[Bioclusters] Bioinformatics Benchmark System version 3 release candidate 1 ready

[Joe Landman]

Doug Shubert wrote:

> Hello Joe,
> Getting a Module error.
>
> [root@opteron bbsv3rc1]# bbsrun --help
> Can't locate Object/MultiType.pm in .......
>
> Was this Module compiled with bbs3?


Hi Doug:

  Updated tarball fixed this.  This module is a dependancy of 
XML::Smart, and was not caught on my initial pass.  New tarball has it.

Joe

>
> Doug
>
> Joe Landman wrote:
>
>> Folks:
>>
>>  Much delayed as version 2 went through many rewrites, and we did not
>> release early or often.  This will be corrected.
>>
>>  http://scalableinformatics.com/BBS/
>>
>> and
>>
>>  http://bioinformatics.org/bbs
>>
>> (they are identical)
>>
>>  Much is new in version 3.
>>
>> 1)  You no longer need to modify program source
>> to setup your benchmark.  A simple XML input file will do.
>> 2) A number of examples are included.  We need to document the
>> format better, though if you read the format, you will see that it 
>> really isn't complex (this is what took so long
>> oddly enough)
>>
>> 3) A bbsv1.xml input deck that replicates the original benchmarks from
>> last year is included.
>>
>> 4) New baseline example tests have been created using HMMer, multiple
>> BLAST runs, and others.  Further baseline tests will be added (and
>> suggestions are always welcome).  We are looking at a number of codes
>> including ClustalW, and various chemistry and proteomics codes.
>>
>> 5) Output in multiple formats: plain text, csv (comma separated values),
>> and XML.
>>
>> 6) A dryrun option.  Does everything but the final execution.  Uses a 
>> random sleep rather than a run. 
>> Much more code, some of it hinting at things to come.  Quite scalable:
>> we ran 100 simultaneous tests on a laptop (learning some surprising
>> things about DBM and performance loss in the process).  Documentation
>> has been created at least in the form of man pages.  More documentation
>> should be available soon, with details of the formats, configuration,
>> and so forth
>>
>> The code is heavily commented.  It is GPLed for GPL 
>> projects/products. For commercial products which need to be non-GPL 
>> and supported efforts,
>> please contact us.
>>
>> Please give it a spin, and send us a note as to how you found it, what
>> else you might like on it, and what tests you would like to see.  If you
>> want to contribute an idea for a test, or even better, a test, please
>> send a note.  If you want to help out on coding, please send a note as
>> well.
>>
>> Thanks!
>>
>>  
>>
>
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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615