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List:       bioclusters
Subject:    Re: [Bioclusters] bio data mirroring
From:       Matthew Dublin <mdublin () genomeweb ! com>
Date:       2008-01-15 22:19:03
Message-ID: 9BF07ADC-513E-4F97-93FC-29A4007343BA () genomeweb ! com
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Hi David,

Matthew Dublin here with Genome Technology magazine based in New  
York, sounds interesting, is there documentation on this you could  
send me?

Thanks,

Matthew
On Jan 15, 2008, at 12:20 PM, David Allouche wrote:

> Hi ,
>
> concerning the concept :
>
> BioMAJ (BIOlogie Mises A Jour) is a workflow engine dedicated to data
> synchronization and processing.The Software automates the update cycle
> and the supervision of the locally mirrored databank repository.
>
> BioMAJ is designed to carry out update cycles for a data source. Each
> cycle has five stages.
>
> *1.**Initialisation: *
>
>
>
> The engine loads the properties file containing the workflow  
> description
> and looks at the current status of the bank by running through the
> associated status file. After determining the bankÕs status, the
> application opens the full cycle or, if necessary, tries to finish the
> previously incomplete cycle (in the event of an error correction).
>
>
>
> *2.**Pre-processing*
>
>
>
> This is a sub-workflow run before the data update. It has the same
> properties as the post-processing part explained below. Its purpose is
> simple: to start tasks, controls and alerts prior to the rest of the
> updating process.
>
>
>
> *3.**Synchronisation*
>
> During this stage, the engine connects to the source and checks for  
> new
> data compared to data already present locally. It determines the  
> list of
> files to be downloaded and assigns a version name. It then carries out
> the download followed by extraction. Finally, it consolidates the data
> by producing a full version of the bank, adhering to the restrictions
> defined by the properties file.
>
>
>
> *4.**Post-processing*
>
> During this stage, the motor runs the post-processing sub-workflow.  
> The
> form can describe relatively complex workflows. It is a succession of
> task blocks that contain one or several sub-collections of meta-tasks
> that can themselves be made up of several processes. Each block is run
> in sequence. In a given block, the meta-tasks that make it up are  
> run in
> parallel. In a meta-task, processes are run in sequence. If there  
> is an
> error in a process, only the branch that it belongs to is stopped.  
> This
> creates a Directed Acyclical Graph (DAG).
>
>
>
> *5.**Deployment*
>
> If the previous stages have completed without error, the application
> puts the new version of the source online. Then it deletes the  
> obsolete
> versions and the temporary files produced when running the post- 
> processes.
>
>
>
> All stages in a session are written up into the status file. If  
> there is
> an error, during the following session, the application will try to
> continue the session from the first erroneous stage of the previous
> session to complete the cycle. One cycle is associated with a data
> source. One or more sessions may be necessary to complete a cycle.
>
>
>
> if you want more details , use the following url  :
>
> http://biomaj.genouest.org
>
>
> be careful we did a mistake in the application packaging.
> the Manuel included into to download is in French !
> the full English documentation is available on the web site into the
> support pull down.
>
> (http://biomaj.genouest.org/index.php? 
> option=com_content&task=view&id=59&Itemid=68)
>
>
>
> let me known if you have questions.
>
> sincerly david
>
> ps: more properties files ( i.e bank update cylce description ) are
> available in the web presentation (  ressources pulldown )
>
> example of application results can be browse  on the following url :
> The application is in production  on  the 3 parteners sites.
> no major problem have been notified.
>
> history of data processing (daily update ) is available on the  
> following
> url :
>
> http://bioinfo.genopole-toulouse.prd.fr/biomaj/
> http://genoweb.univ-rennes1.fr/Serveur-GPO/rapport_biomaj/
> http://genome.jouy.inra.fr/biomaj/
>
> there are daily generated with xslt from the xml statefiles proceed by
> the program.
>
>
>
> Tony Travis a écrit :
>
>> David Allouche wrote:
>>
>>
>>> [...]
>>> we are looking for  more beta-test for feed back. ( publication  
>>> is going
>>> to be submit very soon).
>>>
>>>
>>
>> Hello, David
>>
>> I'm interested in beta-testing your software. Please let me know  
>> where I
>> can download it?
>>
>> Thanks,
>>
>> 	Tony.
>>
>>
>
>
> _______________________________________________
> Bioclusters maillist  -  Bioclusters@bioinformatics.org
> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>


_______________________________________________
Bioclusters maillist  -  Bioclusters@bioinformatics.org
http://www.bioinformatics.org/mailman/listinfo/bioclusters

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