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Bioinformatics Carrer Opportunities

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Bioinformatics is the somewhat new and rather unfortunate term that is commonly employed for referring to the use of computers in biological research. Bioinformatics now looks like a hot cake. The number of jobs advertised for bioinformatics in Nature and Science magazine has increased by 96% bioinformatics job advertisements. According to the U.S. Bureau of Labor Statistics (BLS), the median annual salary for biological scientists, including bioinformatics scientists, was about $71,000 in 2011. Expected job growth for scientists in this category (including biochemists and biophysicists) is 31% between 2010 and 2020. According to BLS data, bioinformatics technicians are included under the umbrella of statistical assistants, whose mean salary was about $39,000 in 2011. The Department of Labor reports bioinformatics technicians will have job growth of 3% to 9% between 2010 and 2020. According to PayScale.com , however, the median salary for biotechnology research scientists with bioin...
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Find and Delete Core Dumps using PHP and Shell

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Linux sometimes dumps a huge file when a script crashes. These core files can build up and eat away valuable disk space. Some other methods of deleting core files will damage your server. Here are a few simple commands I use to find and delete these core dump files safely.
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Replacing form fields by text in PHP

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In PHP, the form field has replaced with the custom text after processing by either using an HTML file or hiding the form fields using the PHP script. This method can also be used for applying static header and footer on the web page. In the following example, I have used an HTML file and PHP script to add two numbers. The HTML file content has replaced during the execution. Before Execution After Execution Source Code: form.html <form method="post" action="<?php print $_SERVER['PHP_SELF']; ?>" > First Number: &nbsp;&nbsp;&nbsp;&nbsp;<input type="text" name="first"><br> Second Number: <input type="text" name="second"><br><br> <input type="reset" value="Reset"><input type="submit" value="Submit"> </form> addition.php <html> <head> <title>Adding two number...
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Running Swiss-PdbViewer on Ubuntu

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DeepView – Swiss-PdbViewer (or SPDBV) is an bioinformatics application that provides a user friendly graphical interface allowing to view and analyze protein and nucleic acid structure. This program is associated with Swiss-Model (an automated homology modeling server running in the Geneva Glaxo Welcome Experimental Research), accessible via the ExPASy web server. Through this application, proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and ...
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Embedding Perl into Perl

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This article describes embedding a Perl script into a Perl script. The program executes through Common Gateway Interface (CGI), which reads ASCII file through file upload method and displays content of the file. The Perl script upload.pl is called through the Perl script file-upload.pl using function eval{} . This program can be modified to call by reference function, to access other system programs too. file-upload.html <html> <head> <title>File Upload</title> </head> <body> <form method="post" action="/cgi-bin/file-upload.pl" enctype="multipart/form-data"> Enter the file to upload:<br> <input name="file" size="45" type="file"><br> <p> <input name="reset" type="reset"> <input name="submit" value="Upload" type=...
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RNA to Protein Translation in PERL

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In PERL programming, an RNA sequence can be translated to a protein sequence by substituting equivalent amino acid characters to triplet characters of RNA. This method has followed to find six reading frames (three in the forward direction, and three in the reverse direction). In this program, I have used the associative array (also known as a hash array) to associate triplet characters with amino acid characters. The associate array corresponding to codon table is arranged to 20 amino acid character. The triplet codon table is shown below: Source Code: print "Enter the RNA sequence: "; $rna = <>; chomp($rna); $rna =~s/[^acgu]//ig; my $rna = uc($rna); my(%genetic_code) = ( 'UCA' => 'S', # Serine 'UCC' => 'S', # Serine 'UCG' => 'S', # Serine 'UCU' => 'S', # Serine 'UUC' => 'F', # Phenylalanine 'UUU' => 'F...
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Running JAVA program in Linux Ubuntu

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The tutorial bellow explains simple procedure to compile, interpret, and execute Java program in Ubuntu using JDK sofware. Steps to run Java program in Ubuntu: 1. Go to Applications > Accessories > Terminal, to open terminal window. 2. Type the following in command line gedit Add.java 3. Enter the code bellow in the editor. /* Addition of two numbers – Add.java */ import java.io.*; class Add { public static void main(String args[]) { InputStreamReader ISR = new InputStreamReader(System.in); BufferedReader BR = new BufferedReader(ISR); int a = 0, b = 0; try { System.out.print("Enter the first number: "); a = Integer.parseInt(BR.readLine()); System.out.print("Enter the second number: "); b = Integer.parseInt(BR.readLine()); } catch(Exception e) { System.out.println("Check the program."); } System.out.println("Addition of " + a + " + " + b + " is " + (a+b)...
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