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	<title><![CDATA[BOL: Related items]]></title>
	<link>https://bioinformaticsonline.com/related/21703?offset=340</link>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/10841/ra-at-iisr-kozhikode</guid>
  <pubDate>Thu, 15 May 2014 10:08:09 -0500</pubDate>
  <link></link>
  <title><![CDATA[RA at IISR Kozhikode]]></title>
  <description><![CDATA[
<p>INDIAN INSTITUTE OF SPICES RESEARCH<br />(Indian Council of Agricultural Research)<br />Marikunnu P.O., Kozhikode – 673 012, Kerala</p>

<p>Walk- in- Test cum Interview (based on test) for the selection of Research Associate</p>

<p>under the scheme “Distributed Information Sub Centre –DISC” &amp; Research Assistant under scheme “Phytophthora, Fusarium and Ralstonia diseases of Horticultural and Field Crops” will be held at this Institute as per details indicated below.</p>

<p>WALK -IN- TEST CUM INTERVIEW</p>

<p>Name of the post : Research Associate</p>

<p>Date of Interview : 21-05-2014 at 10.00 AM</p>

<p>No. of posts : One</p>

<p>Qualifications : a)Essential</p>

<p>Ph.D Degree in Bioinformatics OR :  Masters degree in Bioinformatics with a minimum of<br />60% marks or equivalent OGPA with at least two years research experience as evidenced from fellowship/ associateship/training/published papers etc.</p>

<p>b)Desirable: Experience in NGS data analysis.</p>

<p>Emoluments : Rs. 23,000/- per month + HRA (Masters Degree Holders)</p>

<p>Rs. 24,000/- per month + HRA (Ph.D Degree Holders)</p>

<p>Upper age limit : 40 years for Men &amp; 45 years for Women as on date of Interview (Upper Age limits are relaxable for SC, ST and OBC candidates as per Govt. of India norms (at present 5 years for SC/ST and 3 years for OBC)</p>

<p>Duration of Project : Till 31-03-2017.</p>

<p>Title of Assigment : Research Assistant (on contract basis)</p>

<p>No. of vacancy : One</p>

<p>Qualification : Essential : Post Graduation in Bioinformatics and  Minimum one year experience in NGS data analysis</p>

<p>Desirable : Experience in Perl/Python/R</p>

<p>Remuneration : Rs. 20,000/- per month (consolidated)</p>

<p>Scope of work :</p>

<p>1. Analysis of different file formats and their conversions.</p>

<p>2. Assessing the quality of data and filtering of raw reads.<br />3. Assembling the raw reads-de novo as well as reference  mapping.<br />4. Compression of aligned reads using Jam tools<br />5. RNA-seq. Analysis<br />6. Differential expression testing involving Normalization,  Statistical testing, heat map generation &amp; hierarchical  clustering<br />7. Annotating the assembled genome and geneet testing  and their validation<br />8. Metabolic pathway analysis<br />9. Comparative genomics<br />10. Setting up of genome browsers.</p>

<p>Period of Assigment : Initially for six months.</p>

<p>Date &amp; Venue of Interview : 21-05-2014 at IISR, Kozhikode at 10.00 AM</p>

<p>More at http://www.spices.res.in/pdf/disc-advtmnt.pdf</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>
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  <guid isPermaLink='true'>https://bioinformaticsonline.com/opportunity/view/11000/professorassociate-professor-assistant-professor-at-chettinad-academy-of-research-and-education</guid>
  <pubDate>Sat, 24 May 2014 00:00:15 -0500</pubDate>
  <link></link>
  <title><![CDATA[Professor/Associate Professor/ Assistant Professor at Chettinad Academy of Research and Education]]></title>
  <description><![CDATA[
<p>OPEN FACULTY POSITION</p>

<p>Chettinad Academy of Research and Education (CARE) invites applications from eligible and translational research-oriented candidates to the posts of Professor/Associate Professor/ Assistant Professor  Computational Biology, Bioinformatics, and Pharmaceutical Chemistry.</p>

<p>Emoluments: As per UGC norms (Adequate Compensation for Postdoctoral/Teaching experience)</p>

