[Biojava-dev] Fwd: BioJava Project - Google Summer of Code 2012 - How to get involved

Mon Jul 9 07:04:36 UTC 2012

Hi Everyone,

   sorry for the last email. I am forwarding a message to you that is a
kind of example on how to get involved with the BioJava project.

Best regards,
Marco Vaz

---------- Forwarded message ----------
From: Andreas Prlic <andreas.prlic at gmail.com>
Date: Fri, Jul 6, 2012 at 5:41 PM
Subject: Re: BioJava Project - Google Summer of Code 2012
To: Marco Vaz <marcovaz1 at gmail.com>

Hi Marco,

You probably know best what is interesting for you and what about
suggesting something you would like to contribute from your side? You can
also take a look at the feature requests e.g. here:
http://biojava.org/wiki/BioJava3_Feature_Requests It is probably best to
start with something small to gain some experience with the project first.
Do you already have a checkout and are you using biojava for one of your
projects?

Andreas

On Wed, Jul 4, 2012 at 1:02 AM, Marco Vaz <marcovaz1 at gmail.com> wrote:

>
> Hi Andreas,
>
>    thanks a lot for your reply. I am really interested in contributing on
> more technical related things such as fixing bugs or adding new features
> such the ones proposed for GSOC. So, how can I start collaborating? Do you
> want me to send you mi CV? Can you send me a set of possible things to do?
>
>
> I look forward to hear from you,
> Best regards,
> Marco Vaz
>
> On Tue, Jul 3, 2012 at 7:54 PM, Andreas Prlic <andreas.prlic at gmail.com>wrote:
>
>> Hi Marco,
>>
>> you missed the deadline for applying for GSOC by a few months :-)
>>
>> Having said that, we are always interested in people who are willing to
>> contribute and location does not matter. This can be simple things like
>> helping out with emails on the mailing lists, fixing bugs, adding
>> documentation on the wiki pages or adding new features such the ones
>> proposed for GSOC. Any contribution is welcome!
>>
>> Andreas
>>
>>
>>
>> On Tue, Jul 3, 2012 at 12:48 AM, Marco Vaz <marcovaz1 at gmail.com> wrote:
>>
>>> Good morning,
>>>
>>>    my name is Marco Vaz, I am a computer scientist by the University of
>>> Coimbra (Portugal) and recently I finish my biomedical engineering MsC by
>>> the University of Barcelona. I saw your project proposals to the Google
>>> Summer of Code 2012 and I am very keen on contributing to the BioJava
>>> project because this kind of projects totally fit in the kind of experience
>>> I seek. So, I would like to know if there is any chance to contribute in
>>> any one of the BioJava projects, such as "Port an Algorithm to Java", from
>>> Barcelona (where I live). Right now I have the possibility to conciliate my
>>> job with this kind of open source projects.
>>>    Let me know if you think I can participate in one of your projects
>>> and/or if you want me to send you my CV to get more information about me.
>>>
>>> I look forward to hear from you,
>>> Best regards,
>>> Marco Vaz
>>>
>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>>
>
>

-- 
------------------------------
-----------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------

Yes, it would be great if you could announce that you will work on the
Stockholm parser.

- Do it as part of the alignment module, since this will be close to
the SimpleProfile
class... also - we should move our discussion to the -dev list because this
can be an example for others of how to get involved :-)

Thanks for your interest and looking forward to your contribution!
A

On Fri, Jul 6, 2012 at 8:37 AM, Marco Vaz <marcovaz1 at gmail.com> wrote:

