BioGPS ideas for GSoC 2013

[Chunlei Wu]

With the deadline for student proposal is approaching (just one and half weeks away), we have seen several proposals coming in already. Idea 1 (genewiki) and 2 (facebook game) have been among the most popular ones so far, and we expect high competitions with these applications. Other BioGPS-related ideas have not been discussed as much as the first 2 ideas in the forum yet. We encourage you consider these ideas as well. Not because they can be less competitions, more importantly, these ideas pose significant impact on our ongoing development of BioGPS application. Specifically, we would like to prompt idea 4 and 7:

Idea 4. BioGPS. Advanced gene annotation tools: ID mapping and user table annotation.

Idea 7. BioGPS. Add plugin to display content from Semantic BioGPS.

Both of these ideas are important features in our roadmap. Even though they are under BioGPS context, the implementation of these two ideas does not require the setup of BioGPS dev environment and they will be implemented as standalone applications. Once the standalone application works, the integration into BioGPS is trivial. So at the end of this round of GSoC, the success outcome from these two ideas will be included in our prod BioGPS application (http://biogps.org) immediately.

And finally, if you have a good idea improving either BioGPS or related MyGene.info, you are welcome to propose your own as well!

Feel free to discuss with us for any further questions.

Chunlei

[Tiff Liang]

Hi Chunlei, 

I'm interested at Idea 4. 

From what I understand, this idea is to build a parsor, taken the input files (different format) and output to a format feed to BioGPS and MyGene, or directly insert into the database, (which kind of database do you prefer? ) , and to display it. I guess the language will be python? I'm professional in Perl, and beginner at Python, do you think I'll be a good fit to the project?

For the application form, would the project description be the two features listed? Or does the applicant need to come up new ideas?

Thanks,

Tiff

[Chunlei Wu]

Hi Tiff,

         Thanks for your interest. Idea 4 is essentially doing ID conversion. Taking user's input ID list, do the conversion by calling a web service (via mygene.info), and then display the conversion result back to the user. There is no need to store the result in BioGPS, no database needs to be involved. Here is an example:

         user's input:

1053_at
117_at
121_at

and this user tells us these are reporter IDs, and wants matching GeneSymbol, GeneID, GeneName back. By calling mygene.info web service, we can get all these needed data back, then we then display the conversion result like this in user's browser:

reporter   symbol  geneid  name
1053_at    RFC2    5982    replication factor C (activator 1) 2, 40kDa
117_at    HSPA6    3310    heat shock 70kDa protein 6 (HSP70B')
121_at    PAX8    7849    paired box 8

The second feature is doing the similar ID conversion as well. The difference is that, instead of users pasting in a ID list, users upload a multi-column table file, and specify which column is the ID column for the ID conversion. Then the same conversion will be done based on this column.


         This project will implement a standalone web application. It requires both server-side backend and browser-side user interface. Yes, we require students to implement the backend in Python. And you may consider to use a web framework like Tornado, Django, etc. Probably even more important is to build a smooth user interface, which requires the knowledge of Javascript/HTML/CSS. If you are a Python beginner, it will be a good opportunity for you to gain experience on building web application in Python. If you have experience with Javascript/HTML/CSS before, I think you will be a good-fit.
        

         For the application form, you may use this one: "Advanced gene annotation tools for BioGPS". In your application, you should describe your implementation plan for these two features. It's not required to come up new ideas in your application, but new ideas are always welcome.

Feel free to ask if any further questions.

Chunlei

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[Tiff Liang]

Thanks Chunlei for the quick reply,

Is it ok I submit the proposal with the mockup picture, and if you can check and see if that's what you are looking for? Just want to make sure I am on the right track.

Thanks,

Tiff

[Chunlei Wu]

Yes, mockups are perfect for proposal.

Chunlei

[Tiff Liang]

Somehow I can't find where to submit my proposal. Can you point me to the right place? Thanks a lot.

Tiff

[Andrew Su]

Tiff,

You should register and submit your proposal at
http://www.google-melange.com/gsoc/events/google/gsoc2013

-andrew