[Biojava-dev] helping biojava

[Steve Darnell]

Hi Tony,

The BioJava Google Summer of Code page lists other projects (http://biojava.org/wiki/Google_Summer_of_Code_2012). I have always liked the HMMER project, but there is a licensing restriction to navigate (http://biojava.org/wiki/Talk:Google_Summer_of_Code_2012#HMMER).

Another opportunity might be to port the new 2011 DSSP C++ rewrite to Java (http://www.cmbi.ru.nl/dssp.html). The code is released under the Boost license, which is compatible with LGPL (http://www.gnu.org/licenses/license-list.html#boost). I believe Boost threading is used in the implementation, so it may not be a "plain vanilla" port. That probably requires the Java concurrency package and might be a Masters level project. I think it would be very useful to have a gold-standard secondary structure assigner in BioJava.

~Steve

-----Original Message-----
From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Tony Power
Sent: Saturday, December 01, 2012 8:51 AM
To: Andreas Prlic
Cc: biojava-dev
Subject: Re: [Biojava-dev] helping biojava

Hi Andreas,

Thank you for your reply.
In the page you suggested I can find the following items:

- Genbank parser
- Balibase
- UniProt (XML/txt)

Do you believe any of these are worthy of a masters project? I am asking this because I don't know what is involved.
I guess a parser should be a "simple" job (1-2 weeks)? I need something that a student would be working during 3-6 months.
The work should result in a small conference publication/poster.

Something that could be done would be an app that needs one of those modules, so the student would need to develop the module and the app.
Which of those 3 itens (if any, or others), in your point of view, would be the most interesting for a masters project? If so, where can I find information about the problem?

Thank you for your time,



On Thu, Nov 29, 2012 at 10:17 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Tony,
>
> A good start might be to write new parsers or work on converting an 
> algorithm to Java....
>
> some of our feature requests are documented here:
>
> http://biojava.org/wiki/BioJava3_Feature_Requests
>
> hope that helps,
>
> Andreas
>
>
>
> On Thu, Nov 29, 2012 at 4:23 AM, Tony Power <power3d at gmail.com> wrote:
>
>> Hi all,
>> I have a student that is looking for ideas for her masters final work.
>> Is there any biojava need that would be an interesting subject to 
>> work on for arround 3 or 4 months?
>> If so, please, let me know so I can propose it to the student. It 
>> might not accept it, but it's worth to try.
>> Cheers,
>> Tony
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
>
>
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