[Bioperl-l] a Main Page proposal

Jason Stajich jason at bioperl.org
Thu Sep 24 12:23:44 EDT 2009

If someone also wants to volunteer to keep up the publications page -  
this is where I *had* been curating a list up by citations and google  
scholar searches for 'bioperl' and things that reference 2002 paper.

Seems like this is where the static copy of that information should go  
- but highlighting things on the a page with a circulating list or  
something that just listed recent additions to the list could be done  
by the web dev gurus and could be kewl.
The current issue is that a) it is large so I think pubmed plugin  
rendering can be slow (or gets broken as it seems to be now).

On Sep 24, 2009, at 2:38 AM, Dave Messina wrote:

>> Not to add yet more to the list, but I also think a concise list of
>> projects using (or 'powered by') bioperl should be front-and- 
>> center; not a
>> lot of users know when/where bioperl is used.  This applies to the  
>> other
>> bio* as well, particularly biopython (seeing it popping up more and  
>> more).
> Along these lines, it'd be great to publicize not only
> BioPerl-*powered*projects, but ones which interface with it, too.
> Just this week, for example, there is this, which could go both on a  
> static
> page and in the newsfeed:
> http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btp554v1
> MOODS: fast search for position weight matrix matches in DNA  
> sequences.
> Korhonen J, Martinmäki P, Pizzi C, Rastas P, Ukkonen E.
> Department of Computer Science and Helsinki Institute for Information
> Technology,
> University of Helsinki, Helsinki, Finland.
> SUMMARY: MOODS (MOtif Occurrence Detection Suite) is a software  
> package for
> matching position weight matrices against DNA sequences. MOODS  
> implements
> state-of-the-art on-line matching algorithms, achieving considerably  
> faster
> scanning speed than with a simple brute-force search. MOODS is  
> written in C++,
> with bindings for the popular BioPerl and Biopython toolkits. It can  
> easily be
> adapted for different purposes and integrated into existing  
> workflows. It can
> also be used as a C++ library. AVAILABILITY: The package with  
> documentation and
> examples of usage is available at http://www.cs.helsinki.fi/group/pssmfind 
> . The
> source code is also available under the terms of a GNU General  
> Public License
> (GPL). CONTACT: janne.h.korhonen at helsinki.fi.
> PMID: 19773334 [PubMed - as supplied by publisher]
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Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org

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