Re: Interested in working on a project with bio4j

[Pablo Pareja Tobes]

Hi Anirudh,

Great to hear about your interest on collaborating to Bio4j project.

Do any of the ideas for GSoC 2014 seem particularly interesting to you?

If so, let me know and we can go on from there ;)

Cheers,

Pablo

On Fri, Oct 3, 2014 at 2:52 PM, Anirudh Subramanian <aniru...@gmail.com> wrote:

Hi all,

My name is Anirudh Subramanian and I am a student in Computer Science at University of Florida. I have taken a course in BioInformatics and have to do a project as part of my coursework. I looked at the gsoc ideas list for 2014 and I found some of them particularly interesting. My interests lie in Data Structures, Algorithms , Distributed Systems . It would be great if you guys could give me pointers for the unimplemented ideas in bio4j.

Thanks and Regards,

Anirudh Subramanian

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[Pablo Pareja Tobes]

Hi Anirudh,

> Do you mean to say that allowing end users to query based on specific bio4j parameters and allowing to return sequences corresponding to the results.

Yeah, we mean that.

> How is the raw sequence data connected to bio4j right now ? How is the sequence data strings linked to the bio4j entities right now ?

Raw sequence data is currently stored at Protein entity level  (as a String vertex property)

> And is there work current going on, for this project.

Yeah, Kim Kovach is currently working on integrating Human genome sequence data into Bio4j (including variants). Also Alexey Alekhin is working on a similar project but related to Drosophila genome.

So if you decide to contribute on this topic it'd be great if you all could get to coordinate.

Cheers,

Pablo

On Tue, Oct 7, 2014 at 6:18 PM, Anirudh <aniru...@gmail.com> wrote:

Hi Pablo,

I looked at the project ideas and these project particularly interest me : "integrate sequence data into bio4j" .  I didnt understand when you say :: "There is however a use case for which this integration would add great value: just being able to select a particular set of sequences based in the result of queries, which can take advantage of the rich model and integrated datasets; basically we are using the Bio4j graph as an index." Do you mean to say that allowing end users to query based on specific bio4j parameters and allowing to return sequences corresponding to the results.

How is the raw sequence data connected to bio4j right now ? How is the sequence data strings linked to the bio4j entities right now ?

And is their work current going on, for this project. 

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