update news

HISTORY.qmd

@@ -1,5 +1,15 @@
 # History {.unnumbered}
 
+## Edition 0.0.11 (2023-01-19)
+
+- Adding some quarto code annotations!
+
+- New chapter on algorithms
+
+- Add a challenge on genome assembly
+
+- Rendering with Q v.1.3
+
 ## Edition 0.0.10 (2022-12-17)
 
 - Update book with new quarto and extension versions

docs/HISTORY.html

@@ -357,7 +357,8 @@ <h1 class="quarto-secondary-nav-title">History</h1>
     <h2 id="toc-title">Table of contents</h2>
 
   <ul>
-  <li><a href="#edition-0.0.10-2022-12-17" id="toc-edition-0.0.10-2022-12-17" class="nav-link active" data-scroll-target="#edition-0.0.10-2022-12-17">Edition 0.0.10 (2022-12-17)</a></li>
+  <li><a href="#edition-0.0.11-2023-01-19" id="toc-edition-0.0.11-2023-01-19" class="nav-link active" data-scroll-target="#edition-0.0.11-2023-01-19">Edition 0.0.11 (2023-01-19)</a></li>
+  <li><a href="#edition-0.0.10-2022-12-17" id="toc-edition-0.0.10-2022-12-17" class="nav-link" data-scroll-target="#edition-0.0.10-2022-12-17">Edition 0.0.10 (2022-12-17)</a></li>
   <li><a href="#edition-0.0.9-2022-09-08" id="toc-edition-0.0.9-2022-09-08" class="nav-link" data-scroll-target="#edition-0.0.9-2022-09-08">Edition 0.0.9 (2022-09-08)</a></li>
   <li><a href="#ed.-0.0.8-2022-08-29" id="toc-ed.-0.0.8-2022-08-29" class="nav-link" data-scroll-target="#ed.-0.0.8-2022-08-29">Ed. 0.0.8 (2022-08-29)</a></li>
   <li><a href="#ed.-0.0.7-2022-08-19" id="toc-ed.-0.0.7-2022-08-19" class="nav-link" data-scroll-target="#ed.-0.0.7-2022-08-19">Ed. 0.0.7 (2022-08-19)</a></li>
@@ -390,6 +391,15 @@ <h1 class="title d-none d-lg-block">History</h1>
 
 </header>
 
+<section id="edition-0.0.11-2023-01-19" class="level2">
+<h2 class="anchored" data-anchor-id="edition-0.0.11-2023-01-19">Edition 0.0.11 (2023-01-19)</h2>
+<ul>
+<li><p>Adding some quarto code annotations!</p></li>
+<li><p>New chapter on algorithms</p></li>
+<li><p>Add a challenge on genome assembly</p></li>
+<li><p>Rendering with Q v.1.3</p></li>
+</ul>
+</section>
 <section id="edition-0.0.10-2022-12-17" class="level2">
 <h2 class="anchored" data-anchor-id="edition-0.0.10-2022-12-17">Edition 0.0.10 (2022-12-17)</h2>
 <ul>

docs/chs-challenges-demos/seq-analysis-challenges.html

@@ -528,23 +528,23 @@ <h1 class="title d-none d-lg-block">Seq. Analysis challenges</h1>
 <dl class="code-annotation-container-hidden code-annotation-container-grid">
 <dt data-target-cell="annotated-cell-2" data-target-annotation="1">1</dt>
 <dd>
-<span data-code-annotation="1" data-code-cell="annotated-cell-2" data-code-lines="2">Change the <code># feature</code> name for simple <code>feature</code>.</span>
+<span data-code-cell="annotated-cell-2" data-code-annotation="1" data-code-lines="2">Change the <code># feature</code> name for simple <code>feature</code>.</span>
 </dd>
 <dt data-target-cell="annotated-cell-2" data-target-annotation="2">2</dt>
 <dd>
-<span data-code-annotation="2" data-code-cell="annotated-cell-2" data-code-lines="3">Select <code>feature</code> and <code>assembly</code> columns.</span>
+<span data-code-cell="annotated-cell-2" data-code-annotation="2" data-code-lines="3">Select <code>feature</code> and <code>assembly</code> columns.</span>
 </dd>
 <dt data-target-cell="annotated-cell-2" data-target-annotation="3">3</dt>
 <dd>
-<span data-code-annotation="3" data-code-cell="annotated-cell-2" data-code-lines="4">Group by these two columns, enabling grouping operations.</span>
+<span data-code-cell="annotated-cell-2" data-code-annotation="3" data-code-lines="4">Group by these two columns, enabling grouping operations.</span>
 </dd>
 <dt data-target-cell="annotated-cell-2" data-target-annotation="4">4</dt>
 <dd>
-<span data-code-annotation="4" data-code-cell="annotated-cell-2" data-code-lines="5">Count the numbers of rows based on the applied grouping.</span>
+<span data-code-cell="annotated-cell-2" data-code-annotation="4" data-code-lines="5">Count the numbers of rows based on the applied grouping.</span>
 </dd>
 <dt data-target-cell="annotated-cell-2" data-target-annotation="5">5</dt>
 <dd>
-<span data-code-annotation="5" data-code-cell="annotated-cell-2" data-code-lines="6">Generate a wide dataset sending row names as columns.</span>
+<span data-code-cell="annotated-cell-2" data-code-annotation="5" data-code-lines="6">Generate a wide dataset sending row names as columns.</span>
 </dd>
 </dl>
 </div>

