RuleBase Perl API Library

This is a perl library to interact with RuleBase http://rulebase.org

Installation

To install this module type the following:

perl Makefile.PL
make
make test
make install

Also, it's on CPAN as Bio-Cellucidate (http://search.cpan.org/~bkaney/Bio-Cellucidate/).

An Example

use Cellucidate;

# Search for a bookshelf, returns an array of bookshelf hashes
$bookshelves = Cellucidate::Bookshelf->find();
$bookshelves = Cellucidate::Bookshelf->find( { name => 'Reference 10' });

# Single bookshelf
$bookshelf = Cellucidate::Bookshelf->show(102);

# Bookshelf properties
$bookshelf->{id}   # => 102
$bookshelf->{name} # => 'Reference 10'


# All books on a bookshelf
$books = $bookshelf->books();

# Search for a book
$books = Cellucidate::Book->find( ... );

# Search for models..
$models = Cellucidate::Model->find( ... );

# Single model
$model = Cellucidate::Model->show( id );

# All models in a book
$model = Cellucidate::Book->models( book_id );

# All model rules in a model
$model_rules = Cellucidate::Model->model_rules( model_id );

# All initial conditions in a model
$initial_conditions = Cellucidate::Model->initial_conditions( model_id );

# All simulation runs in a model
$simulation_runs = Cellucidate::Model->simulation_runs( model_id );

# Create a simulation run for a model
$simulation_run_params = { "model_id" => $model_id  };
$simulation_run = Cellucidate::SimulationRun->create($simulation_run_params);

$csv_data = Cellucidate::SimulationRun->get($simulation_run_id, 'csv');

$plots = Cellucidate::SimulationRun->plots($simulation_run_id);

$plots = $simulation_run->plots();  # Cellucidate::Plot->find( { simulation_run_id => $id } );

A more complete example is located in the /examples directory.

Overview

This library facilitates interaction with RuleBase, a web application for biological modeling and simulation.

The various objects in RuleBase are arranged into books that contain models. The basic hierarchy is:

Bookshelves -> Books -> Agents -> Rules -> Models -> Model Rules -> Initial Conditions -> Rule Observables -> Solution Observables -> Simulation Runs -> Ode Results -> Plots -> Series

Additionally, there are a few resources for auxiliary tasks, like importing data and running various jobs LCellucidate::KappaImportJob.

RESTful Web Services

RuleBase has a RESTful interface. So this library is built upon the REST::Client library. At the core, there are 4 operations over HTTP, including: GET, POST, PUT and DELETE. The encoding is primarily XML, but certain resource can be returned in CSV and Kappa (application/x-kappa).

COMMON METHODS / PATTERN

Around each resource, there are convience methods -

find( { params }, format)
get(id, format)
update(id, { data }, format)
create({ data }, format)

See each subclass for a list of specific methods and examples

Configuration

There are two variables that should be set. These are used by all subclasses.

$Cellucidate::CONFIG

This is a hash of configuration options for the underling REST client. See LREST::Client for more information.

$Cellucidate::CONFIG = { host => 'http://api.rulebase.org' };

$Cellucidate::AUTH

This is a hash of your authentication information from rulebase.org. It includes your email address as your login and API Key.

$Cellucidate::AUTH = { login => 'email@host.com', api_key => '111111' };

Subclasses

Cellucidate::Base

Base class for each resource.

Cellucidate::Bookshelf

Represents a Bookshelf in RuleBase. This is top-level object in RuleBase.

Cellucidate::Book

Represents a Book that may contain models and journal pages. A book can be placed on a Bookshelf and has many Models.

Cellucidate::Agent

Represents an agent in RuleBase. 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.

Cellucidate::Rule

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

Cellucidate::Model

Represents a biological model in RuleBase. 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.

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.

Cellucidate::SolutionObservable

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

Cellucidate::RuleObservable

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

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.

Cellucidate::SimulationRun

A simulation run represents an execution of the RuleBase 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.

Cellucidate::OdeResult

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

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).

Cellucidate::Series

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

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.

Cellucidate::Request

This is the request client, a subclass of LREST::Client. This isn't a RuleBase resource.

Dependencies

This module requires these other modules and libraries:

REST::Client XML::Simple Data::Dumper

Copyright and License

Copyright (C) 2010 by Harvard Medical School

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.