[MOBY-l] My MOBY overview and questions

[Simon Twigger]

Im trying to piece together the information on how things are going 
work, this email is a commentary as I try and work things out!

Here's my understanding so far about classes and wdsl files, etc. I've 
thrown in some file examples from biomoby that I came across just so 
people can see whats in them, they may not be the final versions or even 
the right files at all!

-----------
Moby will have a finite set of Classes, these will represent important 
biological 'things' (sequences, IDs, blast results, citations, etc) and 
the structure of these classes will be defined in the data_type.xsd file 
held at MOBY.(eg. http://www.biomoby.org/MOBY/data_type.xsd)

Services (not to be confused with Servers which are the things that 
serve up services) will be created and will take Class1 as an input and 
convert it to (return) Class2 as the output. The exact details of the 
input and output of a particular service will be contained in the 
service.wsdl held on the service machine. (eg. 
http://bioinfo.pbi.nrc.ca/mwilkinson/MOBY/service.wsdl )

Q. Does a class have to be listed at Moby to be useable or will the 
service just not be fully 'moby-compliant' if it uses non-moby classes?
Q. Can we create new classes by mixing other classes together, how 
complex can a class be, is this limited only by the imagination of the 
service provider?

-----------
Services will also register/publish their services at Moby Central, 
indicating their input and output classes. Clients can then query 
MOBY-central for a service that will take the client's input class and 
return the desired output class. Service information will be stored in 
the port_defs.wsdl file at MOBY-Central. (eg. 
http://www.biomoby.org/MOBY/port_defs.wsdl)

Q. Do we register a service or a server - could we register a server and 
have Moby-Central query the server on a regular basis to get a list of 
services that it currently provides?
Q. How will the registering of a service at Moby-Central work - is this 
a manual step the developer will have to do or can it be done 
automagically?
Q. What happens in the case that there are lots of services for a given 
input/output? Will Moby-Central return all services, order the services, 
favoring geographically-sensible services, or services that aren't 
currently busy, or services that have the largest capacity, all of the 
above?
Q. Will MOBY-central detect when a service is offline and not return it 
to the client or will that be up to the client to detect - it would be 
nice if Moby-Central took care of these things.
Q. Can I use the abbreviation MC for Moby-central, I keep typing it 
differently each time?

-------------------------
My understanding of the Current state of the Moby:
- We have sample clients, servers and services, sample service.wsdl, 
port_defs.wsdl and data_type.xsd files
- We do not have - Moby-Central, a wsdl parser or writer

Q. What other parts of the system need to be in place before the entire 
system can get off the ground as a prototype?
Q. Can we list these parts on biomoby.org so that interested parties can 
start having a crack at them?


Hopefully this hasn't made things less clear than they were before!

Cheers,

	Simon.



--------------------------------------------------------------------------------------------------
Simon Twigger, Ph.D.
Assistant Professor, Bioinformatics Research Center

Medical College of Wisconsin
8701 Watertown Plank Road,
Milwaukee, WI, 53226
tel. 414-456-8802, fax 414-456-6595