docs/chs-command-line/git-and-github.html

@@ -860,7 +860,7 @@ <h1 class="title"><span id="sec-vcs" class="quarto-section-identifier d-none d-l
 <footer class="footer"><div class="nav-footer">
       <div class="nav-footer-center">Made with <a href="https://quarto.org/">Quarto</a>. Under <a href="https://github.com/camilogarciabotero/biocomp-book/blob/main/LICENSE">GNU GPL 3.0</a>. Buy me coffee <a href="https://www.paypal.com/paypalme/camilogarciabotero"><i class="fa-solid fa-mug-saucer" aria-label="mug-saucer"></i></a> and visit me at <a href="https://camilogarciabotero.github.io/"><i class="fa-solid fa-house" aria-label="house"></i></a></div>
   </div>
-</footer><script>var lightboxQuarto = GLightbox({"loop":true,"closeEffect":"zoom","selector":".lightbox","descPosition":"bottom","openEffect":"zoom"});</script>
+</footer><script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","openEffect":"zoom","descPosition":"bottom","loop":true});</script>
 
 
 </body></html>

docs/chs-command-line/welcome-to-command-line.html

@@ -1037,7 +1037,7 @@ <h1 class="title"><span id="sec-cli" class="quarto-section-identifier d-none d-l
 <footer class="footer"><div class="nav-footer">
       <div class="nav-footer-center">Made with <a href="https://quarto.org/">Quarto</a>. Under <a href="https://github.com/camilogarciabotero/biocomp-book/blob/main/LICENSE">GNU GPL 3.0</a>. Buy me coffee <a href="https://www.paypal.com/paypalme/camilogarciabotero"><i class="fa-solid fa-mug-saucer" aria-label="mug-saucer"></i></a> and visit me at <a href="https://camilogarciabotero.github.io/"><i class="fa-solid fa-house" aria-label="house"></i></a></div>
   </div>
-</footer><script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","openEffect":"zoom","selector":".lightbox","loop":true,"descPosition":"bottom"});</script>
+</footer><script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","selector":".lightbox","loop":true,"descPosition":"bottom","openEffect":"zoom"});</script>
 
