[Bioperl-l] Re: I want to construct BioC#. Can you help me?

[Heikki Lehvaslaiho]

Dear Feng Yu,

I'll cc this to the bioperl mailing list as your question really is far beyond 
my capabilities to answer.

Bioperl has been built around sequence classes with interface files 
determining ways to have sequence objects in varying complexity. These are 
created by SeqIO modules; one of which exists for each different text format. 
There is a well written HOWTO document explaining SeqIO in bioperl.

Most of the Bioperl have grown organically around these sequence objects. See  
the models directory in the distribution for some rough graphs. There have 
been some expressions of interests to rewrite everything from scratch which 
is an other reason to post this to the list.

The third reason is that these kind of projects need a community to survive. 
It has to be run in very open way so that new people can continuously join in 
and contribute to it - especially once the people who started it move on.

That principle leads us to a really big problem that I can see your project: 
The C# programming language is not open source and it is bound to closed 
operating system. For a new programming language to take hold is has to have 
some quality which makes people want to start using it. Most of 
bioinformatics is currently done using *NIX operating systems. I can not see 
any reason why MSWindows would quickly become the OS of choice for 
bioinformatics. Quite the contrary as a matter of fact. 

Good luck with your project.
Yours,
		-Heikki





On Monday 08 Dec 2003 12:49 pm, you wrote:
> Hi Heikki Lehvaslaiho:
>   I know you are one of the main contributors to BioPrel. I'm very
> interested in bioinformatics, too. Although there are biojava and bioperl
> now, I think we should have libraries for biological applications written
> by C, the most important computer language, also. So I'm determined to
> advocate the BioC# project, using the latest and most powerful language C#,
> an extensive and enhanced variant of C. Yet since computer has so many
> applications in bioinformatics, with so many classes to be constructed, I'm
> absolutely puzzled. You have made a perfect work in bioPerl. So, can you
> put me out with your experience? Tell me how to design so many classes and
> clarify their relations. I'm waiting for your reply.
>   Thank
>   you! 
>                                   Yours Sincerely
>                                    Feng Yu
>                                    12/08/2003
>
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Feng Yu
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡yfbio at hotmail.com
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2003-12-08
>
>         http://www.biosino.org/members/bioinformatics/

-- 
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     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
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