[BioRuby] GSoC - project "Represent bio-objects and related information with images"

[Raoul Bonnal]

Dear Michal,
thank you for your interest in this project.
I'd like to know more about you, programming experience and why did you chose this project ? Are you interested to work in bioinformatics ?

On 02/apr/2011, at 21.56, Michał Koziarski wrote:

> Hi, my name is Michał Koziarski and I would like to participate in this year
> GSoC on project mentioned in title. I've prepared a short plan and would be
> glad to hear some opinions about it. I have a few questions too:
> 
>   - do I have to be familiar with BioRuby itself?
It would help a bit :-)

>   - in what exactly 'web visualization' consists? Does it simply mean that
>   there should be a way to upload created files, or is it something more?
The projects tries to "attach" the concept of images to "bio objects" or to results of some kind of "bio pipeline" where/when possible.
Most of the time we process data and creates objects but often the final product is an image.
For web visualization, we would like to have images that are ready for the web and that can be integrated in a web application easily.
This project (in the subject) will use bio-gem and a feature I'm developing which will give to the developer the possibility to create in a very smooth way a Rails' engine for his/her library.
> And my current plan, in which I don't mention RoR integration (since I am
> not sure what it will be about):
Currently I'm using RoR for my intenral projects, I know there are other framework but I'd like to use the most common. Btw RoR is not our main scope here.

> 1. Getting familiarized with BioRuby objects, mainly with the way they hold
> data.
ok
> 2. Deciding with features should be visualized.
> 3. In case of presence data with different format but same way of
> visualization, implementing a mechanism converting data to unified format.
yeah here we should spend a bit of time in figuring out similar representation for dataset and results from "bioinformatics analysis"
> 4. Writing a module responsible for creating graphical representation of
> data.
> 5. Writing a documentation.
I agree with the initial plan, don't forget the testing phase.

> 
> Any feedback is appreciated.
You can use the ML, and also the irc channel, usually we are there. and on thursday @14:00 GMT there is a irc meeting feel free to join.

For other BioRuby developer, feel free to post any comment/ideas/suggestion.
--
Ra

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