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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/35534?offset=20</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines</guid>
	<pubDate>Sat, 21 May 2016 22:42:16 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines</link>
	<title><![CDATA[Bpipe - a tool for running and managing bioinformatics pipelines]]></title>
	<description><![CDATA[<p>Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.</p>
<ul>
<li>January 20th, 2016 - New! Bpipe 0.9.9 released!</li>
<li>Download <a href="http://download.bpipe.org/versions/bpipe-0.9.9.tar.gz">latest</a>, <a href="http://download.bpipe.org">all</a></li>
<li><a href="http://docs.bpipe.org">Documentation</a></li>
<li><a href="https://groups.google.com/forum/#%21forum/bpipe-discuss">Mailing List</a> (Google Group)</li>
</ul>
<p>Bpipe has been published in <a href="http://bioinformatics.oxfordjournals.org/content/early/2012/04/11/bioinformatics.bts167.abstract">Bioinformatics</a>! If you use Bpipe, please cite:</p>
<p><em>Sadedin S, Pope B &amp; Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics</em></p><p>Address of the bookmark: <a href="http://docs.bpipe.org/" rel="nofollow">http://docs.bpipe.org/</a></p>]]></description>
	<dc:creator>Radha Agarkar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician</guid>
	<pubDate>Mon, 19 Aug 2013 01:12:38 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/2573/most-commonly-used-awk-by-bioinformatician</link>
	<title><![CDATA[Most Commonly used Awk by Bioinformatician]]></title>
	<description><![CDATA[<p style="text-align: center;">&nbsp;</p><p>Awk is a programming language that is specifically designed for quickly manipulating space delimited data. Although you can achieve all its functionality with Perl, awk is simpler in many practical cases.</p><p>Why awk? You can replace a pipeline of 'stuff | grep | sed | cut...' with a single call to awk. For a simple script, most of the timelag is in loading these apps into memory, and it's much faster to do it all with one. This is ideal for something like an openbox pipe menu where you want to generate something on the fly. You can use awk to make a neat one-liner for some quick job in the terminal, or build an awk section into a shell script. You can find a lot of online tutorials, but here I will only show a few examples which cover most of bioinformatician daily uses of awk.</p><p>choose rows where column 3 is larger than column 5:</p><p>awk '$3&gt;$5' input.txt &gt; output.txt</p><p>extract column 2,4,5:</p><p>awk '{print $2,$4,$5}' input.txt &gt; output.txt</p><p>awk 'BEGIN{OFS="\t"}{print $2,$4,$5}' input.txt</p><p>show rows between 20th and 80th:</p><p>awk 'NR&gt;=20&amp;&amp;NR&lt;=80' input.txt &gt; output.txt</p><p>calculate the average of column 2:</p><p>awk '{x+=$2}END{print x/NR}' input.txt</p><p>regex (egrep):</p><p>awk '/^test[0-9]+/' input.txt</p><p>calculate the sum of column 2 and 3 and put it at the end of a row or replace the first column:</p><p>awk '{print $0,$2+$3}' input.txt</p><p>awk '{$1=$2+$3;print}' input.txt</p><p>join two files on column 1:</p><p>awk 'BEGIN{while((getline&lt;"file1.txt")&gt;0)l[$1]=$0}$1 in l{print $0"\t"l[$1]}' file2.txt &gt; output.txt</p><p>count number of occurrence of column 2 (uniq -c):</p><p>awk '{l[$2]++}END{for (x in l) print x,l[x]}' input.txt</p><p>apply "uniq" on column 2, only printing the first occurrence (uniq):</p><p>awk '!($2 in l){print;l[$2]=1}' input.txt</p><p>count different words (wc):</p><p>awk '{for(i=1;i!=NF;++i)c[$i]++}END{for (x in c) print x,c[x]}' input.txt</p><p>deal with simple CSV:</p><p>awk -F, '{print $1,$2}'</p><p>substitution (sed is simpler in this case):</p><p>awk '{sub(/test/, "no", $0);print}' input.txt</p><p>&nbsp;</p><p>OK now here's where to read this stuff properly explained. roll</p><p>Two thorough tutorials:</p><p>http://www.gnu.org/software/gawk/manual/gawk.html</p><p>http://www.grymoire.com/Unix/Awk.html</p><p>A famous list of useful one-liners - though they're short, many are quite tricky:</p><p>http://www.pement.org/awk/awk1line.txt</p><p>And some nice explanations of those one-liners. After reading this you'll have a pretty good grasp!</p><p>http://www.catonmat.net/blog/awk-one-li &hellip; -part-one/</p><p>http://www.catonmat.net/blog/ten-awk-ti &hellip; -pitfalls/</p>]]></description>
	<dc:creator>Neel</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/44669/bioinformatician-at-qub-uk</guid>
  <pubDate>Tue, 01 Oct 2024 21:43:23 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatician at QUB, UK]]></title>
  <description><![CDATA[
<p>The post-holder will work under the direction of the Precision Medicine Centre of Excellence's (PMC) Bioinformatics lead and collaborate closely with the Scientific and Clinical leads. The primary responsibilities will be to develop, validate and maintain data analysis pipelines and algorithms that enable the comprehensive analysis of genomic information derived from cancer specimens, within the context of clinical studies. The PMC is an ISO 15189:2012 accredited medical laboratory (Ref 20634), providing an integrated cancer diagnostic and clinical research service that combines high throughput genomics and digital pathology (www.qub.ac.uk/research-centres/PMC).</p>

