[BioRuby] BioRuby Wrapper for Command line application (GSOC 2011)

Francesco Strozzi francesco.strozzi at gmail.com
Thu Apr 7 18:07:30 UTC 2011 

Excellent! To me the timeline looks good and the working plan is fine.

Anyone else have some comment on this?

Cheers
Francesco

On Thu, Apr 7, 2011 at 18:24, Алесь <ales.guzik at gmail.com> wrote:

> Sorry for this dellay. I just wanted to polish timeline and better
> understand for myself how will I undertake this project.
>
> ** Timeline
>
> * getting in (4 weeks) 27 apr - 24 may
>
>  - getting familiar with BioRuby project (2-3 weeks)
>    - getting into bioinformatics basics (at least 1 week)
>    - getting into project goals and project usage (1 week)
>       - reading articles about BioRuby
>       - reading usage documentation
>       - checking out usage examples
>    - getting into source codebase (1 week)
>       - reading source code documentation (4 days)
>       - looking through source code (2 days)
>       - defining coding guidelines (1 evening)
>    - getting into comunity (in parallel with above)
>       - reading mailing list archive (2-3 days)
>       - hanging up on IRC (all the time)
>
>  - getting familiar with problem (1-2 weeks)
>    - finding examples of applications that will be used with this wrapper
>    - getting familiar with EMBOSS and ACD configuration files
>    - exploring ways to define wrapper configuration
>
> * coding-1 (7 weeks) 25 may - 11 july
>  - writing specs (4 weeks)
>    - defining complete API/DSL for end-users (1 week)
>    - defining interface for adding new CLI tools and EMBOSS suites. (1
> week)
>    - defining additional specs (1 week)
>  - writing code (3 weeks)
>    - writing code for API generation (1 week)
>    - writing code for interprocess communication and data passing (1-2
> week)
>   0-1 additional week to have for finishing all this stuff.
>
> * mid-term evaluation (5 days) 11 july - 15 july
>  At this moment we have complete API/DSL specs and code wich allows
> us wrapping CLI applications.
>
> * coding 2 (4 weeks) 17 july - 16 aug
>  - writing ACD file parser (1-2 weeks)
>  - writing automatic wrapper generation based on ACD files (2-3 weeks)
>
> * documentation and refactoring (1 week) 16 aug - 21 aug
>
> * final evaluation
>
>
> On Thu, Apr 7, 2011 at 5:33 PM, Francesco Strozzi
> <francesco.strozzi at gmail.com> wrote:
> > Hi Ales,
> > did you had the chance to update your proposal on BioRuby Wrapper for the
> > GSoC ? Deadline is tomorrow for student application and we think with
> this
> > proposal we could be able to get some interesting results. But for your
> > application to have a better chance to be considered and evaluated you
> > should provide an updated timeline (even a draft but a bit more detailed)
> > with the activities and tasks broken down into weeks.
> > If you need some help or advise please write here on the Maling List and
> we
> > will provide our contributions.
> > Cheers
> > Francesco
> >
> > On Wed, Apr 6, 2011 at 11:48, Raoul Bonnal <bonnal at ingm.org> wrote:
> >>
> >> Hello Ales,
> >>  thank you for submitting your proposal,
> >> like Michal:
> >> I quote here the discussion with Chris and Christian, if you could write
> a
> >> better time line in form of days/weeks with tasks/objectives I think it
> >> would be better:
> >>
> >> this is the quote from Christian and Chris
> >>
> >> 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
> >> ----
> >> Michał,
> >>
> >> In general, the proposal should answer the questions below, but should
> >> also have a rough timeline on how you would go about coding the project,
> >> creating deliverables for the community for testing, etc. This should
> come
> >> with the input of your possible mentor for the project or from others in
> the
> >> bioruby community.
> >>
> >> The timeline is a little problematic, but the OBF mentors can further
> >> discuss that.  One thing that will cause a problem is that there is a
> >> significant amount of time (about one month) for community bonding, so
> any
> >> coding on a significant project in that period will be tricky.
> >>
> >> chris
> >>
> >>
> >>
> >> ----- 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
> >> >
> >>
