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.