[Biodevelopers] Proposal for creation of algorithm repository

[Malay Kumar Basu]

Hi Jeff and Bill:

Great! The response is really good. I can't agree more. What I have in my
mind is more like a wiki. No one maintains it but everyone does. That's
the best way to implement quality control. I completely agree that
Bioinformatics.org should play a major role in this.

The repository can be just started anytime. There are plenty of code
around. The core algorithms can be easily picked up from GPLed libraries.
For example all the HMM code can be picked up form Sean Eddy's HMMER. All
we need is to clean up the code from the house-keeping stuff, annotate it
and put it in the repository. In the second phase, for the complicated
stuff we might even ask the author to write the code and submit it to
repository. As the code is nothing but the implemented version of the
pseudocode, I don't think they will have any objection. 

This sort repository can not not be maintained by one persion and the
whole community should perticipate to make the code more readable.

May be whol knows, someday the journals might require to submit the code
to the repository, before publishing the paper.

Everyone, please come out with suggestion.

Malay 

On Wed, 12 Mar 2003, J.W. Bizzaro wrote:

> Mail problems.  This one didn't come through:
> 
> ----------
> From: "Dickinson, Bill" <dickinsw at CMG.MFLDCLIN.EDU>
> To: <biodevelopers at bioinformatics.org>
> 
> What a great idea.  An open source repository.  And like open source =
> development in the operating system and business applications area, this =
> repository would draw on the expertise of folks all over the world =
> interested in promoting tools for the life sciences.  Perhaps the person =
> in charge of bioinformatics.org could provide a web link to and =
> resources for such a repository.  Of course there would have to be some =
> kind of monitoring function to ensure quality and conformance with =
> standards that may need defining.  I am interested in becoming involved =
> in this effort.  There must be others too.
> 
> Bill Dickinson=20
> ----------
> 
> Malay Kumar Basu wrote:
> > Hi Group:
> > 
> > I have already posted this message to bionet-software. If this is a
> > duplicate, I am profusely sorry.
> > 
> > Here what I have to say-
> > 
> > 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    
> > 
> > 
> > _______________________________________________
> > Biodevelopers mailing list
> > Biodevelopers at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/biodevelopers
> 
> 
> -- 
> J.W. Bizzaro                                jeff at bioinformatics.org
> President, Bioinformatics.Org       http://bioinformatics.org/~jeff
> "As we enjoy great advantages from the inventions of others, we
> should be glad of an opportunity to serve others by any invention
> of ours; and this we should do freely and generously."
>                     -- Benjamin Franklin
> --
> 
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