Bio-Cellucidate

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Base class for each resource.

=item L<Bio::Cellucidate::Bookshelf> 

Represents a Bookshelf in Cellucidate.  This is pretty much the top tier
of cellucidate resources.

=item L<Bio::Cellucidate::Book>

Represents a Book in Cellucidate.  This is where Models live.  A book
can be placed on a Bookshelf and has many Models.

=item L<Bio::Cellucidate::Agent>

Represents an agent in Cellucidate.  Agents are used by rules and initial
conditions and solution observables.  Books have zero, one or many agents
and an agent belongs to a book.

=item L<Bio::Cellucidate::Rule>

Represents a rule in Cellucidate. Books have zero, one or many rules
and a rule belongs to a book.  Models have Rules through the ModelRule
resource.

=item L<Bio::Cellucidate::Model> 

Represents a biological model in Cellucidate.  The model belongs to a book
and contains a number of Model Rules and Initial Conditions.  A number of
simulations can be run from a Model, each having a number of settings.

=item L<Bio::Cellucidate::ModelRule> 

Represents a Rule that is used my a model.  Model rules belong to a model and
models have one or more typically many model rules.  ModelRules have an
association to Rules.

=item L<Bio::Cellucidate::SolutionObservable>

Represents an Agent or set of Agents that you want to observe and plot the 
concentration of when the simulation is run.

=item L<Bio::Cellucidate::RuleObservable>

Represents a ModelRule that you want to observe the activity of when the
simulation is run.

=item L<Bio::Cellucidate::InitialCondition>

This is an initial condition in a model.  Models have one by more typically
many initial conditions and an initial condition belongs to a model.

=item L<Bio::Cellucidate::SimulationRun>

A simulation run represents an execution of the Cellucidate simulator and contains
child result resources.  Simulation runs define various settings.
A Model has one or many simulation runs and a simulation run belongs to
a model.

=item L<Bio::Cellucidate::OdeResult>

Represents the set of ODE formulas generated when running a simulation in ODE-mode.
The results can be used directly in MATLAB.

=item L<Bio::Cellucidate::Plot>

A plot contains a single time series and a number of data series representing the
rule and solution observables.  A simulation run has one or many plots (one for
each iteration).

=item L<Bio::Cellucidate::Series>

A collection of datapoints.  A series belongs to a plot and represents an observable
or time.

=item L<Bio::Cellucidate::KappaImportJob>

This is a resource that represents an import job.  This allows the creation
of a Book, including Model Rules and Initial Conditions, from a Kappa 
string.

=item L<Bio::Cellucidate::Request>

This is the request client, a subclass of L<REST::Client>.  This isn't a 
cellucidate resource.

=back

=head1 SEE ALSO

L<http://cellucidate.com>, L<REST::Client>

=head1 AUTHOR

Brian Kaney, E<lt>brian@vermonster.com<gt>

=head1 COPYRIGHT AND LICENSE

Copyright (C) 2010 by Plectix BioSystems Inc 

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.8.9 or,
at your option, any later version of Perl 5 you may have available.

=cut



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