[BioRuby] BioRuby Wrapper for Command line application (GSOC 2011)
Raoul Bonnal
bonnal at ingm.org
Thu Apr 7 18:36:29 UTC 2011
it's a detailed time line for sure.
Emboss is an example with a structured configuration file for parameters, but we are not bound only to that suite.
On 07/apr/2011, at 20.07, Francesco Strozzi wrote:
> 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
>
--
Ra
linkedin: http://it.linkedin.com/in/raoulbonnal
twitter: http://twitter.com/ilpuccio
skype: ilpuccio
irc.freenode.net: Helius
github: https://github.com/helios
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