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Herbert Sauro, Michael Hucka, Andrew Finney,Hamid Bolouri
Principal Investigators: John Doyle, Hiroaki Kitano
JST/ERATO Kitano Systems Biology ProjectCalifornia Institute of Technology
Pasadena, California, USA
http://www.cds.caltech.edu/erato
Intro
Experimental Prototype
This talk will illustrate a prototype version of SBW together with a variety of SBW
compliant modules.
Prototype
Features Omitted from Prototype Implementation:
1. No Auto-Startup of Modules
2. No Registry Facilities
3. No Cross-Internet Hooks
Overview
SBW Broker
SB
W Interface
Main Application
SB
W In
terf
ace
Main Application
SB
W In
terf
ace
SBW Broker
Listening Socket
Dispatcher
Next Slide
SBW/Module Interface
Levels of Operation
Raw Messaging Logic
Low Level API
Low Level API +
High Level OOP API
Message Crackers
Call/Send Messages
1. Destination Handle
2. Message Type (Call, Send, etc)
3. Source Handle
4. Service Id
5. Method Id
6. UID – Unique identifier
7. Payload
UID is used to match a reply to the original sender
Description of the Prototype
SBW Broker
• Less than 1500 lines of Delphi source code• 450K exe footprint, could be made much smaller• Thread use is optimized via a Thread pool• Runs in the background, accessible via the Windows Tool-tray• Uses no detectable CPU resources when Idle• Can be run under Win32 or Linux OS
Module Bindings
• Less than 2000 lines of source code• Implemented as a Delphi Component (cf. Java
Bean) for ease of use. • These bindings are compatible with C++ Builder as
well as Delphi.• Can be used to implement Modules for Windows or
Linux
Delphi Prototype Code (Service Provider)
Implementing a Simple Math Service Provider
function TMathClass.MySin (Data : PDataStream) : TComType;begin result := PackComType (sin (ExtractDouble (Data)));end;
TComType is a variant record which can hold any of the allowable SBW data types
PDataStream is a pointer to a byte array containing the message payload
ExtractDouble is a helper routine to assist in extracting data items from the byte array
PackComType is a routine to pack a data type into the TComType variant
sbw.RegisterService ('trig');
sbw.RegisterMethod ('trig', 'sin', MySin, dtDouble, [dtDouble], 'Compute sin of radian angle');
Delphi Prototype Code (Service User)
Implementing a Simple Math Service User
MySin := sbw.GetMethodObj ('TrigModule', ‘trig’, 'sin');
Answer := UnPackDouble (MySin.Call ([3.1415])));
x.Call() returns data as a TComType, therefore it is necessary to use UnPackDouble to unpack the double value.
x.Call() takes a variable number of arguments of any allowable SBW data type, eg MyMeth.Call ([1.2, True, ‘Hello’])
Prototype Test Modules
Non-visual:
• Trig - Math Service provider• NOM – Network Object Model (SBML Module)
Visual:
• Graph2D - Simple 2D Display• Inspector - Module inspector• JDesigner - Visual designer• Jarnac - Simulator• Gillespsie – Simulator (Baltazar Aguda)
Scripting Modules can automatically wrap up a message interface into a scripting object.
SBW
Request Interface Signature
Object Constructor
Interface Object
User:
>>Obj.doitMessage
Constructor
Interface signature
Object Construction
Script Based Modules
NOM(Network Object Model)
GetSBML
LoadSBMLNOM
{Constructor Interface
Deconstructor Interface{
Conclusion
1. Ease of programming
2. Language independence
3. Small, Network friendly, Extensible
From our own experience with using SBW, the benefits of SBW in order of preference include:
Demonstrations (Private Slide)
1. Startup Broker, show popup menu
2. Basic Access to a simple service provider
3. Example illustrating exception handling (ln(-2))
4. Demonstrate Inspector Tool
5. Demonstrate performance using Graph2D
6. Demonstrate JDesigner and Inspector tool
7. Demonstrate Jarnac proxy facility using JDesigner
8. Introduce NOM
9. Demonstrate JDesigner, Jarnac, NOM, Gillespise working together (Close J/JD before carrying out simulation)