 
 </body></html>

docs/chs-sequence-analysis/introduction-to-sequence-analysis.html

@@ -464,7 +464,7 @@ <h1 class="title"><span id="sec-seq-analysis" class="quarto-section-identifier d
 <span class="header-section-number">8.1</span> Biological information</h2>
 <p>Since the origin, organisms (or molecules) have been the result of different selective processes. An emergent property of successive iterations of survival/decease was the ability of molecules to keep a record of its past in a very stable manner, so that it will pass generation to generation. Although this might not be the first property or molecule to ever exist (see the <a href="https://en.wikipedia.org/wiki/Abiogenesis">:origin of life</a>), the innovation of organisms to pack information of previous events became so advantageous that almost any form of living organism has this property: that is DNA.</p>
 <div id="fig-chromosome" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/chromosome-genes.png" class="lightbox" title="The different scales of information packed in a biological fashion. Figure adapted from @meneely2017 book showing how DNA in a eukaryote is packaged with chromosomal proteins to form the much more compact chromatin. Chromatin is then folded into higher-order structures and eventually into the chromosome" data-gallery="quarto-lightbox-gallery-1"><img src="imgs-seqan/chromosome-genes.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/chromosome-genes.png" class="lightbox" data-gallery="quarto-lightbox-gallery-1" title="The different scales of information packed in a biological fashion. Figure adapted from @meneely2017 book showing how DNA in a eukaryote is packaged with chromosomal proteins to form the much more compact chromatin. Chromatin is then folded into higher-order structures and eventually into the chromosome"><img src="imgs-seqan/chromosome-genes.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;8.1: The different scales of information packed in a biological fashion. Figure adapted from <span class="citation" data-cites="meneely2017">Meneely et al. (<a href="../references.html#ref-meneely2017" role="doc-biblioref">2017</a>)</span> book showing how <em>DNA in a eukaryote is packaged with chromosomal proteins to form the much more compact chromatin. Chromatin is then folded into higher-order structures and eventually into the chromosome</em></figcaption><p></p>
 </figure>
 </div>
@@ -474,29 +474,29 @@ <h1 class="title"><span id="sec-seq-analysis" class="quarto-section-identifier d
 <p>DNA is an organic molecule of <a href="https://en.wikipedia.org/wiki/Nucleic_acid">:nucleic acids</a> that is mainly build out of nitrogen-containing compounds (<a href="https://en.wikipedia.org/wiki/Nucleobase">:nucleobases</a>) or just bases.The four bases are adenine (A), cytosine (C), guanine (G) and (T) and they bind strictly as <span class="math inline">\(A=T\)</span> and <span class="math inline">\(C\equiv{G}\)</span> where each of the lines represents an hydrogen bond.</p>
 <p>DNA nitrogenous bases of are arranged in a very compacted helix structure and too much can be understood from its molecular nature. It is of course governed by the physicochemical properties of the atoms, therefore DNA is a physicochemical entity. But those common bricks have also a very beautiful emergent property that comes out from their order (mainly), and that is to keep the instructions that build the organism from which it belongs. These instructions are nothing else than information, which also follow some informational rules. Then DNA is also an informational entity.</p>
 <div id="fig-doublehelix" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/dna-structure.png" class="lightbox" title="DNA double helix structure and main characteristics. Image adapted from @brown2018 showing the structure with the sugar–phosphate backbone of each polynucleotide drawn as a gray ribbon with the base pairs in green" data-gallery="quarto-lightbox-gallery-2"><img src="imgs-seqan/dna-structure.png" class="img-fluid figure-img" style="width:50.0%"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/dna-structure.png" class="lightbox" data-gallery="quarto-lightbox-gallery-2" title="DNA double helix structure and main characteristics. Image adapted from @brown2018 showing the structure with the sugar–phosphate backbone of each polynucleotide drawn as a gray ribbon with the base pairs in green"><img src="imgs-seqan/dna-structure.png" class="img-fluid figure-img" style="width:50.0%"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;8.2: DNA double helix structure and main characteristics. Image adapted from <span class="citation" data-cites="brown2018">Brown (<a href="../references.html#ref-brown2018" role="doc-biblioref">2018</a>)</span> showing the structure with the <em>sugar–phosphate backbone of each polynucleotide drawn as a gray ribbon with the base pairs in green</em></figcaption><p></p>
 </figure>
 </div>
 <p>The description of DNA bases helped the elucidation of the helicoidal structure as well as the elucidation of the base pairing rules of the nucleotides <a href="#fig-nucleotides">Fig.&nbsp;<span>8.4</span></a>, also called the Chargaff’s rules of base pairing. The first outstanding feature of the DNA structure was indeed highlighted by Watson and Crick in its famous paper about a subtle mechanism of replication. The</p>
 
