svg)
+Size of the out file after encoding.
-![Sample binary file 1KB](/posts/dna-sequence/chart-2.png)
+[Download CSV file with benchmarks](/posts/dna-sequence/benchmarks.csv).
 ## References
diff --git a/content/posts/2023-05-22-crafting-stories-in-zed-editor.md b/content/posts/2023-05-22-crafting-stories-in-zed-editor.md
index a3104b8..86be7c8 100644
--- a/content/posts/2023-05-22-crafting-stories-in-zed-editor.md
+++ b/content/posts/2023-05-22-crafting-stories-in-zed-editor.md
@@ -30,6 +30,7 @@ supported languages is not extensive, but it's still impressive.  It's a great
 example of how to create a product that stays out of your way.
 ![Zed editor](/posts/zed/zed-1.png?style=bigimg)
+C code on a light theme.
 For C development it downloaded [clangd](https://clangd.llvm.org/) and setting
 up missing dependencies in code was rather easy. For this project I use
diff --git a/static/posts/dna-sequence/benchmarks.csv b/static/posts/dna-sequence/benchmarks.csv
new file mode 100644
index 0000000..8645d5e
--- /dev/null
+++ b/static/posts/dna-sequence/benchmarks.csv
@@ -0,0 +1,7 @@
+Packages,Encode to FASTA (ms),FASTA file size (KB),FASTA gzipped (KB)
+1KB,5.625224,4.1,1.4
+10KB,32.679975,40.7,13
+100KB,112.864416,406.7,121
+1MB,872.887675,4100,1200
+10MB,8472.693202,40700,12000
+100MB,85525.178217,406700,118000
diff --git a/static/posts/dna-sequence/benchmarks.ods b/static/posts/dna-sequence/benchmarks.ods
deleted file mode 100755
index 62a8e30..0000000
--- a/static/posts/dna-sequence/benchmarks.ods
+++ /dev/null
Binary files differ
diff --git a/static/posts/dna-sequence/chart-1.png b/static/posts/dna-sequence/chart-1.png
deleted file mode 100644
index c017e43..0000000
--- a/static/posts/dna-sequence/chart-1.png
+++ /dev/null
Binary files differ
diff --git a/static/posts/dna-sequence/chart-2.png b/static/posts/dna-sequence/chart-2.png
deleted file mode 100644
index 80b922b..0000000
--- a/static/posts/dna-sequence/chart-2.png
+++ /dev/null
Binary files differ
diff --git a/static/posts/dna-sequence/chart-encoding-speed.png b/static/posts/dna-sequence/chart-encoding-speed.png
deleted file mode 100755
index 7fb106d..0000000
--- a/static/posts/dna-sequence/chart-encoding-speed.png
+++ /dev/null
Binary files differ
diff --git a/static/posts/dna-sequence/chart-file-sizes.png b/static/posts/dna-sequence/chart-file-sizes.png
deleted file mode 100755
index 31bfa66..0000000
--- a/static/posts/dna-sequence/chart-file-sizes.png
+++ /dev/null
Binary files differ
diff --git a/static/posts/dna-sequence/chart-size.py b/static/posts/dna-sequence/chart-size.py
new file mode 100644
index 0000000..4fc408d
--- /dev/null
+++ b/static/posts/dna-sequence/chart-size.py
@@ -0,0 +1,28 @@
+import csv
+import matplotlib.pyplot as plt
+import pandas as pd
+# Read the data
+df = pd.read_csv("benchmarks.csv")
+# Settings
+plt.title("Encode to FASTA out filesize")
+plt.tight_layout(pad=2)
+fig = plt.gcf()
+fig.set_size_inches(10, 4)
+# Plotting
+plt.plot(df["Packages"], df["FASTA file size (KB)"], label = "Raw", color="black", linestyle="-")
+plt.plot(df["Packages"], df["FASTA gzipped (KB)"], label = "Gzipped", color="black", linestyle="--")
+# Adding x and y axis labels
+plt.xlabel("Size of an input file", fontstyle="italic")
+plt.ylabel("File size (KB)", fontstyle="italic")
+# Legend
+legend = plt.legend()
+legend.get_frame().set_linewidth(0)
+# Export as SVG
+plt.savefig("chart-size.svg", format="svg")
