[Bioperl-l] GSoC proposal

[Chris Fields]

On Apr 12, 2009, at 6:10 AM, Oleksii Nikolaienko wrote:

> Hi all!
> My name is Oleksii, I`m PhD student and I`d like to receive your  
> comments on
> my proposal for Google summer of code. It`s called
> "bioperl-live::Bio::Restriction::* - implementing missing features"  
> and I`m
> going to:
>
> 1)      add support for reading and writing different file formats for
> module Bio::Restriction::IO

You should specify which formats you intend on working with.  It's  
known that several formats don't carry all data, for instance  
prototype information, vendors, etc. so that should be documented for  
end-users.  You should probably suggest a workaround for getting at  
missing data (i.e. a format that carries all info, retrieving  
prototype data separately, etc).

> 2)      add support for multicut/multisite enzymes

Agreed, though you should be more specific on how you intend to  
implement this.  From the Bio::Restriction::Enzyme documentation the  
sequence site is supposed to be a Bio::PrimarySeq (though I would  
probably change that internally so it creates these on the fly from  
the stored string).  Multicut/multisite implies list context return,  
so it may become an API issue (and using wantarray as a workaround is  
fraught with problematic API traps that I suggest avoiding if at all  
possible).

> 3)      add information on recommended buffers, restriction  
> efficiency,
> sensitivity to methylation, etc and corresponding new methods

Much of this should probably be outlined in the corresponding  
interface class prior to implementation.

> 4)      update documentation for Bio::Restriction::* modules

Yes, completely agree.  This should be bumped closer to the top of the  
priority list (and outlined in the interface classes).

> Thanks in advance for your suggestions.
>
> notch
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chris