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

[Raoul Bonnal]

Hi Michal,
thank you for your detailed answer, for me it's fine go ahead with the gsoc procedure.
About IRC, if you find us online msg us, sorry I wasn't online during the w.e.

Yes ML means mailing-list :-)

My nick name on IRC is helios.

On 04/apr/2011, at 16.12, Michał Koziarski wrote:

> 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
>> twitter: http://twitter.com/ilpuccio
>> skype: ilpuccio
>> irc.freenode.net: Helius
>> github: https://github.com/helios
>> 
>> 
>> 
>> 
>> 
>> 
>> 
> 
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--
Ra

linkedin: http://it.linkedin.com/in/raoulbonnal
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skype: ilpuccio
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