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

Tue Apr 5 19:19:35 UTC 2011

Hi, Michal:

I think your project plan needs to be much more detailed.

It might be best in a format similar to the template/example below:

Prior to coding ("community bonding period"):
-Familiarize myself with BioRuby code base 
-Learn about graphics within/from Ruby
-Discuss ... with mentors/BioRuby community
-...
-Learn about git, set up my repository

Week 1:
Goal: Develop necessary utility classes for ...
Anticipated problems: None

Weeks 2 and 3: 
Goal: Develop class to visualize intron/exon structures...
Anticipated problems: Such and such might not ...
Alternatives: If XYZ turns out not feasible, I plan to ... instead

Week X:
Goal: Unit tests for ... 

Week Y:
Documentation ...

Hope this helps,

Christian Zmasek

----- Original Message ----
> From: Michał Koziarski <michalkoziarski at gmail.com>
> To: bioruby at lists.open-bio.org
> Sent: Tue, April 5, 2011 10:24:22 AM
> Subject: [BioRuby] GSoC - project "Represent bio-objects and related 
>information with images"
> 
> 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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