1. Herbert Sauro, Michael Hucka, Andrew Finney,Hamid Bolouri Principal Investigators: John Doyle, Hiroaki Kitano JST/ERATO Kitano Systems Biology Project California Institute of Technology Pasadena, California, USA http://www.cds.caltech.edu/erato Intro Experimental Prototype

2. This talk will illustrate a prototype version of SBW together with a variety of SBW compliant modules.

3. Prototype Features Omitted from Prototype Implementation: 1.No Auto-Startup of Modules 2.No Registry Facilities 3.No Cross-Internet Hooks

4. Overview SBW Broker SBW Interface Main Application SBW Interface Main Application SBW Interface SBW Broker Listening Socket Dispatcher Next Slide

5. SBW/Module Interface

6. Levels of Operation Raw Messaging Logic Low Level API Low Level API + High Level OOP API Message Crackers

7. 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

8. 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

9. 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

10. 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');

11. 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’])

12. 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)

13. Scripting Modules can automatically wrap up a message interface into a scripting object. SBW Request Interface Signature Object Constructor Interface Object User: >>Obj.doit Message Constructor Interface signature Object Construction Script Based Modules

14. NOM (Network Object Model) GetSBML LoadSBML NOM { Constructor Interface Deconstructor Interface {

15. 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:

16. 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)