<p>Candidates fulfilling the eligibility criteria as per the UGC norms can send their full CV with copies of certificates and reference letters to the following address by post or by e-mail on or before 31st May 2014</p>

<p>The Registrar,<br />Chettinad Academy of Research and Education,<br />Chettinad Health City<br />Kelambakkam, Chennai 603 103<br />Tamil Nadu<br />T +91 (0)44 4741 1000<br />F +91 (0)44 4741 1011<br />Email: jobs @chettinadhealthcity.com</p>

<p>Advertisement: http://182.73.176.163/chc/ads2014.pdf</p>
]]></description>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/blog/view/43550/basic-structure-of-snakemake-pipeline-run</guid>
	<pubDate>Thu, 14 Oct 2021 07:01:38 -0500</pubDate>
	<link>https://bioinformaticsonline.com/blog/view/43550/basic-structure-of-snakemake-pipeline-run</link>
	<title><![CDATA[Basic Structure of Snakemake Pipeline Run !]]></title>
	<description><![CDATA[<div>/user/snakemake-demo$ ls</div><div>config.json data envs scripts slurm-240702.out Snakefile</div><ul>
<li>data = mock data for the snakefile to use</li>
<li>Snakefile = name of the snakemake &ldquo;formula&rdquo; file
<ul>
<li>Note: The default file that snakemake looks for in the current working directory is the&nbsp;<code>Snakefile</code>. If you would like to override that you can specify it following the&nbsp;<code>-s</code>
<ul>
<li><code>snakemake -s snakefile.py</code></li>
</ul>
</li>
</ul>
</li>
<li>envs = directory for storing the conda environments that the workflow will use.</li>
<li>scripts = directory for storing python scripts called by the snakemake formula.</li>
<li>config.json = json format file with extra parameters for our snakemake file to use.</li>
<li>cluster.json = json format file with specification for running on the HPC</li>
<li>samples.txt = file we will use later relating to the config.json file.</li>
</ul><p><span>Run the snakemake file as a dry run (the example workflow shown above).</span></p><ul>
<li>This will build a DAG of the jobs to be run without actually executing them.</li>
<li><code>snakemake --dry-run</code></li>
</ul><p>User can e<span>xecute rules of interest.</span></p><ul>
<li><code>snakemake --dry-run all</code>&nbsp;VS.&nbsp;<code>snakemake --dry-run call</code>&nbsp;VS.&nbsp;<code>snakemake --dry-run bwa</code></li>
</ul><p><span>Run the snakemake file in order to produce an image of the DAG of jobs to be run.</span></p><ul>
<li><code>snakemake --dag | dot -Tsvg &gt; dag.svg</code>&nbsp;OR&nbsp;<code>snakemake --dag | dot -Tsvg &gt; dag.svg</code></li>
</ul><p>Run the snakemake (this time not as a dry run)</p><ol>
<li><code>snakemake --use-conda</code></li>
</ol>]]></description>
	<dc:creator>Abhi</dc:creator>
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<item>
  <guid isPermaLink='true'>https://bioinformaticsonline.com/researchlabs/view/11107/the-minerva-research-group-for-bioinformatics</guid>
  <pubDate>Tue, 27 May 2014 15:48:14 -0500</pubDate>
  <link></link>
  <title><![CDATA[The Minerva Research Group for Bioinformatics]]></title>
  <description><![CDATA[
<p>The focus of the bioinformatics group is to use computational approaches to gain an insight into genome evolution in primates.</p>

<p>http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27</p>

<p>Kelso Group<br />Department of Evolutionary Genetics<br />Max Planck Institute for Evolutionary Anthropology<br />Deutscher Platz 6<br />04103 Leipzig<br />Germany<br />Phone: +49 341 3550 500</p>

