Hi Ross,
>
> Thanks very much for your reply. Apologies for the delay in replying,
> there were quite a few things to look at first!
>
>
> And, apologies for the length of this post, there are a lot of questions!
> Particularly on what you want from the Voronoi diagram (details further
> down).
>
> I'm glad that you think that it will be possible to gain enough
> familiarity
> with the domain to be able to do useful work.
>
>
> One of your last points was on the re-use of existing packages. If
> successful, I would prefer to go this route if possible and use libraries
> for the word cloud and voronoi diagram, so that more time can be spent on
> learning the Reactome architecture, GWT, and making sure the interface is
> well done and that it provides a reasonable and useful user experience.
>
Sounds reasonable.
>
> I'm not sure yet where the visualisations would fit into the website.
> Perhaps I could ask a potential user what they would like to see, and
> where? I guess that it should respond to what would be most useful to the
> users. Perhaps that would fit into the project itself, as the first task
> parallel to the 'community bonding period'?
>
If you go to the beta version of our new website here:
http://reactomedev.oicr.on.ca/ReactomeGWT/site.html
...and click on the "Pathway network" button, you will see one overview
that we have already experimented with. So a possibility would be to put
a button onto the front page, leading to, say, the Voronoi map. I think
it might actually be reasonable to put the word cloud on the front page
itself. At least, this would be something to show potential users, and
ask them how useful it could be.
>
> Would there perhaps be a 'visualisation page' where the pathway network
> diagram could co-exist with the new ones? Would it be possible to jump
> from
> one to the other, at the click of a button, each being different
> renderings
> of the same point in the data?
That would be another possibility.
>
>
> I have had a quick look at some available packages that could be used,
> details below. One worry would be licensing – are there any licences that
> Reactome may be allergic to?
We try to be as open source as possible, claiming that anybody can
download our code and use it. So commercial code, or code with a
restrictive license, would be bad.
>
> Word cloud
> At the moment, it looks as if the word cloud would be the easier
> visualisation to implement.
> Perhaps this could be adapted, a small set of classes to provide simple
> word clouds:
> OpenCloud:
http://opencloud.mcavallo.org/index.jsp
It would be good if you could collect together a few packages and review
them in your project proposal. Then select one, and explain why you chose
it.
>
> I will have to look into how how GWT positions things on the page and how
> interactivity is achieved. It looks from the pathway browser that a high
> level of interactivity can be achieved.
> Perhaps there could be more than one word cloud displayed at a time - one
> for the top-level pathways, another for shared proteins when a word in the
> first is clicked on.
It's a thought.
>
> Maybe some animation effects? Drag a slider to see changes? As seen here:
>
http://chir.ag/projects/preztags/
>
>
> Voronoi diagram (query)
> To see if I've understood what you are looking for, would this
> interpretation be correct?
> The top level of cells would be the top-level pathways, size adjusted to
> the amount of proteins they involve (as you said). For example, going by
> the pathway network diagram for Homo Sapiens, the largest cell would be
> Metabolism.
> Sub cells of those, level 2 cells, would be named for the other top-level
> pathways and the size adjusted by the amount of proteins they share with
> the parent cell. So the largest cell within the Metabolism level 1 cell
> would be Disease as that looks to be the thickest line joining the two.
>
> Please put me right if I have misinterpreted you!
Would it be possible to have only level 1 cells representing top level
pathways, with proximity "coding" for the number of shared proteins?
>
> However, once the basic algorithms are in place alternate visualisations
> would likely be achieved without too much trouble.
>
> If the above is the case... It looks to me that the creation of a Voronoi
> map from data that is not inherently geometric will be more complex than
> the simplest case as presented in the Wikipedia entry. I think that I
> would
> have to use a weighted Voronoi map as described here:
>
http://www.inf.uni-konstanz.de/gk/pubsys/publishedFiles/BaDe05b.pdf
>
> This makes the implementation a little more involving and I would like
> adapt a working program, if possible, rather than reimplement it, even if
> the algorithms are established and published.
Do you have something in mind?
>
> Voronto software - MIT licence.
>
http://vis.usal.es/voronto/Intro.html
> Having had a skim of some of the literature referenced here, and assuming
> no misinterpretation, I think that adapting some of the code here may be a
> good option. A fair bit of further evaluation of the source code is
> required!
>
If you could list the different options that you looked at and give the
reasons why you chose Voronto, that would be useful and could also go into
your project proposal.
> Reactome itself
>
> I've quickly tried installing Reactome at home using the instructions on
> the website. However, I have been unable to find an architectural overview
> of the system, such as a developer might use. Would that be available? The
> installation is not complete yet, mysql is having problems, but I should
> get that sorted out soon.
>
Sadly, as with most such projects, documentation is sparse for Reactome.
>
> GWT
>
> I've added this to my Eclipse installation, compiled and ran the
> introductory example code and tested it in a browser. Pretty cool, indeed.
>
> If there is some similarity with using Swing I will hopefully be able to
> pick up the basics without too much trouble. Even if I can't get a
> suitable
> application together I'll still look further into this.
>
OK.
>
> I will try to get a rough proposal worked out by Monday. If the above is
> not too far from what you are looking for, would you be able to have a
> quick look at it? No problem if not! There will probably be more questions
> from me, also...
>
I would certainly be prepared to look at your proposal.
Cheers,
David.