toc.org

Overview

Main features

• doc.pl
• biocham.pl

Biocham files, notebooks and call options

• commandline.pl
• util.pl
• counters.pl

Interpreter top-level

• toplevel.pl
• about.pl
• namespace.pl

Part I: Biochemical Networks

• part1.pl

Biochemical Objects

Syntax

• filename.pl
• objects.pl

Molecules and initial state

• molecules.pl
• initial_state.pl

Parameters

• parameters.pl

Functions

• functions.pl

Aliases

• aliases.pl

Reaction Networks

#** Syntax of reactions and transport rules

• reaction_rules.pl
• kinetics.pl
• types.pl

Reaction editor

• reaction_editor.pl

Reaction graph

• reaction_graphs.pl

Graph visualization and editing

• graph_editor.pl
• graphviz.pl

Influence Networks

#** Syntax of influence systems

• influence_rules.pl

Influence editor

• influence_editor.pl

Influence graph

• influence_graphs.pl
• lemon.pl
• multistability.pl

Events

• events.pl

Importing and Exporting BIOCHAM Models

Biocham files

• models.pl

SBML and SBML-qual files

• sbml_files.pl
• qual_files.pl

Ordinary Differential Equations

• ode.pl

#** Graphics files #** Other files

Part II: Qualitative Analysis and Synthesis

Static Analyses

Dimensional analysis

• units.pl

Conservation laws and invariants

• conservation_laws.pl
• invariants.pl

Detecting model reductions

• sepi_graphs.pl
• sepi_infos.pl
• sepi_util.pl
• sepi_core.pl
• sepi_sat.pl
• sepi_neigh_merge.pl
• sepi_old_merge.pl
• sepi_mapping.pl
• sat.pl

Pattern reduction

• pattern_reduction.pl

Tropical algebra equilibrations

• tropical.pl

Multistability analysis

• multistability_command.pl
• oscilations.pl

Boolean Dynamics, Verification and Synthesis

Boolean attractors

• influence_properties.pl

Computation Tree Logic (CTL) formulae

• ctl.pl
• nusmv.pl

Model reduction from CTL specification

• reduce.pl

Model revision from CTL specification

• revision.pl

PAC Learning influence models from Boolean traces

• pac_learning.pl

Part III: Quantitative Analysis and Synthesis

Numerical Simulations

ODE and stochastic simulations

• arithmetic_rules.pl
• formal_derivation.pl
• c_compiler.pl
• gsl.pl
• numerical_simulation.pl
• markov.pl

Hybrid simulations

• na.pl

Plotting and exporting the result of simulations

• plot.pl

Variations and bifurcations

• variations.pl

Verification of Temporal Behaviors and Parameter Synthesis

Numerical data time series

• tables.pl

Temporal logic FO-LTL(Rlin) formulae

• foltl.pl

Parameter sensitivity, robustness and parameter optimization w.r.t. FO-LTL(Rlin) properties

• search.pl

Synthesis of Reaction Networks

Synthesis from mathematical expressions and simple programs

• odefunction.pl

Synthesis from GPAC circuits

• wgpac.pl

Synthesis from polynomial differential equations

• gpac.pl
• lazy_negation.pl
• lazy_negation_gpac.pl

Synthesis from transfer functions

• transfer_function.pl

#** Synthesis from programs #- analog_digital.pl #* Part IV: Wrap-Up #* Biocham Model Analyzer #- analysis.pl

Index

• index

#* Bibliography #- biocham.bib