<p>Job: <br />http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40</p>
]]></description>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44543/seeing-theory-and-learn</guid>
	<pubDate>Tue, 04 Jun 2024 00:31:54 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44543/seeing-theory-and-learn</link>
	<title><![CDATA[Seeing Theory and Learn]]></title>
	<description><![CDATA[<p>Seeing Theory was created by Daniel Kunin while an undergraduate at Brown University. The goal of this website is to make statistics more accessible through interactive visualizations (designed using Mike Bostock&rsquo;s JavaScript library D3.js).</p><p>Address of the bookmark: <a href="https://seeing-theory.brown.edu/" rel="nofollow">https://seeing-theory.brown.edu/</a></p>]]></description>
	<dc:creator>LEGE</dc:creator>
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	<guid isPermaLink="true">https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server</guid>
	<pubDate>Fri, 06 Jun 2014 16:18:43 -0500</pubDate>
	<link>https://bioinformaticsonline.com/pages/view/11582/monitor-running-jobs-on-linux-server</link>
	<title><![CDATA[Monitor running jobs on Linux server]]></title>
	<description><![CDATA[<p>You as a bioinformatican run lots of program on your servers. Sometime the shared server is also used by your colleague. If server is busy you sometime need to check the running programs and want to monitor the running programs as well. The "top" command will come in handy when you need to find out if things are still running, how long they&rsquo;ve been running, or how much memory is being used.<br /><br />&lsquo;top&rsquo; is very simple to run: type<br /><br />%% top<br /><br />You&rsquo;ll get a screen that looks like this, and is updated regularly:<br /><br /><img src="http://bioinformaticsonline.com/mod/photo/top.png" width="659" height="582" alt="image" style="border: 0px;"><br />Simple, right? Heh.<br /><br />First! Note that you can use &lsquo;q&rsquo; or &lsquo;CTRL-C&rsquo; to exit from &lsquo;top&rsquo;.<br /><br />Now let&rsquo;s read and understand at each line independently.<br /><br />The first line:<br /><br />top - 23:00:48 up 39 days,&nbsp; 2 user,&nbsp; load average: 0.00, 0.00, 0.00<br /><br />The first line tells you the current time, how long the machine has been up, how many users are logged in, and the short/medium/long-term compute load on the machine. If you run something for a long time, you&rsquo;ll see these numbers go up. Right now, the machine is basically just sitting there, so these are all close to 0.<br /><br />The second line:</p><p>Tasks:&nbsp; 239 total,&nbsp;&nbsp; 1 running,&nbsp; 238 sleeping,&nbsp;&nbsp; 0 stopped,&nbsp;&nbsp; 0 zombie<br /><br />This line tells you how many processes are running. If you are using laptops machines it&rsquo;s not so interesting because you really are the only one using this machine.<br /><br />Cpu(s):&nbsp; 0.0%us,&nbsp; 0.0%sy,&nbsp; 0.0%ni,100.0%id,&nbsp; 0.0%wa,&nbsp; 0.0%hi,&nbsp; 0.0%si,&nbsp; 0.0%st<br /><br />This line contains the CPU load. The first two numbers are how busy the system is doing computation (&ldquo;us&rdquo; stands for &ldquo;user&rdquo;) and how busy the system is doing system-y things like accessing disks or network (&ldquo;sy&rdquo; stands for &ldquo;system&rdquo;). We&rsquo;ll talk more about this later.<br /><br />Mem:&nbsp;&nbsp; 49457320k total,&nbsp;&nbsp;&nbsp; 3492174k used,&nbsp; 14535596k free,&nbsp;&nbsp;&nbsp; 1435148k buffers<br /><br />This should be easy to understand &ndash; how much memory you&rsquo;re using! <br /><br />Swap:&nbsp;&nbsp; 539356k total,&nbsp;&nbsp; 28332k used,&nbsp;&nbsp; 836562k free,&nbsp;&nbsp;&nbsp; 29862014k cached<br /><br />Swap is just on-disk memory that can be used to &ldquo;swap&rdquo; out programs from main memory. Again, we&rsquo;ll talk about this later.:<br /><br />PID USER&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PR&nbsp; NI&nbsp; VIRT&nbsp; RES&nbsp; SHR S %CPU %MEM&nbsp;&nbsp;&nbsp; TIME+&nbsp; COMMAND<br />&nbsp; 1 root&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 39 &nbsp; 19&nbsp; 0&nbsp; 0&nbsp; 0 S&nbsp; 0.0&nbsp; 0.0&nbsp;&nbsp; 246:57.22 kipmi0<br />&nbsp; 2 root&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; RT&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp; 0 S&nbsp; 0.0&nbsp; 0.0&nbsp;&nbsp; 0:00.00 migration/0<br /><br />And... finally! What&rsquo;s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing&rsquo;s running so the numbers aren&rsquo;t very interesting, but just wait until we run something...</p>]]></description>
	<dc:creator>Jitendra Narayan</dc:creator>
</item>
<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/44620/diy-transcriptomics</guid>
	<pubDate>Wed, 31 Jul 2024 01:19:26 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/44620/diy-transcriptomics</link>
	<title><![CDATA[DIY Transcriptomics]]></title>
	<description><![CDATA[<p><span>A semester-long course covering best practices for the analysis of high-throughput sequencing data from gene expression (RNA-seq) studies, with a primary focus on empowering students to be independent in the use of lightweight and open-source software using the R programming language and the Bioconductor suite of packages. This course follows a hybrid format in which online lectures are paired with in-person labs where students participate in hands-on, live coding exercises using real &lsquo;omic datasets. The course is focused on datasets and topics central to infectious disease research, immunology, and One-Health, but the concepts and approaches covered are applicable to any genomic study.</span></p>
<p>https://diytranscriptomics.com</p><p>Address of the bookmark: <a href="https://diytranscriptomics.com" rel="nofollow">https://diytranscriptomics.com</a></p>]]></description>
	<dc:creator>Abhi</dc:creator>
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<item>
	<guid isPermaLink="true">https://bioinformaticsonline.com/videolist/watch/11355/genomics-and-personalized-medicine-breakthroughs</guid>
	<pubDate>Sun, 01 Jun 2014 23:40:14 -0500</pubDate>
	<link>https://bioinformaticsonline.com/videolist/watch/11355/genomics-and-personalized-medicine-breakthroughs</link>
	<title><![CDATA[Genomics and Personalized Medicine Breakthroughs]]></title>
	<description><![CDATA[<iframe width="" height="" src="https://www.youtube-nocookie.com/embed/VAR-1vNc0TE" frameborder="0" allowfullscreen></iframe>http://bit.ly/e8QGzY Human genome mapping is now enabling a breakthrough in medical innovation -- personalized medicine. What does this mean for patients? We can now identify predispositions to disease, predict how we metabolize drugs, and figure out what kinds of treatments we may respond to, and even determine when a drug may give us an adverse reaction. All medical specialties benefit from human genome intelligence -- oncology saw the first impacts -- but advances are now being seen in cardiology, obstetrics and gynecology, pediatric diseases, gastroenterology, rheumatology, immunology and other areas. This video covers the areas that genetic medicine is impacting and where the future of genomic medicine is heading.]]></description>
	
