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)