Proposal for creation of algorithm repository

Kevin Karplus karplus at bray.cse.ucsc.edu
Wed Mar 19 21:09:18 EST 2003


In article <Pine.SGI.4.05.10303132219000.176191-100000 at www.ccmb.res.in>, 
	Malay Kumar Basu wrote:
> I don't have the necessary resources. But I think time has come that
> someone should create an algorithm repository for bioinformaics. Most of
> the standard algorithms have matured and several heuristics have been
> developed. The time is ripe to put all in one place. It will be a golden
> resource for everyone.
> 
> The repository should classify the algorithms with their use, e.g. 
> pattern matching, repeat finder, multiple alignment, pair-wise alignment,
> contig-assembly etc.
> 
> It should have state-of-the-art implementation of all algorithm, with all
> the nesessary heuristics. e.g. only implementation of naive Needleman
> Wunch is not enough; it should have all the memory effciency tricks for
> real-life implementaion of the algorithm.
> 
> The repository should give links to the original papers describing the
> algorithm.
> 
> The repository should avoid all pseudocode, and should describe all
> algorithm in standard language, like C/C++.
> 
> The repsiory should also describe which of algorithm is "fairest of them
> all".
> 
> I think a wiki like interface is best for such a venture. 

What you are proposing sounds like a VERY large task.  There are
several open-source projects (BioPerl, BioPython, ... ) that have
started doing things like this, and none of them have managed to do
cover more than a small fraction of the important algorithms.
Perhaps the best thing to do is to join one of the open-source
projects and contribute a few of your favorite algorithms implemented
efficiently.


-- 
Kevin Karplus 	karplus at soe.ucsc.edu	http://www.soe.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Professor of Computer Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
Affiliations for identification only.




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