<p>About the person:</p>

<p>Essential criteria:</p>

<p>Hold or be about to obtain* a PhD in Computational biology, Bioinformatics, computing science or related subjects. (*must be obtained within 3 months of the closing date for the post) or MSc equivalent with at least 3 years' work experience in a relevant role.<br />Significant relevant research experience in genomics or work experience in a relevant technical/scientific role.<br />Significant experience in managing and analysing NGS data and other big data.<br />Experience in developing and maintaining analysis pipelines.<br />Experience working with Linux/UNIX environments.<br />Proficiency with python, bash, R and/or equivalent languages.<br />To be successful at shortlisting stage, please ensure you clearly evidence in your application how you meet the essential and, where applicable, desirable criteria listed in the Candidate Information document linked on our website.</p>

<p>More at https://hrwebapp.qub.ac.uk/tlive_webrecruitment/wrd/run/ETREC107GF.open</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42810/bioinformatics-in-africa-part3-mali</guid>
	<pubDate>Sat, 06 Feb 2021 13:28:44 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42810/bioinformatics-in-africa-part3-mali</link>
	<title><![CDATA[Bioinformatics in Africa: Part3 - Mali]]></title>
	<description><![CDATA[<p>International&nbsp;Center&nbsp;for&nbsp;Excellence&nbsp;in&nbsp;Research&nbsp;(ICER):</p><p>The&nbsp;ICER&nbsp;is&nbsp;a&nbsp;research&nbsp;center&nbsp;composed&nbsp;of&nbsp;the&nbsp;following&nbsp;three&nbsp;programs: 1. The&nbsp;Malaria&nbsp;Research&nbsp;and&nbsp;Training&nbsp;Center&nbsp;&shy;&nbsp;Parasitology&nbsp;Group,&nbsp; 2. The&nbsp;Malaria&nbsp;Research&nbsp;and&nbsp;Training&nbsp;Center&nbsp;&shy;&nbsp;Entomology&nbsp;Group&nbsp; 3. The&nbsp;SEREFO&nbsp;Group.</p><p>The&nbsp;first&nbsp;two&nbsp;programs&nbsp;develop&nbsp;biomedical&nbsp;researches&nbsp;in&nbsp;malaria,&nbsp;Filariasis&nbsp;and&nbsp;Leishmaniasis.&nbsp;The&nbsp; third&nbsp;program&nbsp;develops&nbsp;biomedical&nbsp;researches&nbsp;in&nbsp;tuberculosis&nbsp;and&nbsp;HIV.</p><p>Bioinformatics&nbsp;was&nbsp;introduced&nbsp;recently&nbsp;to&nbsp;the&nbsp;ICER&nbsp;and&nbsp;is&nbsp;constantly&nbsp;growing.&nbsp;The&nbsp;ICER&nbsp;has&nbsp;one&nbsp; team,&nbsp;headed&nbsp;by&nbsp;Sidy&nbsp;SOUMARE,&nbsp;which&nbsp;supports&nbsp;the&nbsp;three&nbsp;programmes&nbsp;in&nbsp;all&nbsp;their&nbsp;needs&nbsp;in&nbsp; informatics&nbsp;and&nbsp;bioinformatics.&nbsp;This&nbsp;team&nbsp;can&nbsp;beneficiate&nbsp;from&nbsp;some&nbsp;computational&nbsp;facilities&nbsp;(4&nbsp; blast&nbsp;servers,&nbsp;15&nbsp;other&nbsp;servers&nbsp;and&nbsp;around&nbsp;200&nbsp;terminals),&nbsp;but&nbsp;the&nbsp;ICER&nbsp;staff&nbsp;needs&nbsp;some&nbsp;training&nbsp;in&nbsp; order&nbsp;to&nbsp;be&nbsp;able&nbsp;to&nbsp;administrate&nbsp;these&nbsp;facilities.</p><p>Research&nbsp;Interest&nbsp;and&nbsp;Activities: The&nbsp;following&nbsp;are&nbsp;the&nbsp;present&nbsp;areas&nbsp;of&nbsp;research&nbsp;interest: 1. Functional&nbsp;genomics 2. Analysis&nbsp;of&nbsp;microarray&nbsp;data 3. Interaction&nbsp;between&nbsp;the&nbsp;vector&nbsp;and&nbsp;the&nbsp;parasite.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics</guid>
	<pubDate>Wed, 20 Aug 2014 22:09:21 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/14218/pimp-your-brain-bioinformatics</link>
	<title><![CDATA[Pimp your brain: Bioinformatics]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/KqelGy6Q8nE" frameborder="0" allowfullscreen></iframe>Jan Lisec from the Max Planck Institute of Molecular Plant Physiology explains, in this "pimp your brain" episode, what bioinformatics is and why bioinformatics is so important and indispensable for biological research.

