[BioPython] Code publications

[Tiago Antao]

I am currently submitting my populations genetics' code into biopython 
and I can talk about my motivations.

Most of the code that I am submitting was used in something that I have 
done in the past (sometimes published). I figured, that if I have the 
code sitting here, I could as well donate it. This has one interesting 
advantage for me: all the code that I know I will try to submit to 
biopython is designed with care, all the code that is a one off is 
really a big mess. For me making code public is a motivator to maintain 
clean code.

It is also a way to get to know people that are interested in this type 
of problems, and I think that, as with all things in life, knowing more 
people is a good thing.

Maybe, in 12/18 months time I might think in suggesting to other people 
writing an article on the popgen work in biopython. Lets face it, that 
is also a good motivator. But, if it is the only one, I would agree that 
is not good (as Chris says, maintenance after publication...)

Last, but not least: ethical and moral issues. Having spent some time 
outside of science I do think most scientific work is done in a very 
closed fashion (it was a shock to me, really). From my personal point of 
view open science and free software are arguments to which I connect 
moral value.

Tiago

Chris Fields wrote:
> This is a question that could be posed for any open-source project.
>
> It differs per person in my opinion.  For instance, I donate time and  
> code to BioPerl based on several factors.  Not reinventing the wheel,  
> giving back to the community, access to the code base, and the joy of  
> programming (believe it or not) are among them, but they aren't the  
> only ones.
>
> Publications don't hurt but they aren't my primary motivation.  It  
> generally isn't the focus of my research, only a means to an end (to  
> parse or generate data).  I don't see anything wrong with it being  
> someone else's primary drive to donate as long as they continue  
> support their code post-publication, an issue that unfortunately pops  
> up quite frequently.
>
> chris
>
> On Oct 10, 2007, at 7:20 AM, Fernando wrote:
>
>   
>> Hi everybody,
>>
>> This might be off-topic, or maybe not:
>>
>> I've been working with biopython for a while and I am curious about  
>> what the
>> authors get from all the exceptional work they are doing... I know  
>> it won't
>> have to do anything with money, but in terms of publication /  
>> copyrihts etc,
>> what are the adventages of having your code in biopython? Is there  
>> a journey
>> / conference where the author publish their works and likewise they  
>> can be
>> referenced or something like that?
>>
>> Thanks,
>> Fernando
>> _______________________________________________
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>>     
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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