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

[Michał Koziarski]

I've completed my application. Chris Fields suggested that I should write it
up, he hasn't specified what parts exactly though. If you have any advice
about it, please let me know.

I use some of my answers to questions asked here in the application, I hope
that's not a problem: I didn't see much point in rewriting it, since the
meaning would be the same.

I don't include the first point, about the address, since it's a public ML
and I don't think it's important here.

I am basing the application on the OBF's template, which I enclose too.


   1. Why you are interested in the project you are proposing and are
   well-suited to undertake it.
   2. A summary of your programming experience and skills.
   3. Programs or projects you have previously authored or contributed to,
   in particular those available as open-source, including, if applicable, any
   past Summer of Code involvement.
   4. A project plan for the project you are proposing, even if your
   proposed project is directly based on one of the proposed project ideas for
   member projects.
   5. Any obligations, vacations, or plans for the summer that may require
   scheduling during the GSoC work period.



   1.      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.
   2.      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.
   3. I can't say much more than what I've written in previous paragraph.
   4. 1. Getting familiarized with BioRuby objects, mainly with the way they
   hold data.
   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.
   4. Writing a module responsible for creating graphical representation of
   data.
   5. Final testing.
   6. Writing a documentation.
   5.      Possibly short vacation (less than one week) around beginning of
   July.
        Also, I am from Poland, which means that my summer vacations starts
   from July. Because of that I won't be able to focus only on the project
   until than. What I can do, however, is to start coding earlier. I would like
   to familiarize myself with documentation before bonding period starts (I've
   already began to do it), and when it does start coding right away. Thanks to
   that I should have just as much time as if I started in May.
        Other than that I am all about the project.


Also, since as I've told I would probably have to start coding a little
earlier, I am trying to slowly browse the documentation. It's a big project
though, and I don't know what's important. Do you have any suggestions about
that? Are there parts that would be especially relevant to the project? Or
maybe even better, are there any easier tasks to complete? I learn best by
exercise, so that would be great. I've looked up at github's issues page,
but haven't found anything like what I am talking about. Maybe I just didn't
know on what I was looking?