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Summary: We describe libSBMLReactionFinder, a C library for retrieving specific biochemical reactions from the curated systems biology markup language models contained in the BioModels database. The library leverages semantic annotations in the database to associate reactions with human-readable descriptions, making the reactions retrievable through simple string searches. Our goal is to provide a useful tool for quantitative modelers who seek to accelerate modeling efforts through the reuse of previously published representations of specific chemical reactions., Availability and Implementation: The library is open-source and dual licensed under the Mozilla Public License Version 2.0 and GNU General Public License Version 2.0. Project source code, downloads and documentation are available at http://code.google.com/p/lib-sbml-reaction-finder.

BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is carefully curated to verify that it corresponds to the reference publication and gives the proper numerical results. Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. This allows the users to search accurately for the models they need. The models can currently be retrieved in the SBML format, and import/export facilities are being developed to extend the spectrum of formats supported by the resource.

Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively., Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others., Availability: The specification of SBML Level 1 is freely available from http://www.sbml.org/

Motivation: Metabolic Control Analysis is one of many disciplines that make use of scaled derivatives. In particular, 'elasticities' are used to quantify the effect of an effector or substrate concentration on an enzyme rate under locally specified conditions. Normally an algebraic expression for the elasticity of an enzyme is obtained by differentiating its rate law, multiplying by the effector concentration and dividing by the rate law itself: this results in considerable expression expansion, and when the results are subsequently simplified it is often at the expense of biological comprehensibility., Results: We present a novel algorithm which not only circumvents the expression expansion, but preserves an elegant separation of the components in enzyme behaviour. Easily implemented, and producing gains in both performance and numerical precision, the algorithm is potentially applicable to a number of existing packages. It also greatly assists the manual derivation and evaluation of elasticities, allowing the elasticity of even quite complex enzyme systems to be written by inspection.

SCAMP is a general-purpose simulator of metabolic and chemical networks. The program is written in C and is portable to all computer systems that support an ANSI C compiler. SCAMP accepts metabolic models described in a biochemical language, and this enables novice as well as experienced users rapidly to build and simulate metabolic systems. The language is sufficiently flexible to enable other types of model to be built, e.g. chemostat or ecological models. The language offers many facilities, including: the ability to describe metabolic pathways of any structure and possessing any kinetics using normal chemical notation; optionally build models directly from the differential equations; differing compartment volumes; access to flux, concentration and rate of change information; detection of conserved cycles; access to all coefficients and elasticities of metabolic control analysis; user-defined forcing functions at the model boundaries; user-defined monitoring functions; user-configurable output of any quantity. From the model description SCAMP can either generate C code for later compilation to produce fast executable stand-alone models or run-time code for input to a run-time interpreter for immediate execution. The simulator also incorporates an inbuilt symbolic differentiator for evaluating the Jacobian and elasticity matrices.