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Re: [ccp4bb] {ccp4bb] CCP4 for bioinformatics?
 

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CCP4bb <-- 2008 <-- January 2008 <-- 22 January 2008
Previous message:
Subject: Organic solvent resistent crystallisation plates
From: "Mark J {- dot -} van Raaij" vanraaij {- at -} USC {- dot -} ES
Date: 2008-01-22 		Next message:
Subject: Re: protein expression problem
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2008-01-22


Subject: Re: {ccp4bb] CCP4 for bioinformatics?
From: Clare Sansom c {- dot -} sansom {- at -} MAIL {- dot -} CRYST {- dot -} BBK {- dot -} AC {- dot -} UK
Date: 2008-01-22
Hi all,

Jacob Keller wrote:
>
>
> Does anyone know of a bioinformatics counterpart of ccp4? It seems
> like there should really be such an entity, so that folks would not
> have to write scripts, reinventing the wheel all of the time. I am
> trying right now to manipulate some sequences into various forms, and
> I was imagining a "moleman" homolog for bioinformatics (perhaps
> seqman....?).
>
There *was* a CCP for the bioinformatics community - CCP11, which
started life in the 1980s (yes, before ever the term "bioinformatics"
was coined) to support software for sequence analysis. It ran
continuously until 2005, when its last grant was rejected, and funded
software development, support and training, but it never managed to
attract CCP4's level of industrial funding.

One of the last things the project supported was EMBOSS (mentioned by
Claudine), which is still being developed; its home page is
http://emboss.sourceforge.net/. It may well have some of the
applications that you are looking for. There is a general mailing list
emboss@emboss.open-bio.org that has much lower traffic than this one.

I was involved in CCP11 for about the last five years of its existence.
I and others are not yet convinced that its ecological niche has been
fully occupied, and plans for a grant re-submission occasionally rumble
on. I would be interested to hear of any others who think that
bioinformatics, as a discipline, is missing the service provided so ably
by CCP4.

Of course, one problem we have now that we didn't have in the 1980s,
when specialist hardware was needed for a simple sequence comparison, is
to define the boundaries of "bioinformatics". But that is another
question, and this list is not the right place to ask it!

Cheers,

Dr. Clare Sansom
c.sansom@mail.cryst.bbk.ac.uk
Senior Associate Lecturer, Birkbeck College, London, UK
Freelance bioinformatics consultant and science writer

CCP4bb navigation

CCP4bb <-- 2008 <-- January 2008 <-- 22 January 2008
Previous message:
Subject: Organic solvent resistent crystallisation plates
From: "Mark J {- dot -} van Raaij" vanraaij {- at -} USC {- dot -} ES
Date: 2008-01-22 		Next message:
Subject: Re: protein expression problem
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2008-01-22


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