[BioRuby] Fwd: GSoC - project "Represent bio-objects and related information with images"
Michał Koziarski
michalkoziarski at gmail.com
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?
> > _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list
> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
>
More information about the BioRuby
mailing list