Introduction

The structural analysis of stoichiometric networks is an important step in a number of computational methods in systems biology. The structure of a network based on the stoichiometry matrix is divided into two areas, structural constraints imposed by moiety conservation and constraints imposed by flux distributions at steady state. The former constraints have important applications in numerical methods for simulation and the analysis of control, while the later constraints have important applications in flux balance analysis. The LibStructural API provides a wide variety of methods that permit access to the constraint information in the stoichiometry matrix.

Stoichiometric Constraints

Moiety constraints concern the conservation of molecular subgroups in stoichiometric networks. Their existence results in dependencies among the model differential equations and the emergence of additional model parameters in the form of moiety mass totals. In the API we provide robust methods for extracting the constraint information and include specific methods to obtain for example the number of moiety cycles, the number of independent and dependent species and all the pertinent matrices such as the link matrix, reduced stoichiometry matrix etc. In addition to moiety constraints the library also provides robust methods for determining the flux constraints in a model. These include the dependent and independent flux, and the K matrix (and corresponding terms) that relates the two.

All matrices provided by the API are fully labeled with reaction and species labels. The API can accept models either directly from standard SBML or by specifying the stoichiometry matrix. In the case of SBML the species and reaction labels are obtained directly from the SBML otherwise they are entered manually.

Further and more detailed information on this work can be found in Reder (1988), Sauro and Ingalls (2004), Vallabhajosyula et al. (2005).