Re: bio data mirroring

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  -  [email protected]
> http://www.bioinformatics.org/mailman/listinfo/bioclusters
>