In the video serial "Pimp your brain" scientists from the Max Planck Institute of Molecular Plant Physiology describe their research. More videos from the 'Pimp your brain' serial are available on www.youtube.com/playlist?list=PL-l9VItC9Gn2Ur2Xj6PTOAkjLUlVPbIOO

More videos are available on www.mpimp-golm.mpg.de]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning</guid>
	<pubDate>Fri, 01 Jul 2016 12:57:12 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/28200/machine-learning</link>
	<title><![CDATA[Machine Learning !!!]]></title>
	<description><![CDATA[<p>In machine learning, computers apply&nbsp;<strong>statistical learning</strong>&nbsp;techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.</p>
<p><em>Keep scrolling.</em>&nbsp;Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.</p><p>Address of the bookmark: <a href="http://www.r2d3.us/visual-intro-to-machine-learning-part-1/" rel="nofollow">http://www.r2d3.us/visual-intro-to-machine-learning-part-1/</a></p>]]></description>
	<dc:creator>Gudiya Pal</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</guid>
	<pubDate>Fri, 26 Apr 2019 16:19:41 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/39307/awk-for-beginners</link>
	<title><![CDATA[AWK for beginners !]]></title>
	<description><![CDATA[<p>AWK is a standard tool on every POSIX-compliant UNIX system. It&rsquo;s like flex/lex, from the command-line, perfect for text-processing tasks and other scripting needs. It has a C-like syntax, but without mandatory semicolons (although, you should use them anyway, because they are required when you&rsquo;re writing one-liners, something AWK excels at), manual memory management, or static typing. It excels at text processing. You can call to it from a shell script, or you can use it as a stand-alone scripting language.</p><p>Why use AWK instead of Perl? Readability. AWK is easier to read than Perl. For simple text-processing scripts, particularly ones that read files line by line and split on delimiters, AWK is probably the right tool for the job.</p><div><pre><span>#!/usr/bin/awk -f</span>

<span># Comments are like this</span>


<span># AWK programs consist of a collection of patterns and actions.</span>
<span>pattern1</span> <span>{</span> <span>action</span><span>;</span> <span>}</span> <span># just like lex</span>
<span>pattern2</span> <span>{</span> <span>action</span><span>;</span> <span>}</span>

<span># There is an implied loop and AWK automatically reads and parses each</span>
<span># record of each file supplied. Each record is split by the FS delimiter,</span>
<span># which defaults to white-space (multiple spaces,tabs count as one)</span>
<span># You can assign FS either on the command line (-F C) or in your BEGIN</span>
<span># pattern</span>

<span># One of the special patterns is BEGIN. The BEGIN pattern is true</span>
<span># BEFORE any of the files are read. The END pattern is true after</span>
<span># an End-of-file from the last file (or standard-in if no files specified)</span>
<span># There is also an output field separator (OFS) that you can assign, which</span>
<span># defaults to a single space</span>

<span>BEGIN</span> <span>{</span>

    <span># BEGIN will run at the beginning of the program. It's where you put all</span>
    <span># the preliminary set-up code, before you process any text files. If you</span>
    <span># have no text files, then think of BEGIN as the main entry point.</span>

    <span># Variables are global. Just set them or use them, no need to declare..</span>
    <span>count</span> <span>=</span> <span>0</span><span>;</span>

    <span># Operators just like in C and friends</span>
    <span>a</span> <span>=</span> <span>count</span> <span>+</span> <span>1</span><span>;</span>
    <span>b</span> <span>=</span> <span>count</span> <span>-</span> <span>1</span><span>;</span>
    <span>c</span> <span>=</span> <span>count</span> <span>*</span> <span>1</span><span>;</span>
    <span>d</span> <span>=</span> <span>count</span> <span>/</span> <span>1</span><span>;</span> <span># integer division</span>
    <span>e</span> <span>=</span> <span>count</span> <span>%</span> <span>1</span><span>;</span> <span># modulus</span>
    <span>f</span> <span>=</span> <span>count</span> <span>^</span> <span>1</span><span>;</span> <span># exponentiation</span>

    <span>a</span> <span>+=</span> <span>1</span><span>;</span>
    <span>b</span> <span>-=</span> <span>1</span><span>;</span>
    <span>c</span> <span>*=</span> <span>1</span><span>;</span>
    <span>d</span> <span>/=</span> <span>1</span><span>;</span>
    <span>e</span> <span>%=</span> <span>1</span><span>;</span>
    <span>f</span> <span>^=</span> <span>1</span><span>;</span>

    <span># Incrementing and decrementing by one</span>
    <span>a</span><span>++</span><span>;</span>
    <span>b</span><span>--</span><span>;</span>

    <span># As a prefix operator, it returns the incremented value</span>
    <span>++</span><span>a</span><span>;</span>
    <span>--</span><span>b</span><span>;</span>

    <span># Notice, also, no punctuation such as semicolons to terminate statements</span>

    <span># Control statements</span>
    <span>if</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span>
        <span>print</span> <span>"Starting with count of 0"</span><span>;</span>
    <span>else</span>
        <span>print</span> <span>"Huh?"</span><span>;</span>

    <span># Or you could use the ternary operator</span>
    <span>print</span> <span>(</span><span>count</span> <span>==</span> <span>0</span><span>)</span> <span>?</span> <span>"Starting with count of 0"</span> <span>:</span> <span>"Huh?"</span><span>;</span>