>
> Hi Andreas,
>
>    I was subscribed in the biojava-l mailing list. But now I am in the
> biojava-dev too.
>    Do I need to send an email to the mailing list announcing that I will
> be developing this feature?
>    Can I create all the files inside the biojava3-structure module,
> org.biojava.bio.structure.io package? Can I follow the same structure as
> the PDBFileParser and PDBFile relatives?
>
> Best regards,
> Marco
>
>
> On Fri, Jul 6, 2012 at 5:20 PM, Andreas Prlic <andreas.prlic at gmail.com>wrote:
>
>> Hi Marco,
>> some intro into the Stockholm file format is here:
>> http://en.wikipedia.org/wiki/Stockholm_format
>>
>> are you on biojava-dev? Who does what is being discussed on that mailing
>> list...
>>
>> Andreas
>>
>> On Fri, Jul 6, 2012 at 2:17 AM, Marco Vaz <marcovaz1 at gmail.com> wrote:
>>
>>>
>>> Hi Andreas,
>>>
>>>    The Stockholm file format parser implementation is fine for me. I can
>>> implement it. Is there any kind of specification or description about it
>>> (like the inputs, the outputs, etc)? Can you, please, pass me resources
>>> about it?
>>>    Is there any list where I can find which features are being
>>> implemented by who?
>>>
>>> Thanks,
>>> Marco Vaz
>>>
>>>
>>> On Thu, Jul 5, 2012 at 6:28 PM, Andreas Prlic <andreas.prlic at gmail.com>wrote:
>>>
>>>> Hi Marco,
>>>>
>>>> did you see the online documentation?  e.g.
>>>> http://biojava.org/wiki/BioJava:CookBook
>>>>
>>>> about getting started, you might want to cross check with the list to
>>>> make sure nobody else is working on some features already. (biojava is
>>>> de-centralised) E.g. Scooter mentioned he would try to get the Genbank
>>>> parser implemented. If you are flexible, perhaps doing a Stockholm file
>>>> format parser might be useful? - that is reading a Multiple Sequence
>>>> alignment from a text file and loading it into a SimpleProfile class...
>>>>
>>>> Andreas
>>>>
>>>>
>>>> On Thu, Jul 5, 2012 at 8:10 AM, Marco Vaz <marcovaz1 at gmail.com> wrote:
>>>>
>>>>>
>>>>> Hi Andreas,
>>>>>
>>>>>    I already have a checkout of the project in my laptop, via
>>>>> anonymous SVN (not via developer SVN). I am not using biojava in any
>>>>> project I am working right now.
>>>>>    I sincerely don't know with which feature to start.. I could start
>>>>> with the Genbank parser or porting the Blast algorithm to Java. What do you
>>>>> think? Where can I find more information about the feature that I will
>>>>> implement? There is any kind of technical documentation about what is
>>>>> already done? (apart from the JavaDocs?)
>>>>>
>>>>> Best regards and thanks,
>>>>> Marco
>>>>>
>>>>>
>>>>> On Wed, Jul 4, 2012 at 9:54 PM, Marco Vaz <marcovaz1 at gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>    I'll take a look to the new features requests and I'll choose
>>>>>> something. I'll let you know.
>>>>>> Best regards,
>>>>>> Marco Vaz
>>>>>>
>>>>>> On 4 Jul 2012 17:57, "Andreas Prlic" <andreas.prlic at gmail.com> wrote:
>>>>>>
>>>>>> Hi Marco,
>>>>>>
>>>>>> You probably know best what is interesting for you and what about
>>>>>> suggesting something you would like to contribute from your side? You can
>>>>>> also take a look at the feature requests e.g. here:
>>>>>> http://biojava.org/wiki/BioJava3_Feature_Requests It is probably
>>>>>> best to start with something small to gain some experience with the project
>>>>>> first. Do you already have a checkout and are you using biojava for one of
>>>>>> your projects?
>>>>>>
>>>>>> Andreas
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Wed, Jul 4, 2012 at 1:02 AM, Marco Vaz <marcovaz1 at gmail.com>
>>>>>> wrote:
>>>>>> >
>>>>>> >
>>>>>> > Hi Andreas,
>>>>>> >
>>>>>> >    th...
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> -----------------------------------------------------------------------
>>>> Dr. Andreas Prlic
>>>> Senior Scientist, RCSB PDB Protein Data Bank
>>>> University of California, San Diego
>>>> (+1) 858.246.0526
>>>> -----------------------------------------------------------------------
>>>>
>>>
>>>
>>
>>
>> --
>> -----------------------------------------------------------------------
>> Dr. Andreas Prlic
>> Senior Scientist, RCSB PDB Protein Data Bank
>> University of California, San Diego
>> (+1) 858.246.0526
>> -----------------------------------------------------------------------
>>
>
>

-- 
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------