> >> _______________________________________________
> >> BioRuby Project - http://www.bioruby.org/
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> >> On 06/apr/2011, at 11.27, Алесь wrote:
> >>
> >> > Hello. My name is Ales and I'd like to implement BioRuby wrapper for
> >> > command line applications as my Google Summer of Code 2011 project.
> >> >
> >> >
> >> > 1. Your complete contact information, including full name, physical
> >> > address, preferred email address, and telephone number, plus other
> >> > pertinent contact information such as IRC handles, etc.
> >> >
> >> > Ales Guzik
> >> > 4th year student at Belarusian State University of Informatics and
> >> > Radioelectronics.
> >> > Belarus, Minsk, P.Brovki st. 3-1 46
> >> > ales.guzik at gmail.com
> >> > +375 25 902 8190 (Belarus)
> >> > +1 650 336 5853 (Google Voice)
> >> > skype: ales-guzik
> >> > IRC, twitter, facebook, github etc.: nekotwi
> >> >
> >> > 2. Why you are interested in the project you are proposing and are
> >> > well-suited to undertake it.
> >> >
> >> > This project is interesting for me because it requires metaprogramming
> >> > - thing I most like in ruby and
> >> > because it's BioRuby - project I wanted to get familiar with long time
> >> > ago.
> >> > I use Ruby more than 2 years for most of my university tasks and daily
> >> > linux scripting. 2 month ago I
> >> > started working as Ruby on Rails developer. I have pretty good
> >> > experience in ruby metaprogramming which
> >> > is needed for this project.
> >> >
> >> > 3. A summary of your programming experience and skills.
> >> >
> >> > I have well experience in C, know but not heavily used C++ and Qt,
> >> > long time ago learned some Erlang,
> >> > have coded some C# at university but dislike it, played a bit with
> >> > Android/Java programming.
> >> > Know and sometimes use Scheme(Racket), now learning some Perl 5.
> >> > Started learning Ruby somewhere in the beginning of 2nd university
> >> > year and liked it very much.
> >> >
> >> > 4. 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.
> >> >
> >> > I haven't yet contributed to opensource projects (except for some tiny
> >> > projects by myself) but really want to.
> >> >
> >> > 5. 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.
> >> >
> >> >  1) Get familiar with source code, use cases and documentation of
> >> > BioRuby and BioRuby-ngs
> >> >  2) Define specs and write rspec tests for this CLI application
> wrapper
> >> >  3) Code to make all tests pass
> >> >  4) Optimize code for processing BIG ammounts of information
> >> >  5) Refactor
> >> >  6) Document undocumented parts
> >> >
> >> > 6. Any obligations, vacations, or plans for the summer that may
> >> > require scheduling during the GSoC work period.
> >> >
> >> > I work as rails programmer 30 hours a week. It's like 8:00 - 14:00
> >> > GMT+2 DST monday - friday, so I can code for
> >> > my project 14:30 - 22:00 or even more. It will be like this in june
> and
> >> > august.
> >> > In july I'll be at military training. I'll have time and internet
> >> > access but can't tell my schedule for now.
> >> >
> >> > --
> >> > Regards,
> >> > Ales Guzik
> >> > ------------------------------------------------------------
> >> > e-mail: ales.guzik at gmail.com
> >> > skype: ales-guzik
> >> > tel: +375 25 9028190
> >> > _______________________________________________
> >> > BioRuby Project - http://www.bioruby.org/
> >> > BioRuby mailing list
> >> > BioRuby at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/bioruby
> >>
> >> --
> >> Ra
> >>
> >> linkedin: http://it.linkedin.com/in/raoulbonnal
> >> twitter: http://twitter.com/ilpuccio
> >> skype: ilpuccio
> >> irc.freenode.net: Helius
> >> github: https://github.com/helios
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> BioRuby Project - http://www.bioruby.org/
> >> BioRuby mailing list
> >> BioRuby at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioruby
> >
> >
> >
> > --
> >
> > Francesco
> >
> >
>
>
>
> --
> Regards,
> Ales Guzik
> ------------------------------------------------------------
> e-mail: ales.guzik at gmail.com
> skype: ales-guzik
> tel: +375 25 9028190
>



-- 

Francesco

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