    <span># Blocks consisting of multiple lines use braces</span>
    <span>while</span> <span>(</span><span>a</span> <span>&lt;</span> <span>10</span><span>)</span> <span>{</span>
        <span>print</span> <span>"String concatenation is done"</span> <span>" with a series"</span> <span>" of"</span>
            <span>" space-separated strings"</span><span>;</span>
        <span>print</span> <span>a</span><span>;</span>

        <span>a</span><span>++</span><span>;</span>
    <span>}</span>

    <span>for</span> <span>(</span><span>i</span> <span>=</span> <span>0</span><span>;</span> <span>i</span> <span>&lt;</span> <span>10</span><span>;</span> <span>i</span><span>++</span><span>)</span>
        <span>print</span> <span>"Good ol' for loop"</span><span>;</span>

    <span># As for comparisons, they're the standards:</span>
    <span># a &lt; b   # Less than</span>
    <span># a &lt;= b  # Less than or equal</span>
    <span># a != b  # Not equal</span>
    <span># a == b  # Equal</span>
    <span># a &gt; b   # Greater than</span>
    <span># a &gt;= b  # Greater than or equal</span>

    <span># Logical operators as well</span>
    <span># a &amp;&amp; b  # AND</span>
    <span># a || b  # OR</span>

    <span># In addition, there's the super useful regular expression match</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>
    <span>if</span> <span>(</span><span>"boo"</span> <span>!~</span> <span>"^fo+$"</span><span>)</span>
        <span>print</span> <span>"Boo!"</span><span>;</span>

    <span># Arrays</span>
    <span>arr</span><span>[</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>arr</span><span>[</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>

    <span># You can also initialize an array with the built-in function split()</span>

    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo:bar:baz"</span><span>,</span> <span>arr</span><span>,</span> <span>":"</span><span>);</span>

    <span># You also have associative arrays (actually, they're all associative arrays)</span>
    <span>assoc</span><span>[</span><span>"foo"</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>assoc</span><span>[</span><span>"bar"</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>

    <span># And multi-dimensional arrays, with some limitations I won't mention here</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"foo"</span><span>;</span>
    <span>multidim</span><span>[</span><span>0</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"bar"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>0</span><span>]</span> <span>=</span> <span>"baz"</span><span>;</span>
    <span>multidim</span><span>[</span><span>1</span><span>,</span><span>1</span><span>]</span> <span>=</span> <span>"boo"</span><span>;</span>

    <span># You can test for array membership</span>
    <span>if</span> <span>(</span><span>"foo"</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>"Fooey!"</span><span>;</span>

    <span># You can also use the 'in' operator to traverse the keys of an array</span>
    <span>for</span> <span>(</span><span>key</span> <span>in</span> <span>assoc</span><span>)</span>
        <span>print</span> <span>assoc</span><span>[</span><span>key</span><span>];</span>

    <span># The command line is in a special array called ARGV</span>
    <span>for</span> <span>(</span><span>argnum</span> <span>in</span> <span>ARGV</span><span>)</span>
        <span>print</span> <span>ARGV</span><span>[</span><span>argnum</span><span>];</span>

    <span># You can remove elements of an array</span>
    <span># This is particularly useful to prevent AWK from assuming the arguments</span>
    <span># are files for it to process</span>
    <span>delete</span> <span>ARGV</span><span>[</span><span>1</span><span>];</span>

    <span># The number of command line arguments is in a variable called ARGC</span>
    <span>print</span> <span>ARGC</span><span>;</span>

    <span># AWK has several built-in functions. They fall into three categories. I'll</span>
    <span># demonstrate each of them in their own functions, defined later.</span>

    <span>return_value</span> <span>=</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>);</span>
    <span>string_functions</span><span>();</span>
    <span>io_functions</span><span>();</span>
<span>}</span>

<span># Here's how you define a function</span>
<span>function</span> <span>arithmetic_functions</span><span>(</span><span>a</span><span>,</span> <span>b</span><span>,</span> <span>c</span><span>,</span>     <span>d</span><span>)</span> <span>{</span>

    <span># Probably the most annoying part of AWK is that there are no local</span>
    <span># variables. Everything is global. For short scripts, this is fine, even</span>
    <span># useful, but for longer scripts, this can be a problem.</span>

    <span># There is a work-around (ahem, hack). Function arguments are local to the</span>
    <span># function, and AWK allows you to define more function arguments than it</span>
    <span># needs. So just stick local variable in the function declaration, like I</span>
    <span># did above. As a convention, stick in some extra whitespace to distinguish</span>
    <span># between actual function parameters and local variables. In this example,</span>
    <span># a, b, and c are actual parameters, while d is merely a local variable.</span>

    <span># Now, to demonstrate the arithmetic functions</span>

    <span># Most AWK implementations have some standard trig functions</span>
    <span>localvar</span> <span>=</span> <span>sin</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>cos</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>atan2</span><span>(</span><span>b</span><span>,</span> <span>a</span><span>);</span> <span># arc tangent of b / a</span>

    <span># And logarithmic stuff</span>
    <span>localvar</span> <span>=</span> <span>exp</span><span>(</span><span>a</span><span>);</span>
    <span>localvar</span> <span>=</span> <span>log</span><span>(</span><span>a</span><span>);</span>

    <span># Square root</span>
    <span>localvar</span> <span>=</span> <span>sqrt</span><span>(</span><span>a</span><span>);</span>

