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Proposal for creation of algorithm repository

rebaia ahmed.rebai at cbs.rnrt.tn
Thu Mar 13 08:03:42 EST 2003


Very very good idea Malay,
I was in fact looking for a good enough starting-point implementation of the
Smith-Waterman algorithm on the web but
 found nothing really satisfactory (if anyone have one to reccomend many
thanks).
 However, I do not have enough 'broad shoulders' to do the job..
 Any volunteers?
Ahmed Rebai
Head of Bioinformatics Unit
Centre of Biotecnology of Sfax
 B..P 'K', 3038 Sfax, Tunisia

Malay Kumar Basu wrote:

> Hi Groups:
>
> 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 has 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.
>
> I am eager to hear from you guys-what do you think of such a project? Is
> anyone out there has broad enough shoulder.
>
> Cheers,
>
> Malay
>
> Malay Kumar Basu
> Centre for Cellular and Molecular Biology
> Hyderabad 500007
> I N D I A
>
> Fax: +91-40-7160591 or +91-40-7160311
> Phone: +91-40-7160222
> -----
> curiouser at gene.ccmbindia.org
>
> ---





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