 <div class="no-row-height column-margin column-container"><div id="fig-phosphodiester" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/phosphdiester.png" class="lightbox" title="A phosphodiester bond bind two nitrogenous bases as in the backbone of the DNA helix" data-gallery="quarto-lightbox-gallery-3"><img src="imgs-seqan/phosphdiester.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/phosphdiester.png" class="lightbox" data-gallery="quarto-lightbox-gallery-3" title="A phosphodiester bond bind two nitrogenous bases as in the backbone of the DNA helix"><img src="imgs-seqan/phosphdiester.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;8.3: A phosphodiester bond bind two nitrogenous bases as in the backbone of the DNA helix</figcaption><p></p>
 </figure>
 </div></div><p>This idea of the duality of the DNA (and of course of other biological molecules as well) is the source of the study of many bioinformatic fields. But a question remains open: how do we capture the informational nature of a DNA sequence so that we end up with a sequential file of characters <code>ATCGCTATC...</code>. This is not a trivial question in fact.</p>
 <div id="fig-nucleotides" class="quarto-layout-panel">
 <figure class="figure"><div class="quarto-layout-row quarto-layout-valign-top">
 <div id="fig-gc" class="quarto-figure quarto-figure-center anchored" style="flex-basis: 43.5%;justify-content: center;">
-<figure class="figure"><p><a href="imgs-seqan/guanine-cytosine.png" class="lightbox" title="Guanine and cytosine base pair" data-gallery="quarto-lightbox-gallery-4"><img src="imgs-seqan/guanine-cytosine.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/guanine-cytosine.png" class="lightbox" data-gallery="quarto-lightbox-gallery-4" title="Guanine and cytosine base pair"><img src="imgs-seqan/guanine-cytosine.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">(a) Guanine and cytosine base pair</figcaption><p></p>
 </figure>
 </div>
 <div class="quarto-figure-spacer quarto-layout-cell" style="flex-basis: 5.4%;justify-content: center;">
 <p>&nbsp;</p>
 </div>
 <div id="fig-at" class="quarto-figure quarto-figure-center anchored" style="flex-basis: 51.1%;justify-content: center;">
-<figure class="figure"><p><a href="imgs-seqan/adenine-thymine.png" class="lightbox" title="Adenine and thymine base pair" data-gallery="quarto-lightbox-gallery-5"><img src="imgs-seqan/adenine-thymine.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/adenine-thymine.png" class="lightbox" data-gallery="quarto-lightbox-gallery-5" title="Adenine and thymine base pair"><img src="imgs-seqan/adenine-thymine.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">(b) Adenine and thymine base pair</figcaption><p></p>
 </figure>
 </div>
@@ -508,7 +508,7 @@ <h1 class="title"><span id="sec-seq-analysis" class="quarto-section-identifier d
 <span class="header-section-number">8.3</span> The central <del>dogma</del> theory of molecular biology extended</h2>
 <p>So far we have addressed that DNA is a very stable molecule that stores biological (i.e., evolutionary) information. Also, that DNA could represent a sequential object of characters as in a computer digital object or file as well. But how is it that this order has an underlying biological sense? This was a very though question that required the accumulation of many experimental discoveries and the meeting of genetics and molecular biology.</p>
 <div id="fig-central-mb" class="quarto-figure quarto-figure-center anchored">
-<figure class="figure"><p><a href="imgs-seqan/central-theory-mb.png" class="lightbox" title="An extended representation of the central theory of molecular biology. Image from @makinen2015" data-gallery="quarto-lightbox-gallery-6"><img src="imgs-seqan/central-theory-mb.png" class="img-fluid figure-img"></a></p>
+<figure class="figure"><p><a href="imgs-seqan/central-theory-mb.png" class="lightbox" data-gallery="quarto-lightbox-gallery-6" title="An extended representation of the central theory of molecular biology. Image from @makinen2015"><img src="imgs-seqan/central-theory-mb.png" class="img-fluid figure-img"></a></p>
 <p></p><figcaption class="figure-caption">Figure&nbsp;8.5: An extended representation of the central theory of molecular biology. Image from <span class="citation" data-cites="makinen2015">Mäkinen et al. (<a href="../references.html#ref-makinen2015" role="doc-biblioref">2015</a>)</span></figcaption><p></p>
 </figure>
 </div>
@@ -943,7 +943,7 @@ <h1 class="title"><span id="sec-seq-analysis" class="quarto-section-identifier d
 <footer class="footer"><div class="nav-footer">
       <div class="nav-footer-center">Made with <a href="https://quarto.org/">Quarto</a>. Under <a href="https://github.com/camilogarciabotero/biocomp-book/blob/main/LICENSE">GNU GPL 3.0</a>. Buy me coffee <a href="https://www.paypal.com/paypalme/camilogarciabotero"><i class="fa-solid fa-mug-saucer" aria-label="mug-saucer"></i></a> and visit me at <a href="https://camilogarciabotero.github.io/"><i class="fa-solid fa-house" aria-label="house"></i></a></div>
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docs/chs-sequence-analysis/sanger-analysis.html

@@ -856,7 +856,7 @@ <h1 class="title"><span id="sec-sanger" class="quarto-section-identifier d-none
 <footer class="footer"><div class="nav-footer">
       <div class="nav-footer-center">Made with <a href="https://quarto.org/">Quarto</a>. Under <a href="https://github.com/camilogarciabotero/biocomp-book/blob/main/LICENSE">GNU GPL 3.0</a>. Buy me coffee <a href="https://www.paypal.com/paypalme/camilogarciabotero"><i class="fa-solid fa-mug-saucer" aria-label="mug-saucer"></i></a> and visit me at <a href="https://camilogarciabotero.github.io/"><i class="fa-solid fa-house" aria-label="house"></i></a></div>
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