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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/42810?offset=750</link>
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	<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction</guid>
	<pubDate>Wed, 21 Feb 2024 06:19:41 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44472/pipesnake-bioinformatics-best-practice-analysis-pipeline-for-phylogenomic-reconstruction</link>
	<title><![CDATA[pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction]]></title>
	<description><![CDATA[<p dir="auto"><span>ausarg/pipesnake</span>&nbsp;is a bioinformatics best-practice analysis pipeline for phylogenomic reconstruction starting from short-read 'second-generation' sequencing data.</p>
<p dir="auto">The pipeline is built using&nbsp;<a href="https://www.nextflow.io/">Nextflow</a>, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The&nbsp;<a href="https://www.nextflow.io/docs/latest/dsl2.html">Nextflow DSL2</a>&nbsp;implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.</p><p>Address of the bookmark: <a href="https://github.com/AusARG/pipesnake" rel="nofollow">https://github.com/AusARG/pipesnake</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10380/ra-at-alagappa-university</guid>
  <pubDate>Sun, 04 May 2014 23:33:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA at ALAGAPPA UNIVERSITY]]></title>
  <description><![CDATA[
<p>DEPARTMENT OF BIOTECHNOLOGY<br />(UGC SAP and DST-FIST &amp; PURSE Sponsored Department)<br />ALAGAPPA UNIVERSITY<br />(A State University Accredited by NAAC with „A‟ Grade)<br />Karaikudi - 630 004, India</p>

<p>WALK IN INTERVIEW</p>

<p>A walk-in Interview for the following position tenable at the Bioinformatics Infrastructure Facility (BIF), Department of Biotechnology, Alagappa University will be held at the Department of Biotechnology, Alagappa University, Karaikudi 630 003 on 15.05.2014 (Thursday) at 01:00 PM. This national facility is funded by the Department of Biotechnology, Ministry of Science and Technology, Government of India, New Delhi. The main objectives of the Centre involve teaching and research activities in bioinformatics/biotechnology.</p>

<p>RA (One Post):</p>

<p>Salary : Rs. 11000 p.m. plus admissible HRA</p>

<p>Qualification: M.Sc., in Bioinformatics/Biotechnology/Biophysics/Biochemistry/ Life Sciences</p>

<p>Interested candidates are encouraged to send their Curriculum Vitae by email to “sk_pandian@rediffmail.com” in advance. On the day of interview, the candidates must produce original certificates in proof of their educational qualification and experience and a recommendation letter from the Head of the Department/Institution where last studied/worked. Candidates who have already passed the required Degree alone are eligible to appear for interview. No TA&amp;DA will be given for attending the interview.</p>