    <span># Truncate floating point to integer</span>
    <span>localvar</span> <span>=</span> <span>int</span><span>(</span><span>5.34</span><span>);</span> <span># localvar =&gt; 5</span>

    <span># Random numbers</span>
    <span>srand</span><span>();</span> <span># Supply a seed as an argument. By default, it uses the time of day</span>
    <span>localvar</span> <span>=</span> <span>rand</span><span>();</span> <span># Random number between 0 and 1.</span>

    <span># Here's how to return a value</span>
    <span>return</span> <span>localvar</span><span>;</span>
<span>}</span>

<span>function</span> <span>string_functions</span><span>(</span>    <span>localvar</span><span>,</span> <span>arr</span><span>)</span> <span>{</span>

    <span># AWK, being a string-processing language, has several string-related</span>
    <span># functions, many of which rely heavily on regular expressions.</span>

    <span># Search and replace, first instance (sub) or all instances (gsub)</span>
    <span># Both return number of matches replaced</span>
    <span>localvar</span> <span>=</span> <span>"fooooobar"</span><span>;</span>
    <span>sub</span><span>(</span><span>"fo+"</span><span>,</span> <span>"Meet me at the "</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "Meet me at the bar"</span>
    <span>gsub</span><span>(</span><span>"e+"</span><span>,</span> <span>"."</span><span>,</span> <span>localvar</span><span>);</span> <span># localvar =&gt; "m..t m. at th. bar"</span>

    <span># Search for a string that matches a regular expression</span>
    <span># index() does the same thing, but doesn't allow a regular expression</span>
    <span>match</span><span>(</span><span>localvar</span><span>,</span> <span>"t"</span><span>);</span> <span># =&gt; 4, since the 't' is the fourth character</span>

    <span># Split on a delimiter</span>
    <span>n</span> <span>=</span> <span>split</span><span>(</span><span>"foo-bar-baz"</span><span>,</span> <span>arr</span><span>,</span> <span>"-"</span><span>);</span> <span># a[1] = "foo"; a[2] = "bar"; a[3] = "baz"; n = 3</span>

    <span># Other useful stuff</span>
    <span>sprintf</span><span>(</span><span>"%s %d %d %d"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "Testing 1 2 3"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span> <span># =&gt; "oob"</span>
    <span>substr</span><span>(</span><span>"foobar"</span><span>,</span> <span>4</span><span>);</span> <span># =&gt; "bar"</span>
    <span>length</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; 3</span>
    <span>tolower</span><span>(</span><span>"FOO"</span><span>);</span> <span># =&gt; "foo"</span>
    <span>toupper</span><span>(</span><span>"foo"</span><span>);</span> <span># =&gt; "FOO"</span>
<span>}</span>

<span>function</span> <span>io_functions</span><span>(</span>    <span>localvar</span><span>)</span> <span>{</span>

    <span># You've already seen print</span>
    <span>print</span> <span>"Hello world"</span><span>;</span>

    <span># There's also printf</span>
    <span>printf</span><span>(</span><span>"%s %d %d %d\n"</span><span>,</span> <span>"Testing"</span><span>,</span> <span>1</span><span>,</span> <span>2</span><span>,</span> <span>3</span><span>);</span>

    <span># AWK doesn't have file handles, per se. It will automatically open a file</span>
    <span># handle for you when you use something that needs one. The string you used</span>
    <span># for this can be treated as a file handle, for purposes of I/O. This makes</span>
    <span># it feel sort of like shell scripting, but to get the same output, the string</span>
    <span># must match exactly, so use a variable:</span>

    <span>outfile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>

    <span>print</span> <span>"foobar"</span> <span>&gt;</span> <span>outfile</span><span>;</span>

    <span># Now the string outfile is a file handle. You can close it:</span>
    <span>close</span><span>(</span><span>outfile</span><span>);</span>

    <span># Here's how you run something in the shell</span>
    <span>system</span><span>(</span><span>"echo foobar"</span><span>);</span> <span># =&gt; prints foobar</span>

    <span># Reads a line from standard input and stores in localvar</span>
    <span>getline</span> <span>localvar</span><span>;</span>

    <span># Reads a line from a pipe (again, use a string so you close it properly)</span>
    <span>cmd</span> <span>=</span> <span>"echo foobar"</span><span>;</span>
    <span>cmd</span> <span>|</span> <span>getline</span> <span>localvar</span><span>;</span> <span># localvar =&gt; "foobar"</span>
    <span>close</span><span>(</span><span>cmd</span><span>);</span>

    <span># Reads a line from a file and stores in localvar</span>
    <span>infile</span> <span>=</span> <span>"/tmp/foobar.txt"</span><span>;</span>
    <span>getline</span> <span>localvar</span> <span>&lt;</span> <span>infile</span><span>;</span> 
    <span>close</span><span>(</span><span>infile</span><span>);</span>
<span>}</span>

<span># As I said at the beginning, AWK programs consist of a collection of patterns</span>
<span># and actions. You've already seen the BEGIN pattern. Other</span>
<span># patterns are used only if you're processing lines from files or standard</span>
<span># input.</span>
<span>#</span>
<span># When you pass arguments to AWK, they are treated as file names to process.</span>
<span># It will process them all, in order. Think of it like an implicit for loop,</span>
<span># iterating over the lines in these files. these patterns and actions are like</span>
<span># switch statements inside the loop. </span>

