[BioRuby] Ensembl API

[jan aerts (RI)]

OK. 

-----Original Message-----
From: Toshiaki Katayama [mailto:ktym at hgc.jp] 
Sent: 10 May 2007 11:14
To: jan aerts (RI)
Cc: Michael Han; bioruby at lists.open-bio.org
Subject: Re: [BioRuby] Ensembl API

Jan,

In that case, I would like you to consider to use the rubyforge
repository 'bioruby-annex' which Nakao-san had set up.

  http://lists.open-bio.org/pipermail/bioruby/2007-April/000355.html

When your modules matured and we, core developers, have decided how to
integrate Rails dependent modules in BioRuby, you can put them in the
BioRuby distribution.

Toshiaki

On 2007/05/10, at 18:09, jan aerts (RI) wrote:

> I actually just started working on this API last night (in between 
> some deadlines I got to catch), so haven't gotten so far as to think 
> about caching. I'm basically working through the perl API tutorial
> (http://www.ensembl.org/info/software/core/core_tutorial.html) and try

> to implement all those examples. (At the moment, I'm at the bit that 
> says "Break chromosomal slices into smaller 100k component slices"...)
>
> Some hurdles that I see coming are the caching and projecting features

> from one coord system to another. We'll see what happens when we get 
> there.
>
> As for a public place: I would _very_ much appreciate help with the 
> API, although
>
> QUESTION FOR BIORUBY COMMUNITY AND DEVELOPERS:
> * Do you think it would be best to create a sourceforge project for 
> this, or should I add it directly into bioruby (e.g.
Bio::Api::Ensembl)?
> I suppose the second option would be best, but the stuff I have is 
> probably not polished enough yet... and *far* from complete.
> * Secondly: if a new release is coming: would it be best to wait 
> untill _after_ that release?
>
> jan.
>
>
> -----Original Message-----
> From: Michael Han [mailto:mh6 at sanger.ac.uk]
> Sent: 10 May 2007 09:51
> To: jan aerts (RI)
> Subject: Re: [BioRuby] Ensembl API
>
>
> On 10 May 2007, at 08:58, jan aerts ((RI)) wrote:
>> Michael,
>>
>> As you mention that we maybe won't be able to cover everything with 
>> the default activerecord behaviour: what problems are you thinking
of?
>>
>> Note: I'd like to use the perl API as a guide. And indeed working out

>> the Slice object was quite simple...
>
> Yes, I was thinking of the slices in combination with the different 
> assembly levels.
> A change to the mapping part of that broke the last EnsEMBL release.
> There were some cases where a seq_region maps one-to-many to other 
> seq_regions (also with gaps).
> Did you put all the caching stuff from the Perl API into it? And if 
> not, is the performance ok?
>
> It would be also great if you could put the code into some public 
> place (RubyForge as example), then it would be easier to see what is 
> already working/being worked at and what not.
>
>> jan.
>>
>> -----Original Message-----
>> From: Michael Han [mailto:mh6 at sanger.ac.uk]
>> Sent: 09 May 2007 14:38
>> To: jan aerts (RI)
>> Subject: Re: [BioRuby] Ensembl API
>>
>> On 9 May 2007, at 14:14, jan aerts ((RI)) wrote:
>>> Has anyone worked on an Ensembl API? There is a perl API and the 
>>> database schema is well-documented. On first impression, it seems 
>>> straightforward to make one using ActiveRecord, but I wouldn't want 
>>> to
>>
>>> waste efforts on that if someone else is already working on it.
>>>
>>> See http://www.ensembl.org/info/software/core/index.html
>>>
>>> Dr Jan Aerts
>>> Bioinformatics Group
>>
>> Hi Jan,
>>
>> I am not sure if you can cover everything with a the default active- 
>> record behavior.
>> But I would be a happy user of a ruby EnsEMBL API.
>> If you need/want help with it, I would also volunteer.
>>
>> Michael
>