[Biopython] Intel Python distribution

[Gunning, Don]

Peter

Thanks for the reply.

Regarding disk i/o, this is a universal issue.  The main solution available is code restructuring and the use of SSD's to hide latency.  

Regarding Pairwise2, we are looking for packages that we can include in our distribution.  Can anyone advise how widely it is used and Is there an need for further performance improvement?

Regards

Don

-----Original Message-----
From: Peter Cock [mailto:p.j.a.cock at googlemail.com] 
Sent: Thursday, September 01, 2016 5:31 AM
To: Gunning, Don <don.gunning at intel.com>
Cc: biopython at biopython.org; Biopython-Dev Mailing List <biopython-dev at mailman.open-bio.org>
Subject: Re: [Biopython] Intel Python distribution

Hi Don,

Biopython covers so many topics that everyone using it probably
has a different bottleneck. I tend to do basic sequence manipulations
where disk IO is the main bottleneck - although often problems
in this area are more on the end user script (e.g. taking advantage
of Python sets rather than lists for membership checking).

I do know that the old Bio.pairwise2 code was performing poorly
on larger sequences (this has a C backend), but that has been
improved with a rewrite in our latest release, Biopython 1.68.

Hopefully some of our community will volunteer to talk about
where they think Biopython needs some optimisation?

Regards,

Peter

On Wed, Aug 31, 2016 at 2:34 PM, Gunning, Don <don.gunning at intel.com> wrote:
>
>
> Intel has just announced the Intel Python distribution.   An open source
> version with many packages optimized for performance
>
>
>
> https://software.intel.com/en-us/python-distribution
>
>
>
> The life sciences market is an area we are trying to help with.  And your
> project seemed interesting as it is aligned with our thinking.
>
>
>
> Could someone write me back and discuss how we could contribute to your
> project and get our distribution more widely used in your community?  One
> thought is for Intel to optimize and include packages that are regularly
> used in your community.
>
>
>
> We look forward to hearing from you and potentially collaborating.
>
>
>
> Regards
>
>
>
> Don
>
> Don Gunning
>
> Software Program Manager
>
> Technical computing group
>
> Developer Product Division
>
> Intel Corporation
>
> 1906 Fox Dr
>
> Champaign Il 61820
>
> 217 403 4213
>
>
>
>
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