[Biojava-dev] Biojava3 and BioSQL

Thu May 31 03:53:45 UTC 2012

Hi Thiago, 

I haven't written JEE code in a while, but I think in theory you could use the JPA API, and let the user decide which provider to use (OpenJPA, Hibernate, TopLink, EclipseLink, etc). This way the user wouldn't be required to use Hibernate. Just my 0.02 cents :-)

Cheers,

Bruno P. Kinoshita
http://kinoshita.eti.br
http://tupilabs.com

>________________________________
> From: Thiago Satake <maruco at gmail.com>
>To: Scooter Willis <HWillis at scripps.edu> 
>Cc: "biojava-dev at lists.open-bio.org" <biojava-dev at lists.open-bio.org> 
>Sent: Thursday, 31 May 2012 12:21 AM
>Subject: Re: [Biojava-dev] Biojava3 and BioSQL
> 
>Hi Scooter,
>
>I have worked with bioperl-db before and
 I have a good understanding about
>that, but now I need to work with Java, it is my first time I am working on
>biojava3 and I could not find any support to BioSQL.
>
>Basically, I am going to create a web interface using JEE. My first task I
>need to read GenBank, GFF and Fasta file and store the data into the BioSQL.
>
>In order to maintain my JEE application easy to support/robust I am using
>Spring and Hibernate. However, I could not find Hibernate or Spring support
>in BioJava3 and I thought that it would not sound good for everyone,
>because we need to have a good knowledge of external API.
>
>If hibernate will help the application to be robust I believe that I need
>to use Spring too.  Easy to maintain, but the architecture will be more
>complex.
>
>I can change my decision and use hibernate if everyone likes :-)
>
>
>
>Thanks
>
>Thiago Seito Satake
>
>
>On 30 May 2012 23:43, Scooter Willis
 <HWillis at scripps.edu> wrote:
>
>> Thiago
>>
>> The Biojava3-BioSQL module will be standalone so you should pick database
>> tools like hibernate or others that make your implementation easy to
>> support/robust. Did you check how other Bio languages support BioSQL? I
>> would follow their API to allow for familiarity with already established
>> packages.
>>
>> Do you have a specific requirement for BioSQL support for code you are
>> working on?
>>
>> Scooter
>>
>> From: Thiago Satake <maruco at gmail.com>
>> To: Scooter Willis <hwillis at scripps.edu>
>> Cc: Andreas Prlic <andreas at sdsc.edu>, "biojava-dev at lists.open-bio.org" <
>> biojava-dev at lists.open-bio.org>
>> Subject: Re: [Biojava-dev] Biojava3 and BioSQL
>>
>> Hi,
>>
>> I was wandering if I should use hibernate or not in my BioSQL module. In
>> my point of the view we should avoid a lot of dependency to make things
>> easy to set up. But I am not sure it would be good for everyone...
>>
>> In this module I am thinking to create a data access object strategy
>> typically exchange data with clients using Transfer Objects, and also, I
>> believe we need to create DAOFactory to encapsulate multiple types of data
>> source ( Oracle, Mysql and Postgres).
>>
>>
 I will expose read() and write() functions using an session façade which
>> will encapsulate reused biojava3 component an data access object.
>>
>> Is everything making sense ? ;-)
>>
>>
>>
>> Thanks
>>
>>
>> Thiago Seito Satake
>>
>>
>>
>>
>>
>> On 29 May 2012 12:00, Scooter Willis <HWillis at scripps.edu> wrote:
>>
>>> Thiago
>>>
>>> If you get a chance can you look at the UniprotProxySequenceReader as a
>>> potential model for BioSQL integration. The underlying sequence objects in
>>> Biojava3-core don't care about the storage container for sequence data,
>>> annotations etc. You should be able to do a BioSQLProxySequenceReader
>>> which has knowledge of the BioSQL schema and connection parameters that
>>> you pass into the
 appropriate Sequence object.
>>>
>>> I think this makes the most sense to integrate BioSQL into Biojava3.
>>>
>>> Let me know what I can do to help.
>>>
>>> Scooter
>>>
>>> On 5/28/12 9:34 AM, "Thiago Satake" <maruco at gmail.com> wrote:
>>>
>>> >Thanks Andreas,
>>> >
>>> >
>>> >In my current project I will work with Java and BioSQL. I think that an
>>> >biojava3-biosql API would be very useful. Now I am getting a good
>>> >understanding of  biojava3 and deciding what is the best solution for
>>> >that.
>>> >Any suggestions would be good!!
>>> >
>>> >
>>> >For now, I have created a simple project in my local environment called
>>> >biojava3-biosql, after I've finished, I
 would like to share with all of
>>> >you. Is possible include in BioJava project ?
>>> >
>>> >
>>> >
>>> >Thanks,
>>> >
>>> >
>>> >Thiago Seito Satake
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >On 26 May 2012 20:34, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> >
>>> >> No, biojava 3 does not have biosql bindings currently. Any patches are
>>> >> welcome...
>>> >>
>>> >> Andreas
>>> >>
>>> >> On Sat, May 26, 2012 at 12:13 PM, Thiago Satake <maruco at gmail.com>
>>> >>wrote:
>>> >> > Hi,
>>> >>
 >
>>> >> > I have noticed that there is a componet called biosql 1.8.1 which
>>> >>works
>>> >> > with biojava 1.8.
>>> >> >
>>> >> > Quick question, I would like to work with biojava3 and BioSQL. Is
>>> >>there a
>>> >> > componete for that ?
>>> >> >
>>> >> > Thanks
>>> >> >
>>> >> >
>>> >> > --
>>> >> > Thiago Seito Satake
>>> >> > _______________________________________________
>>> >> > biojava-dev mailing list
>>> >> > biojava-dev at lists.open-bio.org
>>> >> > http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> >>
>>> >
>>> >
>>> >
>>> >--
>>> >Thiago Seito Satake
>>> >Tel: (041) 88428444
>>> >_______________________________________________
>>> >biojava-dev mailing list
>>> >biojava-dev at lists.open-bio.org
>>> >http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>>
>>
>>
>> --
>> Thiago Seito Satake
>> Tel: (041) 88428444
>>
>
>
>
>-- 
>Thiago Seito Satake
>Tel: (041) 88428444
>
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