[BioBrew Users] BioBrew Vs Bio-linux

[Glen Otero]

On Jan 28, 2004, at 8:17 AM, Mamoon Kundi wrote:

> Hi Dan,
> Thanks for the explanation.  Another question though:
>
> Bioinformatics apps shipped with BioBrew are about the same shipped 
> with
> Bio-Linux, correct ?
> I mean, both linux distributions comes shipped with same/similar
> bioinformatics software ?

I believe Bio-Linux has a lot more software than BioBrew.
>
> One can get the open-source software anyway, correct.

I hope so. I'm going to try and get their software and put it into 
BioBrew ; )
>
> Is it optimized in any way on BioBrew, cuz as I understand it has to be
> recompiled with specific libs to be able to run on the cluster, do you
> know ?

Many of the programs don't need any parallel communication libraries 
like MPICH, but those programs that do, e.g. mpiBLASt, Gromacs, are 
built with them so that they will run  on a cluster.

Glen

>
> -Rgds
> Mamoon.
> -----Original Message-----
> From: BioBrew-Users-admin at bioinformatics.org
> [mailto:BioBrew-Users-admin at bioinformatics.org] On Behalf Of Dan Swan
> Sent: Wednesday, January 28, 2004 2:10 AM
> To: BioBrew-Users at bioinformatics.org
> Subject: Re: [BioBrew Users] BioBrew Vs Bio-linux
>
>
> On Tue, 27 Jan 2004, Mamoon Kundi wrote:
>
>> Glen,
>> How do u compare BioBrew with Bio-Linux
>>
>> http://bio-linux.net
>>   or
>> http://envgen.nox.ac.uk/biolinux.html
>>
>> I have read your faq and theirs, but wanted to know ur input/comments
>> on this topic.
>>
>> What r the pros/cons of BioBrew that I need to be aware of ? What
>> applications programmatically lend themselves to be run efficiently on
>
>> a BioBrew machine ?
>
> Hi maybe I can hop in here and make some points.  My name is Dan Swan
> and
> I am the Bio-Linux developer.
>
> The way I see it BioBrew is aimed at cluster deployment, Bio-Linux is
> squarely aimed at desktop use, although we do include Condor for loose
> clustering.
>
> BioBrew is a full Linux distribution, whereas Bio-Linux is currently
> (although this is changing) is distributed as a system image
> (see www.systemimager.org).
>
> Bio-Linux was designed to meet the needs of a single scientific
> community, but interest outside the community is causing
> us to change our development model.  Our focus has been, and always 
> will
>
> be, building bioinformatics workstations for bench scientists.
>
> If you are  looking for a cluster optimised 'proper' Linux distribution
> Bio-Linux is probably not what you are looking for.  If you are looking
> for a customised Linux desktop with bioinformatics applications with an
> easy route to loose clustering, it might be!
>
> Glen feel free to disagree as you see fit :)
>
> cheers!
>
> Dan
>
> -- 
> Dr Dan Swan - Bio-Linux Developer | RHCE
> EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
> Tel: 01865 281 658 Fax: 01865 281 696
> http://bio-linux.net/ | dswan at ceh.ac.uk
>
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>
Glen Otero, Ph.D.
Linux Prophet
619.917.1772