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	<guid isPermaLink="true">https://bioinformaticsonline.com/bookmarks/view/43273/understanding-kmer</guid>
	<pubDate>Wed, 18 Aug 2021 04:27:51 -0500</pubDate>
	<link>https://bioinformaticsonline.com/bookmarks/view/43273/understanding-kmer</link>
	<title><![CDATA[Understanding kmer !]]></title>
	<description><![CDATA[<p><a href="https://en.wikipedia.org/wiki/k-mer">What is a&nbsp;<em>k-mer</em>&nbsp;anyway?</a><span>&nbsp;A&nbsp;</span><em>k-mer</em><span>&nbsp;is just a sequence of&nbsp;</span><em>k</em><span>&nbsp;characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get&nbsp;</span><em>all k-mers</em><span>&nbsp;from a sequence you need to get the first&nbsp;</span><em>k</em><span>&nbsp;characters, then move just a single character for the start of the next&nbsp;</span><em>k-mer</em><span>&nbsp;and so on. Effectively, this will create sequences that overlap in&nbsp;</span><code>k-1</code><span>&nbsp;positions.</span></p><p>Address of the bookmark: <a href="https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/" rel="nofollow">https://bioinfologics.github.io/post/2018/09/17/k-mer-counting-part-i-introduction/</a></p>]]></description>
	<dc:creator>BioStar</dc:creator>
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