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

Tue Apr 5 20:37:02 UTC 2011

I have to agree, my plan isn't very specific. But mainly coming up with a
timeline is kind of a guesswork: maybe it's just me, I don't like saying
anything unless I am certain of it, and there's no way at this point to do
this. Anyway, I will prepare what I am able to today, and hopefully catch
someone tomorrow on irc to further discuss some specifics.

Chris: could you explain why any coding at community bonding period would be
hard? I assumed that a big part of it is getting familiar with
documentation, and with that done before I would have some more time to
code. Of course, it wouldn't be a full-time coding, but I thought that at
this point I would have all the knowledge to start writing, so why not to.
Maybe I am missing something, in that case tell me please.

Christian: yes, it was very helpful, I've read some example plans before,
but I couldn't really relate them to my project. Now I have a little clearer
picture of what to write. Thanks for that, hopefully tomorrow I will present
something in that manner.

2011/4/5 Christian Zmasek <cmzmasek at yahoo.com>

> 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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> >
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