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

Wed Apr 6 18:14:55 UTC 2011

W dniu 5 kwietnia 2011 22:56 użytkownik Chris Fields
<cjfields at illinois.edu>napisał:

> 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.
>

I believe that I understand it better now. I attach something more specific.
I am still working on it, but there are some questions I would like to ask
about what I've completed so far. But first, the timeline:

Prior to coding:

   -         Familiarize myself with BioRuby code in general perspective.
   -         Prepare my environment to work with and learn about Rubyvis.
   -         Take a closer look at how BioRuby objects stores data.
   -         Prepare ideas on how to unify that data format. The goal is to
   create one format that would easily allow to base visualization module on
   it. If that turn out to be impossible divide objects in as small number of
   groups as possible and propose formats for each one of them.
   -         Discuss these ideas, decide which one to choose.
   -         Discuss what set of functions user should have access to.
   -         Discuss which features should be visualized, and in which order
   it should be implemented.
   -         Decide if there are any other tools that could help with
   developing the project, if so learn about them.
   -         Final preparation for coding: preparing environment, creating
   git repo.

    Week 1:
    Goal: choose one representative type of BioRuby object and develop class
that would convert its data to proposed format. That should come along with
unit tests.

    Week 2:
    Goal: develop graphical module that would create image files based on
data in unified format and provide user interface, write unit tests.

    On this point it should be possible to fully visualize chosen BioRuby
object.

    Weeks 3 to 8:
    Goal: basing on first weeks work, prepare similar classes for all of the
remaining BioRuby objects. Each class should have unit tests.

    Week 9:
    Goal: develop mechanism of browsing images in shell. It should include
simple search and a way of opening images.

    Week 10:
    Goal: write integration tests.

    Weeks 11 and 12:
    Goal: write documentation.

I would like to be more specific about what should be done from weeks 3 to
8, though. It would be nice to plan some time for every object that needs
visualization, but I don't know which that would be exactly. Could you give
me a hand with this?

And in general, as always I would be happy to hear some feedback.

>
> > 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 do understand your point. However, I didn't mean to spend less time on
getting to know the codebase, I just wanted to start doing it earlier.
Anyhow, maybe you have some suggestions about how to solve this time issue?
It's a matter of coding for one month for about 30 hours a week.

I based my proposition on something I read on one of GSoC suggestions page.
But yes, you may be right that BioRuby is to big project for such a
approach.

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