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| +--------------------------------------------------------------------+