<span>/^fo+bar$/</span> <span>{</span>

    <span># This action will execute for every line that matches the regular</span>
    <span># expression, /^fo+bar$/, and will be skipped for any line that fails to</span>
    <span># match it. Let's just print the line:</span>

    <span>print</span><span>;</span>

    <span># Whoa, no argument! That's because print has a default argument: $0.</span>
    <span># $0 is the name of the current line being processed. It is created</span>
    <span># automatically for you.</span>

    <span># You can probably guess there are other $ variables. Every line is</span>
    <span># implicitly split before every action is called, much like the shell</span>
    <span># does. And, like the shell, each field can be access with a dollar sign</span>

    <span># This will print the second and fourth fields in the line</span>
    <span>print</span> <span>$</span><span>2</span><span>,</span> <span>$</span><span>4</span><span>;</span>

    <span># AWK automatically defines many other variables to help you inspect and</span>
    <span># process each line. The most important one is NF</span>

    <span># Prints the number of fields on this line</span>
    <span>print</span> <span>NF</span><span>;</span>

    <span># Print the last field on this line</span>
    <span>print</span> <span>$</span><span>NF</span><span>;</span>
<span>}</span>

<span># Every pattern is actually a true/false test. The regular expression in the</span>
<span># last pattern is also a true/false test, but part of it was hidden. If you</span>
<span># don't give it a string to test, it will assume $0, the line that it's</span>
<span># currently processing. Thus, the complete version of it is this:</span>

<span>$</span><span>0</span> <span>~</span> <span>/^fo+bar$/</span> <span>{</span>
    <span>print</span> <span>"Equivalent to the last pattern"</span><span>;</span>
<span>}</span>

<span>a</span> <span>&gt;</span> <span>0</span> <span>{</span>
    <span># This will execute once for each line, as long as a is positive</span>
<span>}</span>

<span># You get the idea. Processing text files, reading in a line at a time, and</span>
<span># doing something with it, particularly splitting on a delimiter, is so common</span>
<span># in UNIX that AWK is a scripting language that does all of it for you, without</span>
<span># you needing to ask. All you have to do is write the patterns and actions</span>
<span># based on what you expect of the input, and what you want to do with it.</span>

<span># Here's a quick example of a simple script, the sort of thing AWK is perfect</span>
<span># for. It will read a name from standard input and then will print the average</span>
<span># age of everyone with that first name. Let's say you supply as an argument the</span>
<span># name of a this data file:</span>
<span>#</span>
<span># Bob Jones 32</span>
<span># Jane Doe 22</span>
<span># Steve Stevens 83</span>
<span># Bob Smith 29</span>
<span># Bob Barker 72</span>
<span>#</span>
<span># Here's the script:</span>

<span>BEGIN</span> <span>{</span>

    <span># First, ask the user for the name</span>
    <span>print</span> <span>"What name would you like the average age for?"</span><span>;</span>

    <span># Get a line from standard input, not from files on the command line</span>
    <span>getline</span> <span>name</span> <span>&lt;</span> <span>"/dev/stdin"</span><span>;</span>
<span>}</span>

<span># Now, match every line whose first field is the given name</span>
<span>$</span><span>1</span> <span>==</span> <span>name</span> <span>{</span>

    <span># Inside here, we have access to a number of useful variables, already</span>
    <span># pre-loaded for us:</span>
    <span># $0 is the entire line</span>
    <span># $3 is the third field, the age, which is what we're interested in here</span>
    <span># NF is the number of fields, which should be 3</span>
    <span># NR is the number of records (lines) seen so far</span>
    <span># FILENAME is the name of the file being processed</span>
    <span># FS is the field separator being used, which is " " here</span>
    <span># ...etc. There are plenty more, documented in the man page.</span>

    <span># Keep track of a running total and how many lines matched</span>
    <span>sum</span> <span>+=</span> <span>$</span><span>3</span><span>;</span>
    <span>nlines</span><span>++</span><span>;</span>
<span>}</span>

<span># Another special pattern is called END. It will run after processing all the</span>
<span># text files. Unlike BEGIN, it will only run if you've given it input to</span>
<span># process. It will run after all the files have been read and processed</span>
<span># according to the rules and actions you've provided. The purpose of it is</span>
<span># usually to output some kind of final report, or do something with the</span>
<span># aggregate of the data you've accumulated over the course of the script.</span>

