Proposal for creation of algorithm repository

Malay Kumar Basu curiouser at gene.ccmbindia.org
Thu Mar 13 11:50:33 EST 2003


Hi Rebaia:

Thanks. I am getting very positive replies from others. We would start
soon. And we want your participation too. Look at the discussion in
Biodevelopers mailing list on www.bioinformatics.org. 

As far as SW is concerned, if you have not found an implementation yet,
let me know. I might be able to help you.

Malay

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Did I tell you? I am looking for a job. I am penniless now!

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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On Thu, 13 Mar 2003, rebaia wrote:

> 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
> >



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