Re: [Genome Informatics] GSoC 2013. Reactome.

[David Croft]

Hi Elena,
>
> I am Elena Lopatina, a student of the Department of Molecular and
> Biology Physics in the Moscow Institute of Physics and Technology.
> I do research in bioinformatics, it's about chromosome rearragements that
> occurs during the evolution history of different bacteria. In my
> everyday work
> I develop applications for data processing in Java. Also I am familiar
> with Javascript
> and web technology as well as with the VCS, XML, SQL, CSS and another
> technologies used in software development.
>
> I am interested in working on project "Reactome Big Picture
> Visualization" or "Reactome Search" because I am familiar with this
> area of knowledge
> and want to contribute to bioinformatics software development.
>
> I don't have experience in using GWT but I would highly appreciate in
> opportunity to extend my expertise.
>
> Could you please advise me which project would be better to join?
>
It depends on what you are most interested in. The search project is
more server-side oriented, and would give you experience in using
Lucene. The visualization project is more client oriented, and would
give you experience in GWT and possibly HTML5 (depending on how you
chose to do the visualization).

Cheers,

David Croft.

[David Croft]

Hi Elena,

I think, that "Big Picture Visualization" is more interesting for me.
How can I contribute to the project before submitting proposal?

We can discuss what you would like to put into the proposal.  You can change the proposal at any time, even after it has been submitted, so don't worry about getting things perfect.

And what should I have in my project proposal?

1. A discussion of the design of the visualization, and how it would integrate into the existing Reactome website;
2. A discussion of the technologies you would use, and how you would familiarize yourself with them, if you had not used them before;
3. A timeline, where you break down the implementation of the project into a linear sequence of tasks.

You could start by taking a look at:

http://reactomedev.oicr.on.ca/ReactomeGWT/site.html

Click on the button marked "Pathway network".  That shows you more or less the information that we would like to show in the word cloud and the Voronoi map.  It depicts our top-level-pathways as blobs, with their size depending on the number of proteins in the pathway.  The lines you see criss-crossing on the web page represent the number of proteins shared by any given pair of pathways, which you could use in a distance metric.

We use the Google Web Toolkit (GWT) for building our web pages.  If you are not familiar with this, take a look at:

https://developers.google.com/web-toolkit/overview

It allows you to program web clients in pure Java, in a similar style to AWT.  This Java then gets compiled to Javascript and is then incorporated into your web page.

You need to look over the Reactome website that you see in the above link (this is our new website) and have a think about where you would fit the work cloud and the Voronoi map into this.  You would need to research the trechnologies that you will need to understand, such as GWT, RESTful web services.  You would need to investigate existing packages for creating word clouds and Voronoi maps, and decide whether to re-implement yourself or whether you can use them.  Finally, you would need to come up with a design proposal. This would form the technical part of a proposal.

Then you would need to decide how to break down the tasks into a linear sequence, and make a timeline out of them.  Don't forget to include time needed to research/learn new stuff.

All of this would become the proposal you submit to the GSoC Melange system.

Cheers,

David Croft.

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