diff --git a/static/posts/dna-sequence/chart-size.svg b/static/posts/dna-sequence/chart-size.svg
new file mode 100644
index 0000000..1a2d127
--- /dev/null
+++ b/static/posts/dna-sequence/chart-size.svg
@@ -0,0 +1,1553 @@
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+   <cc:Work>
+    <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
+    <dc:date>2023-08-05T13:29:17.701350</dc:date>
+    <dc:format>image/svg+xml</dc:format>
+    <dc:creator>
+     <cc:Agent>
+      <dc:title>Matplotlib v3.5.2, https://matplotlib.org/</dc:title>
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diff --git a/static/posts/dna-sequence/chart-speed.py b/static/posts/dna-sequence/chart-speed.py
new file mode 100644
index 0000000..c07b057
--- /dev/null
+++ b/static/posts/dna-sequence/chart-speed.py
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+import csv
+import matplotlib.pyplot as plt
+import pandas as pd
+# Read the data
+df = pd.read_csv("benchmarks.csv")
+# Settings
+plt.title("Encode to FASTA speed over time")
+plt.tight_layout(pad=2)
+fig = plt.gcf()
+fig.set_size_inches(10, 4)
+# Plotting
+plt.plot(df["Packages"], df["Encode to FASTA (ms)"], label = "ALB", color="black", linestyle="--")
+# Adding x and y axis labels
+plt.xlabel("Size of an input file", fontstyle="italic")
+plt.ylabel("Encoding time (ms)", fontstyle="italic")
+# Export as SVG
+plt.savefig("chart-speed.svg", format="svg")
diff --git a/static/posts/dna-sequence/chart-speed.svg b/static/posts/dna-sequence/chart-speed.svg
new file mode 100644
index 0000000..7bb0c29
--- /dev/null
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diff --git a/templates/base.html b/templates/base.html
index f5cb386..6e0e50e 100644
--- a/templates/base.html
+++ b/templates/base.html
@@ -95,6 +95,19 @@
                  font-family: monospace;
          }
+          figure {
+                  margin-inline-start: 0;
+                  margin-inline-end: 0;
+          }
+          figcaption {
+                  text-align: center;
+          }
+          figcaption p {
+                  margin: 0.3em 0 0 0;
+          }
+          
          img, video, audio {
                  max-width: 100%;
          }
@@ -167,14 +180,14 @@
                You can write me an email
                at <a href="mailto:m@mitjafelicijan.com">m@mitjafelicijan.com</a> or
                catch up with me <a href="https://telegram.me/mitjafelicijan"
-                target="_blank">on Telegram</a>.
+                                                        target="_blank">on Telegram</a>.
          </p>
          <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 specified
+                           target="_blank" rel="noreferrer">CC BY 4.0 license</a> unless specified
                otherwise. Blog is also available as <a href="/index.xml"
-                target="_blank">RSS feed</a>.
+                                                                                                target="_blank">RSS feed</a>.
          </p>
        </footer>
  </body>
author	Mitja Felicijan <m@mitjafelicijan.com>	2023-08-05 13:41:36 +0200
committer	Mitja Felicijan <m@mitjafelicijan.com>	2023-08-05 13:41:36 +0200
commit	057be23acf19acae0683c59b0a346b411a04880a (patch)
tree	852fcf2ca92060b2e70401df446b572b7fd8d874
parent	2f5ea5f4982d6276881c9a3342ed8847ebc7d326 (diff)
download	mitjafelicijan.com-057be23acf19acae0683c59b0a346b411a04880a.tar.gz