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Programming Language of Choice

Everything on bioinformatics, the science of information technology as applied to biological research.

Moderator: BioTeam

Perl or Java or Awk or Python ?

Poll ended at Wed May 11, 2005 3:54 am

Perl
0
No votes
Java
1
33%
Awk
0
No votes
Python
2
67%
Other(plz Specify)
0
No votes
 
Total votes : 3

Programming Language of Choice

Postby cytochromeP » Wed May 04, 2005 3:54 am

Which is the programming language of choice for doing Bio-informatics research ?
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Postby mith » Wed May 04, 2005 4:29 am

Perl and java can be used online, dunno about the others though.
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Postby Chris4 » Thu May 05, 2005 9:03 am

Does anyone here use programming in biology?
I want to get started with a language but im pretty much a beginner when it comes to programming. So I need something fairly easy. I am fairly confident with computers and this will just be a hobby. for now.
I am looking at python as i used it at a workshop i went to and i know its used a lot in biology.
I initially want to use for it for Systems Biology. Creating models of pathways and systems. And then making predictions about the pathway etc.
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A Simple Perl DNA profile script

Postby cytochromeP » Thu May 05, 2005 12:22 pm

#!/usr/bin/perl

$dnaseq='ggggaccccattggggcccc';

$counter=0;

while($dnaseq=~/a/g){
$counter++;
}

print 'adenine: '.$counter*100/length($dnaseq).' %';

#the above code wud print the % of adenine in the given DNA sequence
#to run the programme save the code in a file 'dnaseq.pl'
#and execute it by the command
# perl dnaseq.pl
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Postby ac83 » Sat May 07, 2005 6:19 am

I'm doing a bioinformatics degree in uni right now. It doesn't seem like there's really anyone out there with the training that knows what is going on truly with both the computer side and the bio side.
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Postby cyberpostdoc » Fri Jun 03, 2005 2:57 am

Perl > java > c/c++

JSP PHP

MySQL oracle
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Postby Chris4 » Fri Jun 03, 2005 8:39 am

ac83 wrote:I'm doing a bioinformatics degree in uni right now. It doesn't seem like there's really anyone out there with the training that knows what is going on truly with both the computer side and the bio side.


lol. Thats true. Same with systems biology. Should be a problem really, but im not sure it is at the moment. As long as it works. :o
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Postby biostudent84 » Mon Jun 13, 2005 6:35 pm

cyberpostdoc wrote:Perl > java > c/c++


EEEEEK! A linux zealot! Kill it! Kill it!!!!!!!!!!

hahahahaha
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Postby b_d_41501 » Mon Jun 13, 2005 7:28 pm

I program with Visual Basic 6.0. lol, i know this is different from the topic right?. lol
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Postby biostudent84 » Mon Jun 13, 2005 7:41 pm

b_d_41501 wrote: lol, i know this is different from the topic right?. lol


*shrugs* No worries.
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Postby b_d_41501 » Mon Jun 13, 2005 7:43 pm

lol. I'm not very good at the whole programming thing. :lol:
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Postby biostudent84 » Mon Jun 13, 2005 8:14 pm

b_d_41501 wrote:lol. I'm not very good at the whole programming thing. :lol:


Me neither. But if you want to go into pure biology, not medicine, you really need to learn a little programming. It is becoming more and more needed in the biological world. Especially with the advent of bioinformatics.
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