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

[Chris Fields]

Michał,

In general, the proposal should answer the questions below, but should also have a rough timeline on how you would go about coding the project, creating deliverables for the community for testing, etc. This should come with the input of your possible mentor for the project or from others in the bioruby community.

The timeline is a little problematic, but the OBF mentors can further discuss that.  One thing that will cause a problem is that there is a significant amount of time (about one month) for community bonding, so any coding on a significant project in that period will be tricky.

chris

On Apr 5, 2011, at 12:24 PM, Michał Koziarski wrote:

> 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?
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