Bioprogramming

Bioinformatics

In bioinformatics, all biological data are regarded as information. So, by combining various fields such as computer science and statistics, the information is analyzed and studied.

 

Bioprogramming

Bioprogramming is all programming activities for analyzing biological data.

 

Programming

Programming is a process that makes new algorithm from programming languages called codes through a compiler. It can convert a set of programming languages into executable programs. Programs can perform various activities like computation, analysis, algorithmic flow, and more.

The computer is the electrical machine or device that carries out the programs. Computers exist in many different forms such as desktop, laptop, tablet, and etc.

 

Compiler

Compiler is a program that transforms programming languages into computer languages. With this process, computer can recognize the commands. The compilers have own specific programming language. C⁺⁺, for example, has c language. They are classified according to the languages and the operating systems.

 

Programming language

Programming languages are generally high-level languages that are used in coding by programmers.If you compare the programming to a country, then the language is the communication medium. The 3 major types of bioprogramming languages are S, R, and Matlab. All of them are for statistical and computational use. Grammar is the rule of the languages.

 

Perl programming

Perl is a programming language that supports scripts called a script lanuguage. It is developed by Larry wall in 1987. It is a powerful tool for varied applications such as network programming, finance, and bioinformatics. An operating system of perl is basically Linux but almost systems support the program. 

site(perl.org)

 

BioPerl programming

BioPerl is a collection of Perl modules for biological data processing. It is an open source software for biological applications in bioinformatics. In the Human Genome Project, the program has played a central role.

site(bioperl.org)

Homework source:

 #!/usr/bin/perl
use strict;
use warnings;

use Path::Class;
use autodie; # die if problem reading or writing a file

my $dir = dir("C:/Temp"); # C:/Temp
print "The Fasta File will be generated in C:/Temp\n";
print "The name of file is FASTA20131369.txt.\n";
my $file = $dir->file("file.txt"); # C:/Temp/FASTA20131369.txt

# Get a file_handle (IO::File object) you can write to
my $file_handle = $file->openw();

my @list = ('>Your_first_seq', 'ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA
ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA
ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA
ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA');

foreach my $line ( @list ) {
    # Add the line to the file
    $file_handle->print($line . "\n");
}

BioOS

BioOS denotes an operationg system for bioinformatics

site(bioos.org) 

 

Other languages for Bioinformatics

• R
• S
• Matlab

 

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Perl tutorial:  http://raven.iab.alaska.edu/~ntakebay/teaching/programming/perl1st/index.html