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* Getting Started
** Overview
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- doc.pl
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- biocham.pl
- about.pl
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SBML  
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- platform/current/platform.pl
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** Installing and Running Biocham Locally
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- commandline.pl
- util.pl
- counters.pl
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** About this manual
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- filename.pl
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* Syntax of Biocham Reaction Systems
** Biochemical objects
- objects.pl
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** Reaction and transport rules
- reaction_rules.pl
- kinetics.pl
- types.pl
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* Syntax of Biocham Influence Systems
- influence_rules.pl
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* Syntax of Biocham Temporal Specifications
**  Boolean temporal properties
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- ctl.pl
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**  Numerical temporal properties
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* Commands at Top-level
- toplevel.pl
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- namespace.pl
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** Loading, listing, importing and exporting models
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*** Biocham files
- models.pl
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*** SBML files
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- sbml_files.pl
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- sbml_qual_files.pl
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*** ODE files
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- ode.pl
- odefunction.pl
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*** GPAC files
- wgpac.pl
*** Transfer function files
- transfer_function.pl
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*** Graphics files
*** Other files
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** Listing and editing reactions, influences and events
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*** Reactions
- reaction_editor.pl
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*** Influences
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- influence_editor.pl
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- influence_properties.pl
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*** Events
- events.pl
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** Listing and defining initial states, molecules and locations
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*** Molecules
- molecules.pl
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*** Initial state
- initial_state.pl
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** Listing and declaring parameters, functions, aliases and invariants
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*** Parameters
- parameters.pl
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*** Functions
- functions.pl
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*** Aliases
- aliases.pl
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*** Algebraic invariants, conservation laws and P-invariants
- conservation_laws.pl
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- invariants.pl
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** Simulations
*** ODE and stochastic simulations
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- arithmetic_rules.pl
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- formal_derivation.pl
- gsl.pl
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- numerical_simulation.pl
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FOLTL  
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*** Traces and tables
- tables.pl
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*** Plotting the result of simulations
- plot.pl
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** Listing and editing graphs
- reaction_graphs.pl
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- influence_graphs.pl
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- graph_editor.pl
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- graphviz.pl
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** Temporal properties
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*** FOLTL(R) constraints, validity domains, sensitivity and robustness
- foltl.pl
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*** CTL model-checking and revision
- nusmv.pl
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- revision.pl
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* Index
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- index
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* Bibliography
- biocham.bib