<p>Advertisement: http://www.alagappabiotech.org/Walk%20in%20interview.pdf</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</guid>
	<pubDate>Mon, 24 Nov 2025 05:16:49 -0600</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44930/bioinformatics-the-bridge-between-curiosity-and-discovery</link>
	<title><![CDATA[Bioinformatics: The Bridge Between Curiosity and Discovery]]></title>
	<description><![CDATA[<p>In the sprawling universe of modern science, bioinformatics stands as one of the most transformative and empowering fields of our time. It is where biology meets computation, where data becomes meaning, and where curiosity becomes discovery. If you&rsquo;ve stepped into this world&mdash;or are considering it&mdash;here&rsquo;s your reminder: you&rsquo;re part of a revolution.</p><p><strong>Why Bioinformatics Matters More Than Ever</strong></p><p>Every day, our world generates massive amounts of biological data&mdash;from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.</p><p>Bioinformatics isn&rsquo;t just a skill.<br />It&rsquo;s the language of the future of biology.</p><p>By mastering it, you give yourself the power to:</p><p>Decode genomes and understand life at its most fundamental level</p><p>Identify patterns no microscope could ever reveal</p><p>Predict disease outbreaks before they occur</p><p>Accelerate drug discovery with computational precision</p><p>Contribute to open-source tools that empower scientists worldwide</p><p>You don&rsquo;t just follow science&mdash;you drive it.</p><p><strong>Every Expert Was Once a Beginner</strong></p><p>Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.</p><p>But here&rsquo;s the truth: every bioinformatician started exactly where you are now&mdash;curious, unsure, but excited.</p><p>No one writes perfect code on day one.</p><p>No one understands genomics pipelines immediately.</p><p>What makes you a bioinformatician is not perfection, but perseverance.</p><p>When your script throws a cryptic error&hellip;<br />When your data refuses to format&hellip;<br />When your pipeline runs for 6 hours only to crash&hellip;</p><p>Remember: this is part of the journey.<br />Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.</p><p>Bioinformatics Is Not Just a Career&mdash;It&rsquo;s a Mindset</p><p>It&rsquo;s the mindset of:</p><p>Problem-solving.</p><p>Continuous learning.</p><p>Turning chaos into clarity.</p><p>Seeing what others can&rsquo;t.</p><p>Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.</p><p><strong>Your Contribution Matters</strong></p><p>As you work on your script, pipeline, genome, or model, remember:</p><p>Somewhere, your analysis might contribute to:</p><p>A new therapy</p><p>A faster diagnostic test</p><p>A better understanding of a pathogen</p><p>A more resilient crop</p><p>An open-source dataset that helps thousands</p><p>A discovery that rewrites textbooks</p><p>Your code may be small, but its ripple effect is powerful.</p><p>The Future Is Bioinformatics&mdash;And You Are Part of It</p><p>The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.</p><p>This is a golden era&mdash;and you are not late.<br />You are exactly where you need to be.</p><p>Keep Pushing. Keep Learning. Keep Discovering.</p><p>Bioinformatics is a journey filled with challenges, but also with unmatched rewards.</p><p>So the next time you feel stuck, frustrated, or overwhelmed, remember:<br />You&rsquo;re building the science of tomorrow.</p><p>Be proud. Stay curious. Keep going.<br />Your work matters more than you think.</p>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10459/associate-professor-bio-informatics-at-university-of-allahabad-in-allahabad</guid>
  <pubDate>Wed, 07 May 2014 00:26:53 -0500</pubDate>
  <link></link>
  <title><![CDATA[Associate Professor - Bio-Informatics at University of Allahabad in Allahabad]]></title>
  <description><![CDATA[
<p>No of vacancies: 01</p>

<p>Pay scale: Pay Band of Rs. 37400-67000 with AGP of Rs. 9000.</p>

<p>i. Educational Qualification: Good academic record with a Ph.D. Degree in the concerned/allied/relevant disciplines.</p>

<p>ii. A Master's Degree with at least 55% marks (or an equivalent grade in a point scale wherever grading system is followed).</p>

<p>iii. A minimum of eight years of experience of teaching and/or research in an academic/research position equivalent to that of Assistant Professor in a University, College or Accredited Research Institution/industry excluding the period of Ph.D. research with evidence of published work and a minimum of 5 publications as books and/or research/policy papers.</p>

<p>iv. Contribution to educational innovation, design of new curricula and courses, and technology - mediated teaching learning process with evidence of having guided doctoral candidates and research students.</p>

<p>v. A minimum score as stipulated in the Academic Performance Indicator (API) based Performance Based Appraisal System (PBAS), set out in UGC Regulation.</p>

<p>Download application form from website: http://www.allduniv.ac.in/</p>

<p>Send your application to the Registrar, University of Allahabad, Allahabad-211002 (U.P.) on or before 30th April 2014</p>

<p>For more details: http://www.allduniv.ac.in/images/adv/backlog/advt-details.pdf OR http://www.allduniv.ac.in/images/news/extension-notice.pdf</p>

<p>Last Apply Date: 30 May 2014</p>
]]></description>
</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>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation</guid>
	<pubDate>Sat, 10 May 2014 04:41:22 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/10664/dna-replication-process-3d-animation</link>
	<title><![CDATA[DNA Replication Process [3D Animation]]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/27TxKoFU2Nw" frameborder="0" allowfullscreen></iframe>See an organised list of all the animations: http://doctorprodigious.wordpress.com/hd-animations/]]></description>
	
