Interest in Idea 7: Google Summer of Code

[Neeti Pokharna]

Hello,

I'm a student at BITS Pilani, India pursuing dual degree - Masters of Science in Biological Sciences and Bachelors of Engineering in Electrical and Electronics. Due to my passion for coding, I have had been learning and practicing various computer languages.

I am interested in doing a project under NRNB for Google Summer of Code 2013. I went through the ideas page, and  I would be interested in working on any of these :

idea 11: New features for Online Tutorial System

I have some experience with PHP and would like to work with Open Tutorials which contribute to immense pool of knowledge.
I have looked at Open tutorial and converter and think that features like Mix and Match would be really useful.

idea 7:  Web interface for Querying the Virtual Cell database
I have checked SBML specifications. Since the format is XML development of a web application for querying VCell database should be quite do-able.

I would like to know if we are allowed to work on 2 ideas.

I am very keen on working on a project which would help biologists, being a student of Biology myself.

Please let me know of any further required details, and any references which might prove helpful for me.

Looking forward to work on these.

Thank you.

--

Regards,

Neeti Pokharna

3rd Year, B.E.(Hons.) Electrical and Electronics Engineering and M.Sc.(Hons.) Biological Sciences 

Voice : +91 946 222 2522

Birla Institute of Technology & Science, Pilani
Pilani Campus, Rajasthan 333 031, INDIA

[Jim Schaff]

Hi Neeti,

idea 7:  Web interface for Querying the Virtual Cell database
I have checked SBML specifications. Since the format is XML development of a web application for querying VCell database should be quite do-able.

Our Oracle database stores models decomposed into a relational database schema, and individual models are cached in VCML format (very closely related to SBML).  We would like to query for entire models by various attributes and annotations.  We would also like to directly search for model components (e.g. reactions) across all available models.  In addition, if a VCell user authenticates, the user's private models and those models that are shared with him will be included.  A user may decide to share a model with others or make it "public" with a stable URI.  

If time allows, some integration with the Pathway Commons services could be introduced and allow viewing and manipulation of model reaction diagrams (there are some Javascript "graph" engines that could be used to display networks in a browser). 

Architecturally, I would like this web app to tie into the same infrastructure as our RESTful web API which will provide authentication and authorization (to ensure privacy of user's models).  So the database queries will be relayed through the provided API (the infrastructure for this is already in place).  There exists a Restlet API for GWT (Google Web Toolkit) that would integrate easily with our server if you were considering using GWT - but this is not a requirement.

More about the Web API: 

An JSON/HTML web API for retrieving simulation job status has been developed (using Restlet server-side framework).  A very simple Android app has been created (using the Restlet client-side framework) which only lists the simulations, and a small browser client is served up directly. (for more details including current API spec and screenshots, see posting https://groups.google.com/forum/?fromgroups=#!topic/vcell-discuss/y0_k5ufMm2k) 

 

I would like to know if we are allowed to work on 2 ideas.

I am very keen on working on a project which would help biologists, being a student of Biology myself.

I don't think it is advisable to work on two projects (and probably not allowed).