[Biojava-dev] GSOC-2012 Port an Algorithm to Java

[Steve Darnell]

Hi Hannes,

You make a fair point. I know that JNA requires distributed libraries to interact with native libraries. I made a quick (and unsupported) assumption that javacpp did the same.

If javacpp also requires distribed libraries to work, there would be an issue with GPL licensing. As you note, there should not be any problems if javacpp is just generating JNI code (like SWIG).

Thanks for clarifying the point.

~Steve

Sent from my HTC Merge

-----Original Message-----
From: Hannes Brandstätter-Müller [biojava at hannes.oib.com]
Received: Wednesday, 04 Apr 2012, 3:35pm
To: Steve Darnell [darnells at dnastar.com]; biojava-dev [biojava-dev at lists.open-bio.org]
Subject: Re: [Biojava-dev] GSOC-2012 Port an Algorithm to Java

I think it is important to distinguish between:

- Including GPL'd code, porting it or otherwise "improve" it
- using a GPL'd (with Classpath exception, which would be important in
this case, if I understand it correctly) software to produce something
of your own

You make it sound like GPL also extends on stuff you create with GPL'd
software (e.g. an image you draw in a GPL's editor). The viral nature
of GPL does not extend that far.

Hannes

On Wed, Apr 4, 2012 at 17:51, Steve Darnell <darnells at dnastar.com> wrote:
> I would be careful with suggesting the use of javacpp. It is licensed under GPLv2, while BioJava is licensed under LGPLv2. There was a recent discussion on the list on the topic of HMMER and its GPL related to this year's GSoC. I don't believe there would be strong support for using a GPL utility when other non-GPL options exist (e.g. SWIG, JNA, etc.).
>
> ~Steve
>
> -----Original Message-----
> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-bounces at lists.open-bio.org] On Behalf Of Sai Teja Jammalamadaka
> Sent: Wednesday, April 04, 2012 8:37 AM
> To: biojava-dev at lists.open-bio.org
> Subject: [Biojava-dev] GSOC-2012 Port an Algorithm to Java
>
> Hello.
>
> My name is Sai Teja Jammalamadaka.
> I'm a Student of Computer Science and Engineering (B.Tech.) at Vishnu Institute of Technology, Bhimavaram, India.
>
> I am interested to participate in GSOC this year.
> I've taken a look at the ideas page, and I see that you are wanting to port some algorithms into Java from C++.
>
> I've found an open source project called "javacpp"
> http://code.google.com/p/javacpp/
> JavaCPP provides efficient access to native C++ inside Java Would this be more useful instead of a hard conversion into java?
>
>
> To be frank, I have never worked on an open source project before.
> I have worked on Java based web projects which I've submitted for Competitions like Oracle's ThinkQuest International Competition and IBM's The Great Mind Challenge. I created a small side scrolling java game using the JGame Java Library. So I do have a good exposure to the Java Language.
> But I've never channeled my time into working with a public open source project, as of yet.
>
> I would like your advice and feedback.
> I mean is there scope for you to select a project related to algorithm porting compared to other projects? And since I've never worked before on open source projects, will that affect my chance of getting accepted? What else can I do to overcome that drawback?
>
> Eagerly Awaiting Your Reply,
> Sai Teja Jammalamadaka,
> Student of Computer Science and Engineering, Vishnu Institute of Technology, Bhimavaram, 534204 Andhra Pradesh INDIA
>
> Link to CV:
> https://docs.google.com/open?id=0B3KNacfHUN6OamJwWGFuQ0FULWlmLUxab25yejhaQQ
> Website: www.saiteja.in<http://www.saiteja.in> (undergoing maintenance)
> Email: audiodevelop at gmail.com
> IRC Nick: audiodevelop
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