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43431/code-golf</guid>
	<pubDate>Wed, 06 Oct 2021 04:17:29 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43431/code-golf</link>
	<title><![CDATA[Code Golf]]></title>
	<description><![CDATA[<p>Code Golf is a game designed to let you show off your code-fu by solving problems in the least number of characters.</p>
<p>Since this is your first time here, I suggest starting with something simple like&nbsp;<a href="https://code.golf/fizz-buzz">Fizz Buzz</a>.</p><p>Address of the bookmark: <a href="https://code.golf/" rel="nofollow">https://code.golf/</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>

<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10748/bioinformatics-phd-at-cuk-kerala</guid>
  <pubDate>Sat, 10 May 2014 20:21:22 -0500</pubDate>
  <link></link>
  <title><![CDATA[Bioinformatics PhD at CUK Kerala]]></title>
  <description><![CDATA[
<p>Applications are invited from highly motivated students (UGC-CSIR-JRF) with a background in Genomics/ Biotechnology/ Molecular Microbiology/ Biochemistry and Bioinformatics to pursue research leading to Ph.D. in the following areas;</p>

<p>    1. Cancer Genomics</p>

<p>    2. Microbial Genetics and Metagenomics</p>

<p>    3. Human Infective Diseases</p>

<p>    4. Computational Drug Design</p>

<p>Interested candidates may apply to Dr. Ranjith N. Kumavath, Assistant Professor &amp; Head, Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Padannakad (PO), Nileshwar, Kasaragod-671328,Kerala. Email: RNkumavath@gmail.com</p>
]]></description>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43681/a-guide-to-machine-learning-for-biologists</guid>
	<pubDate>Tue, 28 Dec 2021 01:43:25 -0600</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43681/a-guide-to-machine-learning-for-biologists</link>
	<title><![CDATA[A guide to machine learning for biologists]]></title>
	<description><![CDATA[<p>Because of the increasing size and inherent complexity of biological data, there has been an increase in the application of machine learning in biology to create useful and predictive models of the underlying biological processes. All machine learning techniques fit models to data; nevertheless, the specific methods are highly variable and can appear baffling at first glance. In this Review, we hope to give readers a moderate introduction to a few fundamental machine learning techniques, including the most recently created and frequently used deep neural network techniques. We illustrate how different algorithms may be adapted to specific types of biological data, as well as some best practises and points to consider when embarking on machine learning studies. There is also discussion of several upcoming directions in machine learning methodology.</p><p>Address of the bookmark: <a href="https://www.nature.com/articles/s41580-021-00407-0" rel="nofollow">https://www.nature.com/articles/s41580-021-00407-0</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</guid>
	<pubDate>Tue, 06 Aug 2024 23:51:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/44633/learn-python-with-example</link>
	<title><![CDATA[Learn python with example]]></title>
	<description><![CDATA[<div><div><div><p>There are over 21 unique&nbsp;Python project&nbsp;walkthroughs in this content that range from beginner to advanced. See below for the timestamps for these projects:</p><p><span>00:00:00 | How To Navigate These Projects</span><br /><span>---</span><br /><span>00:01:46 | #1 - Quiz Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fquiz_game.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/quiz_game.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:22:00 | #2 - Number Guessing Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fnumber_guesser.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/number_guesser.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:39:49 | #3 - Rock, Paper, Scissors (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Frock_paper_scissors.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/rock_paper_scissors.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>00:54:40 | #4 - Choose Your Own Adventure Game (Easy)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2Fblob%2Fmain%2Fchoose_your_own_adventure.py" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/blob/main/choose_your_own_adventure.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:06:47 | #5 - Password Manager (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F5-Python-Projects-For-Beginners%2F" target="_blank">https://github.com/techwithtim/5-Python-Projects-For-Beginners/</a><span>&nbsp;</span><br /><span>Fernet Cryptography Documentation:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fcryptography.io%2Fen%2Flatest%2Ffernet%2F" target="_blank">https://cryptography.io/en/latest/fernet/</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:37:37 | #6 - PIG (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject1.