<span>END</span> <span>{</span>
    <span>if</span> <span>(</span><span>nlines</span><span>)</span>
        <span>print</span> <span>"The average age for "</span> <span>name</span> <span>" is "</span> <span>sum</span> <span>/</span> <span>nlines</span><span>;</span>
<span>}</span>
</pre><p><span>&nbsp;</span></p></div>]]></description>
	<dc:creator>BioJoker</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/view/19838</guid>
	<pubDate>Sat, 27 Dec 2014 13:30:15 -0600</pubDate>
	<link>https://bioinformaticsonline.com/view/19838</link>
	<title><![CDATA[Interview with a bioinformatician series ...]]></title>
	<description><![CDATA[<p>The aim of this series to interviews some notable bioinformaticians to get their views on various aspects of bioinformatics research. Hopefully these answers will prove useful to others in the field, especially to those who are just starting their bioinformatics careers.<br /><br />This series will be available at BOL every fortnight.<br /><br /><br /><br /></p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/35798/an-introduction-to-applied-bioinformatics</guid>
	<pubDate>Fri, 02 Mar 2018 04:26:38 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/35798/an-introduction-to-applied-bioinformatics</link>
	<title><![CDATA[An Introduction to Applied Bioinformatics]]></title>
	<description><![CDATA[<p>IAB is primarily being developed by&nbsp;<a href="http://caporasolab.us/people/greg-caporaso/">Greg Caporaso</a>(GitHub/Twitter:&nbsp;<a href="https://github.com/gregcaporaso">@gregcaporaso</a>) in the&nbsp;<a href="http://www.caporasolab.us/">Caporaso Lab</a>&nbsp;at&nbsp;<a href="http://www.nau.edu/">Northern Arizona University</a>. You can find information on the courses I teach on&nbsp;<a href="http://www.caporasolab.us/teaching">my teaching website</a>&nbsp;and information on my research and lab on&nbsp;<a href="http://www.caporasolab.us/">my lab website</a>.</p>
<p>&nbsp;</p><p>Address of the bookmark: <a href="http://readiab.org/" rel="nofollow">http://readiab.org/</a></p>]]></description>
	<dc:creator>Jit</dc:creator>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/42813/bioinformatics-in-africa-part5-nigeria</guid>
	<pubDate>Sat, 06 Feb 2021 21:13:47 -0600</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/42813/bioinformatics-in-africa-part5-nigeria</link>
	<title><![CDATA[Bioinformatics in Africa: Part5 - Nigeria]]></title>
	<description><![CDATA[<p>Covenant University (CU)&shy;Ota:<br />Covenant University (with her enriching and growing state&shy;of&shy;the&shy;art laboratories in the area of &nbsp;science and technology, arts, business and social sciences) is presently the Best University in &nbsp;Nigeria (Private University category), based on the recent over&shy;all rating just concluded by the &nbsp;Nigeria &nbsp; University &nbsp; Commission &nbsp; (NUC). &nbsp; Recently, &nbsp; Covenant &nbsp; University &nbsp; has &nbsp; initiated &nbsp; the &nbsp;establishment of a Centre for Applied Biotech, Bio&shy;Informatics and Microbiology (CBBM) to be &nbsp;situated at the University. The institute has been designed to be a Public&shy;Private Partnership for a productive synergy b/w Academia, Industry and Government. The whole concept is still evolving &nbsp;and more details will be release soon. As regards CBBM, a dedicated computing lab is in plan, but even our computing capacity is &nbsp;presently enormous. In the department of Computer and Information Sciences, we have more than &nbsp;250 Pentium 4 PCs set aside for teaching and research purposes. Furthermore, we have several &nbsp;moderate speed PCs at the Postgraduate research lab and our engineering departments and units. &nbsp;Our wet lab facilities is presently minimal (basic for teaching), the Centre requirement as it touches &nbsp;the wet&shy;laboratories is also set to upgrade this to basic tools expected at an international centre of learning.