[BioRuby] BioRuby Wrapper for Command line application (GSOC 2011)
Francesco Strozzi
francesco.strozzi at gmail.com
Thu Apr 7 14:33:10 UTC 2011
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
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