Chronological Thread 

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On his question about practices for modular modelling, I have sent Lucian a
list of our publications in this area over the last 3-4 years from me,
Sarala Wimalaratne, David Nickerson, and Jonna Terkildsen. I also included
our latest work on a repository-enabled modular model library, in this case
for Synthetic Biology, made available on Advance Access just over a week
ago. I include a link here in case there are others similarly interested who
cannot be at the talks tomorrow.



http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq063



Cheers,



Mike.





From: cellml-discussion-bounces at cellml.org
[mailto:cellml-discussion-bounces at cellml.org] On Behalf Of Catherine Lloyd
Sent: Wednesday, 24 February 2010 11:49 a.m.
To: Andrew Miller
Cc: CellML Discussion List
Subject: [cellml-discussion] Fwd: Evo connection



Dear Andrew



I am forwarding Lucian's questions onto you in case you feel you have to
file tracker items for any of them or need to get in touch with Lucian
again.



I am also opening it up to the discussion list in case anyone else would
like to comment.



Best wishes

Catherine





Begin forwarded message:





From: Lucian Smith <lpsmith at spod-central.org>

Date: 24 February 2010 9:38:13 AM

To: Catherine Lloyd <c.lloyd at auckland.ac.nz>

Subject: Re: [cellml-discussion] Evo connection



-Currently, I must run my program from the directory with the 'components/'
subdirectory. Is there a way I can set things up so I can run my program
from anywhere?

-In the model bertram_satin_pedersen_luciani_sherman_2007.cellml, 'lambda'
gets translated into infix with a '$' before it. Is this because 'lambda'
is also a function name? Does this happen with any other variables?

-Is there documentation about how you define your infix?

-If I get a 'failed to load external entity' exception, it SIGABRTs me,
despite being supposedly wrapped in one of those 'nsresult' thingummies, and
try/catch doesn't seem to work. What do I need to do to catch this?

code:
bool Registry::LoadCellML(nsCOMPtr<cellml_apiIModel> model)
{
if (model == NULL) return true;
nsresult rv;
nsCOMPtr<cellml_servicesICeVASBootstrap>
cevasboot(do_GetService(CEVAS_BOOTSTRAP_CONTRACTID, &rv));
NS_ENSURE_SUCCESS(rv, true);

nsCOMPtr<cellml_servicesICeVAS> cevas;
try {
rv = cevasboot->CreateCeVASForModel(model, getter_AddRefs(cevas));
}
catch (...){
return true;
}


result:
I/O warning : failed to load external entity
"/home/lpsmith/CellML/models/.\ImportExample2.cellml"
terminate called after throwing an instance of
'iface::cellml_api::CellMLException'
what(): std::exception

Program received signal SIGABRT, Aborted.
0xb7f5b430 in __kernel_vsyscall ()

-Speaking of, the above problem was due to the imported file name being
called ".\ImportedExample2.cellml" instead of "./ImportedExample2.cellml"
(and me running on a unix platform). Is there a good cross-platform method
for fixing this problem?

-Can I get a zip file of all the cellml models on cellml.org from anywhere?

-hypertrophy_or_deterioration_parent.cellml
-faville_model_2008: This model is recursive. When I loop over its
components, some components come up multiple times, every time under the
original name. My code then sees the same thing again, and fails. How
would I get the *new* name for the component? Here's the current code:

while (component != NULL) {
numcomps++;
//Each CellML 'component' becomes its own Antimony 'module'
nsString cellmltext;
rv = component->GetName(cellmltext);
string cellmlname = "cellmlmod_" + ToThinString(cellmltext.get());
NewCurrentModule(&cellmlname);
CurrentModule()->LoadCellMLComponent(component);
RevertToPreviousModule();
rv = cmpi->NextComponent(getter_AddRefs(component));
}



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• [cellml-discussion] Fwd: Evo connection, Catherine Lloyd, 02/24/2010
  • [cellml-discussion] Fwd: Evo connection, Mike Cooling, 02/24/2010
  • [cellml-discussion] Lucian's questions, Lucian Smith, 02/24/2010
  • [cellml-discussion] Fwd: Evo connection, Mike Cooling, 02/24/2010

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