</p><p>University&nbsp;of&nbsp;Ibadan&nbsp;(UIB)&shy;Ibadan:<br />There&nbsp;has&nbsp;been&nbsp;significant&nbsp;increase&nbsp;in&nbsp;the&nbsp;number&nbsp;of&nbsp;bioinformatics&nbsp;activities&nbsp;in&nbsp;Nigeria&nbsp;(and&nbsp;West Africa)&nbsp;since&nbsp;2003&nbsp;when&nbsp;the&nbsp;program&nbsp;was&nbsp;initiated&nbsp;by&nbsp;the&nbsp;West&nbsp;African&nbsp;Biotechnology&nbsp;Workshops Series&nbsp;(WABWS,&nbsp;http://www.wabw.org)&nbsp;at&nbsp;the&nbsp;University&nbsp;of&nbsp;Ibadan,&nbsp;Nigeria&nbsp;(in&nbsp;collaboration&nbsp;with&nbsp; the&nbsp;South&nbsp;African&nbsp;National&nbsp;Bioinformatics&nbsp;Institute&nbsp;(SANBI,&nbsp;http:/www.sanbi.ac.za).&nbsp;Workshops&nbsp; that&nbsp;were&nbsp;open&nbsp;to&nbsp;scientists&nbsp;from&nbsp;all&nbsp;African&nbsp;countries&nbsp;have&nbsp;seen&nbsp;a&nbsp;very&nbsp;high&nbsp;number&nbsp;of&nbsp;applications&nbsp; from&nbsp;scientists&nbsp;based&nbsp;in&nbsp;West&nbsp;Africa.&nbsp;The&nbsp;encouraging&nbsp;desire&nbsp;to&nbsp;acquire&nbsp;cutting&shy;edge&nbsp;skills&nbsp;to&nbsp; computational&nbsp;process&nbsp;data&nbsp;and&nbsp;extract&nbsp;useful&nbsp;knowledge&nbsp;from&nbsp;genome&nbsp;projects&nbsp;led&nbsp;to&nbsp;the&nbsp;interest&nbsp;of&nbsp; the&nbsp;West&nbsp;African&nbsp;Biotechnology&nbsp;Workshops&nbsp;(WABW)&nbsp;to&nbsp;develop&nbsp;an&nbsp;agenda&nbsp;to&nbsp;address&nbsp;the&nbsp; bioinformatics&nbsp;skills&nbsp;gap&nbsp;among&nbsp;scientists&nbsp;in&nbsp;West&nbsp;Africa.&nbsp;An&nbsp;increased&nbsp;commitment&nbsp;from&nbsp;agencies&nbsp; like&nbsp;NEPAD&nbsp;would&nbsp;be&nbsp;required&nbsp;in&nbsp;the&nbsp;provision&nbsp;of&nbsp;infrastructure&nbsp;to&nbsp;establish&nbsp;and&nbsp;sustain&nbsp;regional&nbsp; and&nbsp;national&nbsp;networks.</p><p>University&nbsp;of&nbsp;Ilorin&nbsp;(UIL)&shy;Ilorin:<br />The&nbsp;University&nbsp;of&nbsp;Ilorin&nbsp;was&nbsp;established&nbsp;in&nbsp;1976&nbsp;by&nbsp;the&nbsp;Federal&nbsp;Government&nbsp;of&nbsp;Nigeria.&nbsp; Bioinformatics&nbsp;activities&nbsp;started&nbsp;at&nbsp;the&nbsp;University&nbsp;in&nbsp;February&nbsp;2003&nbsp;with&nbsp;the&nbsp;establishment&nbsp;of&nbsp;the&nbsp; West&nbsp;African&nbsp;Bioinformatics&nbsp;Research&nbsp;Initiative&nbsp;(WABRI).&nbsp;However,&nbsp;progress&nbsp;has&nbsp;been&nbsp;rather&nbsp;slow&nbsp; due&nbsp;to&nbsp;inadequate&nbsp;funding.&nbsp;We&nbsp;are&nbsp;mainly&nbsp;engaged&nbsp;in&nbsp;Bioinformatics&nbsp;training&nbsp;at&nbsp;the&nbsp;introductory&nbsp; level&nbsp;and&nbsp;proteomics&nbsp;studies&nbsp;on&nbsp;various&nbsp;species&nbsp;of&nbsp;malaria&nbsp;parasites.&nbsp;Recently,&nbsp;we&nbsp;became&nbsp;interested&nbsp; in&nbsp;comparative&nbsp;genome&nbsp;analysis&nbsp;of&nbsp;various&nbsp;species&nbsp;of &nbsp;Plasmodium&nbsp; and&nbsp;the&nbsp;comparison&nbsp;of&nbsp; chloroquine&nbsp;sensitive&nbsp;and&nbsp;chloroquine&nbsp;resistant&nbsp;strains&nbsp;of&nbsp;Plasmodium&nbsp;falciparum.&nbsp;Other&nbsp;activities&nbsp; and&nbsp;areas&nbsp;of&nbsp;interest&nbsp;can&nbsp;be&nbsp;seen&nbsp;on&nbsp;our&nbsp;website,&nbsp;http://www.wabri.org,&nbsp;although&nbsp;not&nbsp;all&nbsp;our&nbsp; proposed&nbsp;interests&nbsp;have&nbsp;been&nbsp;fully&nbsp;implemented&nbsp;due&nbsp;to&nbsp;our&nbsp;level&nbsp;of&nbsp;funding.</p><p>Training:<br />The&nbsp;University&nbsp;of&nbsp;Ilorin&nbsp;has&nbsp;introduced&nbsp;M.Sc.&nbsp;and&nbsp;Ph.D.&nbsp;programmes&nbsp;in&nbsp;Computer&nbsp;Science&nbsp;(with&nbsp; options&nbsp;in&nbsp;Bioinformatics).&nbsp;The&nbsp;programme&nbsp;is&nbsp;based&nbsp;in&nbsp;the&nbsp;Department&nbsp;of&nbsp;Computer&nbsp;Science&nbsp;and&nbsp; emphasis&nbsp;is&nbsp;on&nbsp;the&nbsp;development&nbsp;of&nbsp;algorithms&nbsp;to&nbsp;solve&nbsp;problems&nbsp;in&nbsp;bioinformatics. The&nbsp;Covenant&nbsp;University&nbsp;offers&nbsp;M.Sc.&nbsp;and&nbsp;Ph.D&nbsp;in&nbsp;Computer&nbsp;Science&nbsp;with&nbsp;option&nbsp;in&nbsp;Bioinformatics&nbsp; (Computational&nbsp;Biology).&nbsp;Furthermore,&nbsp;through&nbsp;affiliated&nbsp;departments,&nbsp;the&nbsp;CBBM&nbsp;is&nbsp;been&nbsp;design&nbsp;to&nbsp;award&nbsp;Diploma&nbsp;and&nbsp;Degree&nbsp;certificates&nbsp;in&nbsp;Biotechnology.</p><p>Web&nbsp;sites&nbsp;and&nbsp;links: http://www.covenantuniversity.com http://www.run.edu.ng http://www.uniben.edu http://www.wabri.org http://www.wabw.org http://www.unilorin.edu.ng http://www.wabri.org http://www.asopah.org</p>]]></description>
	<dc:creator>BioStar</dc:creator>
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