[BioRuby] GSoC - project "Represent bio-objects and related information with images"
Christian Zmasek
cmzmasek at yahoo.com
Tue Apr 5 19:19:35 UTC 2011
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?
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