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

[Michał Koziarski]

2011/4/4 Raoul Bonnal <bonnal at ingm.org>

> 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 ?
>

I have fairly strong Ruby knowledge, I have been using it for about a year
and a half. There were no really big projects there though, the biggest I've
got was probably small LAN IM. Nevertheless, I use Ruby on daily basis and I
am familiar with most of its, even complex, features.

Also, from the beginning of this year I work as a RoR developer. I've worked
on a bigger, team project and now I am developing one solo. I've learned a
lot here: working with version control systems, developing in team,
operating on other people's code, testing... not to mention further
developing my Ruby knowledge.

Other than that, I know C++ pretty well: it was my first language and I
still use it whenever I see fit. I also have some basic Python and C#
knowledge.

About why I've chosen this project: I find the problem of representing
computer data in format readable by humans interesting, partially because
it's so significant: we could have the best algorithms, the fastest
computers, but the output would be useless if we wouldn't be able to read
it. Additionally, I love the idea of writing code for organisation such as
OBF: it makes me think that I do have, even slightest, impact on science. I
must also admit that working with Ruby is very tempting :) I really enjoy
writing Ruby code.

I am certainly interested in programming for scientific purposes. To be
honest I haven't thought much about in what area exactly, but since I do
have some interest in biology that would seem like a logical choice.

>
> 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 :-)
>

Well, then I am starting to getting know it right know. :)

>   - 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.
>

Actually, I was thinking about trying some test-driven development, I am not
100% sure if that would work for this project though. But anyway, yes, I
haven't included that in my plan, thank you for pointing that out.

I guess it would be the best to do the final testing before writing a
documentation, with some smaller scaled testing after each milestone
completed.

>
>
> 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.
>

I've joined ML (it stands for mail list, right?) already, and visited the
irc a day or two before, unfortunately it seemed no one was online at the
time. As for the meeting, I have classes at this time, so I am not sure if I
will be able to be there, but for sure I will visit irc if any other
questions come to my mind.

And thank you for answering my questions, I have much clearer picture now.


>
> For other BioRuby developer, feel free to post any
> comment/ideas/suggestion.
>    --
> Ra
>
> linkedin: http://it.linkedin.com/in/raoulbonnal
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