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project1.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>01:59:07 | #7 - Madlibs Generator (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject2.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project2.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:15:04 | #8 - Timed Math Challenge (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects%2Fblob%2Fmain%2Fproject3.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects/blob/main/project3.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>02:28:02 | #9 - Slot Machine (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Slot-Machine" target="_blank">https://github.com/techwithtim/Python-Slot-Machine</a><span>&nbsp;</span><br /><span>---</span><br /><span>03:20:43 | #10 - Turtle Racing (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FTurtle-Racing-V2" target="_blank">https://github.com/techwithtim/Turtle-Racing-V2</a><span>&nbsp;</span><br /><span>Turtle Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Flibrary%2Fturtle.html" target="_blank">https://docs.python.org/3/library/turtle.html</a><span>&nbsp;</span><br /><span>---</span><br /><span>04:13:09 | #11 - WPM Typing Test (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FWPM_Typing_Test" target="_blank">https://github.com/techwithtim/WPM_Typing_Test</a><span>&nbsp;</span><br /><span>Curses Docs:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fdocs.python.org%2F3%2Fhowto%2Fcurses.html" target="_blank">https://docs.python.org/3/howto/curses.html</a><span>&nbsp;</span><br /><span>05:09:43 | #12 - Alarm Clock (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>Sound Effects:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fwww.fesliyanstudios.com%2Froyalty-free-sound-effects-download%2Falarm-203" target="_blank">https://www.fesliyanstudios.com/royalty-free-sound-effects-download/alarm-203</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:22:07 | #13 - Password Generator (Easy)</span><br /><span>Python Project Idea Blog:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fhackr.io%2Fblog%2Fpython-projects" target="_blank">https://hackr.io/blog/python-projects</a><span>&nbsp;</span><br /><span>---</span><br /><span>05:39:16 | #14 - Shortest Path Finder (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fpath-finder.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/path-finder.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:14:53 | #15 - NBA Stats &amp; Current Scores (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fnba-scores.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/nba-scores.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>06:38:22 | #16 - Currency Converter (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2F3-Mini-Python-Projects-For-Intermediates%2Fblob%2Fmain%2Fcurrency-converter.py" target="_blank">https://github.com/techwithtim/3-Mini-Python-Projects-For-Intermediates/blob/main/currency-converter.py</a><span>&nbsp;</span><br /><span>API: https://free.currencyconverterapi.com/</span><br /><span>---</span><br /><span>06:58:51 | #17 - YouTube Video Downloader (Medium)</span><br /><span>Code: &nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fyoutube.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/youtube.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:09:50 | #18 - Automated File Backup (Medium)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Beginner-Automation-Projects%2Fblob%2Fmain%2Fbackup.py" target="_blank">https://github.com/techwithtim/Python-Beginner-Automation-Projects/blob/main/backup.py</a><span>&nbsp;</span><br /><span>---</span><br /><span>07:21:18 | #19 - Mastermind/4 Color Match (Advanced)</span><br /><span>---</span><br /><span>07:48:20 | #20 - Aim Trainer (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Aim-Trainer" target="_blank">https://github.com/techwithtim/Python-Aim-Trainer</a><span>&nbsp;</span><br /><span>---</span><br /><span>08:39:20 | #21 - Advanced Python Scripting (Advanced)</span><br /><span>Code:&nbsp;</span><a href="https://morioh.com/redirect?id=65b0752318cf2dc4d28010e1&amp;own=5ff684ea1a53c42123416f96&amp;l=https%3A%2F%2Fgithub.com%2Ftechwithtim%2FPython-Scripting-Project" target="_blank">https://github.com/techwithtim/Python-Scripting-Project</a><span>&nbsp;</span></p></div></div></div>]]></description>
	<dc:creator>BioStar</dc:creator>
</item>

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