"Use names if consistent and unambiguous across compartments, or identifiers if compartment suffix is present (id in form \"xxx_y\" with xxx as base identifier and y as compartment label).")
publicstrategymergingStrat=null;
publicStringidRegex="^(\\w+)_\\w$";
@Option(name="-me",aliases={"--simple"},usage="merge parallel edges to produce a simple graph",required=false)
return"Metabolic networks used for quantitative analysis often contain links that are irrelevant for graph-based structural analysis. For example, inclusion of side compounds or modelling artifacts such as 'biomass' nodes.\n"+
"While Carbon Skeleton Graph offer a relevant alternative topology for graph-based analysis, it requires compounds' structure information, usually not provided in model, and difficult to retrieve for model with sparse cross-reference annotations.\n"+
"In contrary to the SBML2Graph app that performs a raw conversion of the SBML content, the present app propose a fine-tuned creation of compound graph from predefined list of side compounds and degree² weighting to get relevant structure without structural data."+
"This app also enable Markov-chain based analysis of metabolic networks by computing reaction-normalized transition probabilities on the network.";
}
@Override
publicStringgetShortDescription(){return"Advanced creation of a compound graph representation of a SBML file content";}