1. Systems Science For situations where tools are disjoint
Different developers
Different methods, styles
Independent models to be federated
Need to implement data flow among models
but… not as simple as it may sound

2. Information Flow in Systems Toxicology

3. “Multi-media” Modeling
Air model
Water model
soil model

4. “Multi-media” Modeling
file of int, 5 per line
Air model
file of float,
one per line
with 3 ints after
5 minute steps
Access DB out
Water model
Unix pipe of char in
3 hour steps
soil model
1 month steps

5. Model Federations No scientist has expertise for the whole
Scientists must be able to develop components individually…
i.e., not be software engineers working as a cohesive team
Component models must interoperate
Air model
Water model
soil model

6. Model Federations Mismatch management module Air model Water model
5 minute steps
Water model
3 hour steps
soil model
1 month steps

7. Wat (water model instance)
JDeco Functional Federations
group &
average
concentrations
sed 1
sed 2
sed 3
sed 4
aggrgate
fluxes
Wat (water model instance)
sediment model instances
replicate
& join
soil model
Water model
Air model

8. New Areas
Human lung model… biochemistry, fluid dynamics, protein motors and cilia mechanics, cell physiology… for cystic fibrosis research

9. AOP Infrastructure

10. Model Federations Aspects Mismatch management module Air model
5 minute steps
Aspects
Water model
3 hour steps
soil model
1 month steps

11. Good modularity XML parsing in org.apache.tomcat XML parsing
OOP is an idea about how to structure systems the idea of an “object” has proven to be a powerful
fundamentally about classification and specialization (classes and inheritance)
XML parsing in org.apache.tomcat
red shows relevant lines of code
nicely fits in one box

12. Good modularity URL pattern matching in org.apache.tomcat
red shows relevant lines of code
nicely fits in two boxes (using inheritance)

13. But problems exist… logging in org.apache.tomcat
logging is not modularized
But problems exist…
logging in org.apache.tomcat
red shows lines of code that handle logging
not in just one place
not even in a small number of places

14. Logging, zoomed in // log( "New request " + rrequest );
//From ContextManager
public void service( Request rrequest, Response rresponse ) {
// log( "New request " + rrequest );
try {
// System.out.print("A");
rrequest.setContextManager( this );
rrequest.setResponse(rresponse);
rresponse.setRequest(rrequest);
// wront request - parsing error
int status=rresponse.getStatus();
if( status < 400 )
status= processRequest( rrequest );
if(status==0)
status=authenticate( rrequest, rresponse );
if(status == 0)
status=authorize( rrequest, rresponse );
if( status == 0 ) {
rrequest.getWrapper().handleRequest(rrequest,
rresponse);
} else {
// something went wrong
handleError( rrequest, rresponse, null, status ); }
} catch (Throwable t) {
handleError( rrequest, rresponse, t, 0 );
// System.out.print("B");
rresponse.finish();
rrequest.recycle();
rresponse.recycle();
} catch( Throwable ex ) {
if(debug>0) log( "Error closing request " + ex);
// log( "Done with request " + rrequest );
// System.out.print("C");
return;
// log( "New request " + rrequest );
// System.out.print(“A”);
// System.out.print("B");
if(debug>0)
log("Error closing request " + ex);
// log("Done with request " + rrequest);
// System.out.print("C");

15. Cross Cutting Concerns