NAME
Bio::Metabolic::Network - Perl extension for biochemical reaction networks
SYNOPSIS
use Bio::Metabolic::Network;
my $net = Bio::Metabolic::Network->new($reaction1, $reaction2, ... );DESCRIPTION
This class implements objects representing biochemical reaction networks. A reaction network is defined a number of biochemical reactions.
EXPORT
None
OVERLOADED OPERATORS
String Conversion
$string = "$network";
print "\$network = '$network'\n";
Comparison
if ($network1 <= $network2)...AUTHOR
Oliver EbenhÂŽöh, oliver.ebenhoeh@rz.hu-berlin.de
SEE ALSO
Bio::Metabolic Bio::Metabolic::Substrate Bio::Metabolic::Substrate::Cluster Bio::Metabolic::Reaction.
METHODS
Constructor new
Returns a new Bio::Metabolic::Network object. Passed arguments must be Bio::Metabolic::Reaction objects.
Every network object is associated with a matrx, the stoichiometric matrix. This matrix is defined by the reactions and gets determined upon creation.
Method copy
Returns a clone of the network. However, the references to the reactions point to exactly the same reactions. If one gets modified, it effects all networks with that reaction.
Method reactions
Returns an arrayref of the reactions.
Method has_reaction
Argument is a reaction. Returns 1 if the network contains the raction, 0 otherwise.
Method add_reaction
Argument is a Bio::Metabolic::Reaction. Alters the object in-line, adding the reaction to the list.
Method remove_reaction
Argument is a Bio::Metabolic::Reaction. Altering the object in-line, removeing the reaction from the network. Return undef if network did not have the reaction, 1 on success.
Method network_to_string
Returns a string representation of the network
Method add_networks
Adds an arbitrary number of networks, returning a new object containing all reactions that are contained at least present in one of the networks.
Method is_in
$net1->is_in($net2) Returns 1 if all reactions in $net1 also occur in $net2, i.e. if $net1 is a subnetwork of $net2.
Method dist
Provides a distance measure between networks. Returns the number of reactions that are different in the two networks.
Method substrates
Returns a Bio::Metabolic::Substrate::Cluster containing all substrates participating in at least one reaction.
Method matrix
Returns the stoichiometric matrix of the network as a PD::Matrix object.
Method new_matrix
determines the stoichiometric matrix of the network defined by its reactions.
Method print_matrix
Prints the matrix in a way that describes which substrates are associated with which rows and which reactions with which columns.
Method time_derivative
This method returns a Math::Symbolic tree representing a function which determines the temporal change of the concentration of the substrate passed as the argument. This function is determined by the reaction rates.
Method ODEs
This method returns an array of Math::Symbolic trees. One for each substrate. The optional argument can be a Bio::Metabolic::Substrate::Cluster, an arrayref or an array of Bio::Metabolic::Substrate objects. If no argument is specified, it defaults to what the method substrates() returns.
Method mfile
Dumps a strong which can be used as an mfile for Matlab. The optional argument can be a Bio::Metabolic::Substrate::Cluster, an arrayref or an array of Bio::Metabolic::Substrate objects. If no argument is specified, it defaults to what the method substrates() returns.
The corresponding substrate concentrations are considered to be integration variables.
All parameters within the participating reactions must have a value. The method croaks if one parameter value is not defined.
1 POD Error
The following errors were encountered while parsing the POD:
- Around line 34:
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