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Bioprogramming

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<h1><span style="font-size: x-large"><strong><b><span lang="EN-US"strong>Bioinformatics</span></bstrong></strong></span></h1> <p style="font-family: -apple-system-font; line-height: 16px"><span style="font-size: larger"><span lang="EN-US">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.</span></span></p> <p style="font-family: -apple-system-font; line-height: 16px"><b><span lang="EN-US"strong>&nbsp;</span></bstrong></p> <h1><span style="font-size: x-large"><strong><span lang="EN-US">Bioprogramming</span></strong></span></h1> <p style="font-family: -apple-system-font; line-height: 16px"><bstrong><span style="font-size: larger"><span lang="EN-US">Bioprogramming </span></span></bstrong><span style="font-size: larger"><span lang="EN-US">is all programming</span><span lang="EN-US">&nbsp;activities for analyzing biological data.</span></span></p> <p style="font-family: -apple-system-font; line-height: 16px"><b><span lang="EN-US"strong>&nbsp;</span></bstrong></p> <h2><span style="font-size: larger"><strong><b><span lang="EN-US"strong>Programming</span></bstrong></strong></span></h2> <p style="font-family: -apple-system-font; line-height: 16px"><bstrong><span style="font-size: larger"><span lang="EN-US">Programming </span></span></bstrong><span style="font-size: larger"><span lang="EN-US">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. </span></span></p> <p style="font-family: -apple-system-font; line-height: 16px"><span style="font-size: larger"><span lang="EN-US">The <bstrong>computer </bstrong>is the electrical machine or device that carries out the programs. Computers exist in many different forms such as desktop, laptop, tablet, and etc. <br /></span></span></p> <p style="font-family: -apple-system-font; line-height: 16px"><b><span lang="EN-US"strong>&nbsp;</span></bstrong></p> <h3 style="margin-left: 40px"><span style="font-size: larger"><strong><b><span lang="EN-US"strong>Compiler</span></bstrong></strong></span></h3> <p style="font-family: -apple-system-font; margin-left: 40px; line-height: 16px"><bstrong><span style="font-size: larger"><span lang="EN-US">Compiler </span></span></bstrong><span style="font-size: larger"><span lang="EN-US">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<sup>++</sup>, for example, has c language. They are classified according to the languages and the operating systems.</span></span></p><p style="font-family: -apple-system-font; line-height: 16px">&nbsp;</p><h3 style="margin-left: 40px"><span style="font-size: larger"><strong><b><span lang="EN-US">Programming language</span></b></strong></span></h3><p style="font-family: -apple-system-font; margin-left: 40px; line-height: 16px"><b><span style="font-size: larger"><span lang="EN-US">Programming languages </span></span></b><span style="font-size: larger"><span lang="EN-US">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. <b>Grammar </b>is the rule of the languages.<br /></span></span></p><p style="font-family: -apple-system-font; line-height: 16px">&nbsp;</p><h2><span style="font-size: larger"><strong>Perl programming</strong></span></h2><p><span style="font-size: larger">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.&nbsp;</span><span style="font-size: larger">An operating system of perl is basically Linux but almost systems support the program.&nbsp;</span></p><p><span style="font-size: larger"><a href="http://perl.org">site(perl.org)</a></span></p><p style="margin-left: 40px">&nbsp;</p><h3 style="margin-left: 40px"><span style="font-size: larger"><strong>BioPerl programming</strong></span></h3><p style="margin-left: 40px"><span style="font-size: larger">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.</span></p><p style="margin-left: 40px"><span style="font-size: larger"><a href="http://bioperl.org">site(bioperl.org)</a></span></p><p style="margin-left: 40px">&nbsp;</p><h2><strong><span style="font-size: larger">BioOS</span></strong></h2><p><span style="font-size: larger">BioOS denotes an operationg system for bioinformatics</span></p><p><span style="font-size: larger"><a href="http://bioos.org">site(bioos.org)&nbsp;</a></span></p>
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 <h3 style="margin-left:40px"><span style="font-size:larger"><strong><strong>Programming language</strong></strong></span></h3> <p style="margin-left:40px"><strong><span style="font-size:larger">Programming languages </span></strong><span style="font-size:larger">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. <strong>Grammar </strong>is the rule of the languages.</span></p> <p>&nbsp;</p> <h2><span style="font-size:larger"><strong>Perl programming</strong></span></h2> <p><span style="font-size:larger">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.&nbsp;</span><span style="font-size:larger">An operating system of perl is basically Linux but almost systems support the program.&nbsp;</span></p> <p><span style="font-size:larger"><a href="http://perl.org">site(perl.org)</a></span></p> <p style="margin-left:40px">&nbsp;</p> <h3 style="margin-left:40px"><span style="font-size:larger"><strong>BioPerl programming</strong></span></h3> <p style="margin-left:40px"><span style="font-size:larger">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.</span></p> <p style="margin-left:40px"><span style="font-size:larger"><a href="http://bioperl.org">site(bioperl.org)</a></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive">Homework source:</span></span></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive">&nbsp;#!/usr/bin/perl<br />use strict;<br />use warnings;</span></span></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive">use Path::Class;<br />use autodie; # die if problem reading or writing a file</span></span></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive">my $dir = dir(&quot;C:/Temp&quot;); # C:/Temp<br />print &quot;The Fasta File will be generated in C:/Temp\n&quot;;<br />print &quot;The name of file is FASTA20131369.txt.\n&quot;;<br />my $file = $dir-&gt;file(&quot;file.txt&quot;); # C:/Temp/FASTA20131369.txt</span></span></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive"># Get a file_handle (IO::File object) you can write to<br />my $file_handle = $file-&gt;openw();</span></span></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive">my @list = (&#39;&gt;Your_first_seq&#39;, &#39;ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA<br />ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA<br />ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA<br />ATATATATATATATATAATATATATATATATATAATATATATATATATATAATATATATATATATATA&#39;);</span></span></span></p> <p style="margin-left:40px"><span class="marker"><span style="font-size:8px"><span style="font-family:comic sans ms,cursive">foreach my $line ( @list ) {<br />&nbsp; &nbsp; # Add the line to the file<br />&nbsp; &nbsp; $file_handle-&gt;print($line . &quot;\n&quot;);<br />}</span></span></span></p> <h2><strong><span style="font-size:larger">BioOS</span></strong></h2> <p><span style="font-size:larger">BioOS denotes an operationg system for bioinformatics</span></p> <p><span style="font-size:larger"><a href="http://bioos.org">site(bioos.org)&nbsp;</a></span></p> <p>&nbsp;</p> <h2><span style="font-size: larger"><strong>Other languages for Bioinformatics</strong></span></h2> 
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<li><span style="font-size: larger;"><a href="http://en.wikipedia.org/wiki/R_(programming_language)">R</a></span></li> <li><a href="http://en.wikipedia.org/wiki/S_(programming_language)"><span style="font-size: larger;">S</span></a></li> <li><a href="http://en.wikipedia.org/wiki/MATLAB"><span style="font-size: larger;">Matlab</span></a></li>
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<p>Perl tutorial:&nbsp; http://raven.iab.alaska.edu/~ntakebay/teaching/programming/perl1st/index.html</p>
 
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