[BioRuby] GSoC question (regarding SDI algorithm)
Christian M Zmasek
czmasek at burnham.org
Thu Apr 8 21:39:44 UTC 2010
Hi, Monika:
Remember, the deadline is tomorrow!
> Hello
>
> I think I should first explicitly ask this question: I am not
> experienced in Ruby, but I believe I can improve myself enough during
> the Community Bonding period. Does it make me ineligible to apply?
No. Part of the goals for GSoC is for students to "learn new things".
> If not, please continue with reading: ;)
>
>
> Basically you also need to write a short CV, similar to a job
> application.
>
> Where should I later submit this CV? Should include only education /
> work experience, or also something like a cover letter?
It will all be part of you application (i.e. one document).
You need to write an "abstract" which can can be considered a cover letter.
>
> And a question about the algorithm itself - would it need to be
> accomodated in some application, or just be a separate BioRuby library?
It would be part of BioRuby.
>
> Develop unit tests
>
> I hope this is not stupid question, but where is it possible to get the
> following information about a gene tree: which nodes should receive
> which annotations about 'duplication' and 'specialization', for the
> duplication inference to be considered correct? I mean, as a
> non-biologist I do not know what should be the correct output of the
> algorithm...
You should read (or at least have a look at) some of the references
listed here:
http://evogsoc2010.wordpress.com/2010/03/25/references-for-gene-duplications-proposal/
You can also have a look at my PhD thesis, which explains some of the
background, especially chapter 1.3.2.1.
See:
ftp://selab.janelia.org/pub/publications/Zmasek02/Zmasek02-phdthesis.pdf
Furthermore, I can easily provide you with test gene trees which have
duplications assigned. This is not a big issue.
>
> Regards
> Monika Machunik
>
>
> 2010/4/6 Christian M Zmasek <czmasek at burnham.org
> <mailto:czmasek at burnham.org>>
>
> Hi, Monika:
>
> Thank you for you interest in this proposal.
> Please remember that student applications are due by April 9, 19:00
> UTC -- so, you have not much time left.
>
> I think your lack of experience in Biology is not a problem.
>
> The idea is to implement the algorithm with the BioRuby toolkit
> (http://www.bioruby.org/).
>
> Some more advice:
>
> If you plan to apply, you need to write a very detailed plan on how
> you intend to accomplish this project.
>
> For each step you should list:
> 1. Goal/deliverable
> 2. Approach
> 3. Time estimation
> 4. Anticipated problems & possible alternative approaches
>
> Like so:
>
> A. Prior to coding (from ... to .... )
> 1. Familiarize myself with BioRuby, set up git hub repository
> 2. ...
> 3. 1 week
> 4. Not familiar with git, might need to...
>
> B. Week 1 (from ... to .... )
> 1. Develop unit tests
> 2. Using manually created gene and species trees, I plan to...
> 3. 1 week
> 4. No problem anticipated
>
>
> Basically you also need to write a short CV, similar to a job
> application.
>
> Hope this helps,
>
> Christian
>
>
> Monika Machunik wrote:
>
> Hello
>
> My name is Monika Machunik and I am planing to apply in this
> year's Summer
> of Code. I have read your idea description about "Implementation of
> algorithm to infer gene duplications in BioRuby", and, although my
> background does not include any biology, I got quite interested
> in this
> project (I could not find mentors' email addresses, so I'm
> posting it
> here..).
>
> I would like to shortly introduce myself to get your opinion if
> I would be
> suitable for this project.
>
> I have about a year of work experience in Java programming,
> including some
> internships and last year's GSoC. Besides Java I know C++, some
> C, Php,
> HTML, etc. I am not experienced in Ruby programming (at least
> have seen Ruby
> code;)), but I learn fast. Currently I am doing my Master degree
> in Computer
> Science, so I have some knowlegde about algorithms and data
> structures. I
> have never worked at the intersection of biology and CS, but this
> conjunction has always been intriguing to me.
>
> And now my thoughts about possible content of the workload.
>
> I have read the abstract of the article and, despite of my lack of
> biological knowledge, I managed to comprehend it;). I think I
> also should
> have no problem with understanding the algorithm itself. Apart from
> implementing the algorithm, the project would involve getting
> familiar with
> BioRuby, understanding phyloXML in such extent to be able to
> write an
> algorithm operating on its ready structures.
>
> I am not sure if the algorithm should be implemented inside some
> exisitng
> software, or will it be a kind of standalone algorithm? If it
> should be
> accomodated inside some application, the project would probably
> involve
> doing that too...
>
> ...let it be all for now. Let me know if I have any chances in
> this project
> :)
>
> Best regards
> Monika Machunik
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