Posted by Ashok Kumar on July 3rd, 2010
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. Read the rest of this entry »
Posted by Ashok Kumar on June 6th, 2010
This article describes embedding a Perl script into a Perl script. This program is an Common Gateway Interface, which reads ASCII files through file upload 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 in other programs too.
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Posted by Ashok Kumar on March 9th, 2010
In PERL programing, RNA sequence is converted into protein sequence by substituting equivalent amino acid characters to triplet characters of RNA. This method is followed to find six reading frame (three in forward direction, and three in reverse direction). In this program, I have used associative array (also known as hash array) to associate triplet characters with amino acid character.
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Posted by Ashok Kumar on February 21st, 2010
The protocols and tools under Simulation allow you to run energy calculations, solvation, energy minimization, and molecular dynamics simulations using the CHARMm and other programs.
The protocols under Simulation serve the following types of users:
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Posted by Ashok Kumar on January 18th, 2010
Experimental structure determination involves difficult methods that require a significant amount of expertise and resources. Protein Modeling on the other hand enables access to sensible structural models in much shorter periods of time. The major aim of protein modeling is the prediction of a protein’s tertiary structure from its primary structure. To this end a diverse range of approaches have been developed comparative, de novo or ab initio structure prediction.
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Posted by Ashok Kumar on December 16th, 2009
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 Read the rest of this entry »
Posted by Ashok Kumar on December 14th, 2009
Many people know from their own experience that it’s not easy to install an Apache web server and it gets harder if you want to add MySQL, PHP and Perl.
XAMPP is an easy to install Apache distribution containing MySQL, PHP and Perl. XAMPP is really very easy to install and to use – just download, extract and start.
At the moment there are four XAMPP distributions:
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Posted by Ashok Kumar on December 8th, 2009
HTML with PHP :-
HTML: add.htm
<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<form action=”add.php” method=”post”>
Enter the first number: <input type=”text” name=”a” size=10><br>
Enter the second number: <input type=”text” name=”b” size=10><br>
<input type=”submit” name=”submit” value=”ADD”>
</form>
</body>
</html>
PHP: add.php
<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<?php
$a=$_POST["a"];
$b=$_POST["b"];
$c=$a+$b;
print “Addition of $a and $b is $c.”;
?>
</body>
</html>
Only with PHP :-
<?php
$a = $_POST["a"];
$b = $_POST["b"];
if (!isset($_POST['add']))
{ // If page is not submitted to itself echo the form
?>
<html>
<head><title>Adding Two Numbers</title></head>
<body>
<form method=”post” action=”<?php echo $PHP_SELF; ?>”>
Enter the first number: <input type=”text” size=”12″ maxlength=”12″ name=”a”></br>
Enter the second number: <input type=”text” size=”12″ maxlength=”36″ name=”b”></br>
<input type=”submit” value=”ADD” name=”add”>
</form>
<?
}
else
{
$c=$a+$b;
print “Addition of $a and $b is $c.”;
}
?>
</body>
</html>
HTML with PHP :-
HTML: add.htm
<html>
<head>
<title>Adding two numbers</title>
</head>
<body>
<form action=”add.php” method=”post”>
Read the rest of this entry »
Posted by Ashok Kumar on December 8th, 2009
[Modem0]
Modem = /dev/rfcomm0
Baud = 115200
SetVolume = 0
Dial Command = ATDT
Init1 = ATZ
Init3= ATM0
FlowControl = CRTSCTS
[Dialer vodafone]
Username = “vodafone”
Password = “vodafone”
Phone = *99#
Stupid Mode = 1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
Init3 = AT+CGDCONT=1,”10.10.1.100:9401″,”portalnmms”,”",0,0
Inherits = Modem0
[Dialer three]
Username = “none”
Password = “none”
Phone = *99#
Stupid Mode = 1
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
Init3 = AT+CGDCONT=1,”10.10.1.100:9401″,”portalnmms”,”",0,0
Inherits = Modem0
[Modem0]
Modem = /dev/rfcomm0
Posted by Ashok Kumar on December 4th, 2009
Steps to run C program in Ubuntu:
1. Go to Applications > Accessories > Terminal, to open terminal window.
2. Type the following in command line
sudo gedit first.c Read the rest of this entry »
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