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

Tue Apr 5 20:56:38 UTC 2011

On Apr 5, 2011, at 3:37 PM, Michał Koziarski wrote:

> 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.

Don't think of it as a strict timeline as much as an overall plan for development of your project.  Timelines for projects are meant to be malleable and change based on what occurs during development, but w/o underlying structure then there is no organization of your priorities.

> 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.

In general, little coding occurs during community bonding; the time is spent asking questions on the API, working out final priorities, details on the project, etc with the community (mentor in particular).  I'm not sure of your level of experience with BioRuby, but from my experience with BioPerl and past GSoC projects the codebase and API (and documentation, or lack thereof) can be daunting for a beginner.  So, mentioning that you will use that period to code b/c of time issues during the scheduled period is a bit premature in my opinion w/o more specifics, but that's really for the BioRuby folks to decide.

I think Christian made some more specific notes on what is expected.

chris

> 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/
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> > BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> 
> 