[Pipet Devel] Re: standard API for ISYS, OpenBSA & Piper

[Juha Muilu]

Hi Jeff,
Thanks for the mail! The idea of integrating our systems is great and
we are happy to collaborate.

The openBSA project consist basically two separate systems. 
One is the application server which uses new BSA compliant API and other
one is ALBeanBox components. The ALBeanBox contains Java
beans that can be connected together based on XML metadata to make
analysis pipelines. ALBeanBox framework as such is independent of BSA system,
but
we have made couple of BSA specific beans for running remote applications 
and for visualizing the BSA bio-objects.

Configuration of the BSA server based also on XML metadata, which is used
to describe properties of analysis applications (e.g. input/output data,
command line parameters..) and how the output is adapted (e.g.. conversion
to CORBA or XML bio-objects). Currently the XML metadata is auto generated 
from GCG like configuration files, but Martin is planning to make GUI
tool for that (perhaps same tool can be used also with the ALBeanBox 
components as well)

The system is more or less working and can be found from:
http://industry.ebi.ac.uk/openBSA

The BSA API is already standardized, but it is open for extensions and also 
for small changes, I believe. I wonder is this something you can use or
are you thinking some higher level abstraction!? I do not fully understand
what you meant by XML-based API... Perhaps we can made bridge components
to connect our systems and then have common GUI tools (and XML format) 
for building pipelines. 

Cheers, Juha


"J.W. Bizzaro" wrote:
> 
> Adam and Juha,
> 
> I spoke with both of you at your respective posters during ISMB2000.  I'm the
> coordinator of the Piper project, which is very similar to both ISYS and
> OpenBSA.
> 
> I asked if you would consider developing a standard API that defines how our
> systems could interface with an independent program (client or node).  The
> advantage is that programs wrapped to work with one system will work with all
> 3.  You both said that you thought it would be a good idea :-)
> 
> I don't believe that either of you are familiar with each other's system (ISYS
> and OpenBSA).  At least, Juha told me that he did not see the ISYS poster.
> So, I will quickly summarize where I believe we all stand.  Correct me if I am
> wrong.
> 
>   o  ISYS has developed an API based on what looked to me like
>      C or Java code.  Adam said that he would consider an
>      XML-based API.
> 
>   o  OpenBSA is a replacement for Applab and so uses a similar
>      API.  I don't know what stage of development that API is in.
> 
>   o  Piper is in the process of clearly defining an API based
>      on XML.  Piper uses XML extensively.
> 
> Perhaps we can all work toward defining an XML-based API?  The main
> requirement that Piper has is that we want to automate program wrapping and/or
> have it done graphically by the user.  In other words, have the API be
> straight-forward enough so that a human need not program it by hand.
> 
> What do you think?  If we all agree to work on this, I can create a mailing
> list (and subsequently a CVS module) for this collaborative sub-project.
> 
> Cheers.
> Jeff
> --
> J.W. Bizzaro                                           jeff at bioinformatics.org
> Director, Bioinformatics.org: The Open Lab     http://bioinformatics.org/~jeff
> "Injustice anywhere is a threat to justice everywhere."
>                -- Martin Luther King, Jr.
> --

-- 
 +--------------------------------------------------------------------+
 |Juha Muilu, Ph.D., EMBL Outstation| Email:  muilu at ebi.ac.uk         |
 |European Bioinformatics Institute | Phone:  +44 (0)1223 494 624     |
 |Wellcome Trust Genome Campus      | Fax:    +44 (0)1223 494 468     |
 |Hinxton, Cambridge CB10 1SD, UK   | http://industry.ebi.ac.uk/~muilu|
 +--------------------------------------------------------------------+