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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