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How to use available Bioperl data to build evolutionary software?

Perl Bioinformatics Evolution Bioperl

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#1 Inbox

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Posted 23 August 2012 - 04:12 AM

How to use available Bioperl data to build evolutionary software? How one is supposed to use all available perl module for designing a evolutionary software? information regarding how to initialize with this would be great.
Thanks.

#2 hobglobin

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Posted 27 August 2012 - 08:54 AM

perhaps you should ask perlmunky, I guess he's one of the few here who know about perl

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#3 DELETEMYACCOUNTPLEASE

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Posted 03 September 2012 - 02:36 PM

Hmm, I don't really check this forum much anymore - fallen out of love with science.

How much perl do you know? Do you want to use existing code to write pipelines or do you wish to create your own versions of mr bayes? Perl is a great tool and very well supported by the biological community but ... there are nicer/faster languages if you don't want to make extensive use of bioperl (there is also biopython, biojava, bioclojure and biohaskell). If you are out to implement number crunching algorithms then you may want c/c++ or if you want to do machine learning you should consider python and scikits (also the scipy superpack - google it). Give me moar details ;)

#4 Inbox

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Posted 03 September 2012 - 08:32 PM

Thanks Perlmunky,
I know about Perl (Learner level), I just know how to install Perl strawberry, active perl and Padre. I have read about it in book- Beginning perl for Bioinformatics and now reading Mastering Perl for Bioinformatics. I can write some simple programs one mentioned in Beginning perl for Bioinformatics.
Right now I am interested in understanding how it works. Bioperl is resource of program already designed by programmers. I want to build Evolutionary Program Like one ( MEGA- Molecular Evolutionary Genetics analysis) with Bioperl available resources. Your help would be great importance for understanding.

#5 DELETEMYACCOUNTPLEASE

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Posted 04 September 2012 - 12:17 PM

right, you aren't aiming low then? If you are going to be making use of bioperl then i suspect you are going to want to use some modules to do things like fetching a parsing data - eg going to NCBI and pulling down a load of .fasta files, parsing out the sequences and building some phylogenetic trees, sequence alignments etc. You will find loads of this stuff in bioperl - the trick is mastering searching the bioperl repos - http://www.bioperl.o...i/Main_Page is the best place to start. I am not familiar with the state of Perl, cpan and bioperl but you should get your head around CPAN. You should also take a look at perl moose, testing and *creating and using objects.

* i 100% hate OO perl - even with moose.

TRY HERE http://doc.bioperl.org/bioperl-live/

Edited by perlmunky, 04 September 2012 - 12:25 PM.


#6 Inbox

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Posted 05 September 2012 - 01:06 AM

Hi,
Will I need GUI also?

#7 Inbox

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Posted 05 September 2012 - 02:34 AM

I am following following protocol,

Padre- Tool- Module tool- Install local distribution- BioPerl-1.6.901.tar.gz


But it is showing ,


--> Working on C:\Users\bhaskar\Desktop\perl\BioPerl-1.6.901.tar.gz
Fetching file://C:/Users/bhaskar/Desktop/perl/BioPerl-1.6.901.tar.gz ... OK
Configuring BioPerl-1.006901 ... OK
==> Found dependencies: Data::Stag
! Finding Data::Stag on cpanmetadb failed.
! Finding Data::Stag on search.cpan.org failed.
! cannot open file '/.cpanm/sources/http%search.cpan.org%CPAN/02packages.details
.txt.gz': No such file or directory opening compressed index
! Couldn't find module or a distribution Data::Stag
! Bailing out the installation for BioPerl-1.006901. Retry with --prompt or --fo
rce.
Press any key to continue . . .

#8 DELETEMYACCOUNTPLEASE

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Posted 11 September 2012 - 12:00 PM

Don't bother with a gui until you have got a working algorithm. I also wouldn't consider using perl/tk for a GUI, I would wrap it as a web service (consider looking at something like perl catalyst but much lighter weight, google sinatra for perl)

I don't use windows machines, it's all OS X and Linux. I would strongly advise anyone doing bioinformatics work (or just those with a passing interest) getting a copy of Ubuntu (free, it's linux) and doing your magic there.

#9 Inbox

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Posted 13 September 2012 - 04:55 AM

Don't bother with a gui until you have got a working algorithm. I also wouldn't consider using perl/tk for a GUI, I would wrap it as a web service (consider looking at something like perl catalyst but much lighter weight, google sinatra for perl)

I don't use windows machines, it's all OS X and Linux. I would strongly advise anyone doing bioinformatics work (or just those with a passing interest) getting a copy of Ubuntu (free, it's linux) and doing your magic there.


I will be starting with Ubuntu, I have used it before. Thanks.





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