[Bioperl-l] Fwd: Code to contribute

Chris Fields cjfields at illinois.edu
Fri Aug 15 09:59:42 EDT 2008


Agreed!

We're hoping to move to a more structured core after 1.6 which will  
require decent documentation and tests for inclusion.  My feeling is  
one should free to add code samples to relevant pages/sections in the  
BioPerl wiki, or write up your own HOWTO (it's not terribly hard to  
do, and it adds to your karma).

chris

On Aug 14, 2008, at 8:17 PM, Smithies, Russell wrote:

> You forgot 2 points,
>
> vi) write documentation/examples, and  vii) write tests
>
> ;-)
>
>
>
> Russell
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
> [mailto:bioperl-l-bounces at lists.open-
>> bio.org] On Behalf Of Rutger Vos
>> Sent: Friday, 15 August 2008 11:52 a.m.
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] Fwd: Code to contribute
>>
>> Sounds exciting! I bet the general advice you'll get is to i) check
>> out the latest code from svn ii) see which bioperl objects/interfaces
>> (e.g. Bio::Seq) you'd use to integrate your algorithm into bioperl
>> iii) write a class that performs the algorithm as some sort of
>> analysis factory taking the sequence object (or ideally object
>> interface) as an input iv) run that class by the mailing list v)  
>> check
>> it into svn.
>>
>> On Thu, Aug 14, 2008 at 4:37 PM, Michael Janis <mjanis at chem.ucla.edu>
> wrote:
>>> Hi,
>>>
>>>
>>>
>>> I've had some perl code lying around for what seems like forever and
> I'd
>>> like to contribute it to bioperl, if such facilities don't already
> exist in
>>> bioperl.  The code implements shuffling (DNA or RNA) keeping the
>>> dinucleotide composition (and codon usage) intact through a Eularian
> path
>>> approach as described in Altschul and Erickson (1985).  The code
> seeds the
>>> Eularian paths by keeping the first and last nucleotide invariant in
> the
>>> shuffle - which has minimal detrimental effects to the purpose of
> the
>>> algorithm, in my experience.
>>>
>>>
>>>
>>> A quick search on the bioperl website shows that there is a
> mutation.pls
>>> script, and facilities for using Sean Eddy's SQUID C library, which
>>> implements the same function (I wrote this particular function
> before I knew
>>> how to use C).  As such, it's probably not as elegant as Sean Eddy's
>>> implementation, but it works - and it's entirely in perl.
>>>
>>>
>>>
>>> The bioperl developer pages suggest a post to the mailing list as
> the best
>>> place to start contributing to bioperl.  Is this a useful function
> to add to
>>> the project?
>>>
>>>
>>>
>>> Best Regards,
>>>
>>>
>>>
>>> Michael
>>>
>>>
>>>
>>> -------------------------------
>>>
>>> Michael Janis
>>>
>>> <mailto:mjanis at chem.ucla.edu> mjanis at chem.ucla.edu
>>>
>>> -------------------------------
>>>
>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> Department of zoology
>> University of British Columbia
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>>
>>
>>
>> --
>> Dr. Rutger A. Vos
>> Department of zoology
>> University of British Columbia
>> http://www.nexml.org
>> http://rutgervos.blogspot.com
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> = 
> ======================================================================
> Attention: The information contained in this message and/or  
> attachments
> from AgResearch Limited is intended only for the persons or entities
> to which it is addressed and may contain confidential and/or  
> privileged
> material. Any review, retransmission, dissemination or other use of,  
> or
> taking of any action in reliance upon, this information by persons or
> entities other than the intended recipients is prohibited by  
> AgResearch
> Limited. If you have received this message in error, please notify the
> sender immediately.
> = 
> ======================================================================
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






More information about the Bioperl-l mailing list