MathSBML: a package for manipulating SBML-based biological models

Summary: MathSBML is a Mathematica package designed for manipulating Systems Biology Markup Language (SBML) models. It converts SBML models into Mathematica data structures and provides a platform for manipulating and evaluating these models. Once a model is read by MathSBML, it is fully compatible with standard Mathematica functions such as NDSolve (a differential-algebraic equations solver). Math-SBML also provides an application programming interface for viewing, manipulating, running numerical simulations; exporting SBML models; and converting SBML models in to other formats, such as XPP, HTML and FORTRAN. By accessing the full breadth of Mathematica functionality, MathSBML is fully extensible to SBML models of any size or complexity. Availability: Open Source (LGPL) at http://www.sbml.org and http://www.sf.net/projects/sbml. Supplementary information: Extensive online documentation is available at http://www.sbml.org/mathsbml.html. Additional examples are provided at http://www.sbml.org/software/mathsbml/bioinformatics-application-not

Tradeoffs between AC power quality and DC bus ripple for 3-phase 3-wire inverter-connected devices within microgrids

Visions of future power systems contain high penetrations of inverters which are used to convert power from dc (direct current) to ac (alternating current) or vice versa. The behavior of these devices is dependent upon the choice and implementation of the control algorithms. In particular, there is a tradeoff between dc bus ripple and ac power quality. This study examines the tradeoffs. Four control modes are examined. Mathematical derivations are used to predict the key implications of each control mode. Then, an inverter is studied both in simulation and in hardware at the 10 kVA scale, in different microgrid environments of grid impedance and power quality. It is found that voltage-drive mode provides the best ac power quality, but at the expense of high dc bus ripple. Sinusoidal current generation and dual-sequence controllers provide relatively low dc bus ripple and relatively small effects on power quality. High-bandwidth dc bus ripple minimization mode works well in environments of low grid impedance, but is highly unsuitable within higher impedance microgrid environments and/or at low switching frequencies. The findings also suggest that the certification procedures given by G5/4, P29 and IEEE 1547 are potentially not adequate to cover all applications and scenarios

SBMLToolbox: an SBML toolbox for MATLAB users

We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML

Escalating model sizes and complexities call for standardized forms of representation

The recent work of Kitano et al on a comprehensive EGFR Pathway Map (Mol Systems Biol, this issue) represents a tremendous amount of intellectual effort. The scale of the model is breathtaking. No doubt some readers will assail the effort on the grounds that models of this size and complexity are difficult to verify, but while this may be true for today’s methods, it is an unhelpful criticism. The inescapable reality in systems biology is that models (that is to say, hypotheses cast in a computational form) will continue to grow in size, complexity, and scope. Rather than grouse, we should be thinking about how to developways of analyzing and verifying models of this scale. We also need to improve our methods of sharing and understanding each other’s work in order to facilitate the iterative processes of review and refinement that are fundamental to modeling

Symbolization-based analysis of engineering time series

Data symbolization, derived from the study of symbolic dynamics, involves discretization of measurement data to aid in observing and characterizing temporal patterns. In this study, symbolization-based methods are developed for analysis of time series from experimental engineering systems to test hypotheses concerning stationarity, temporal reversibility, and synchronization. Stationarity is examined in the context of process control and dynamical state matching; temporal reversibility, in the context of model discrimination and selection of control schemes (linear versus nonlinear); and synchronization, in the context of modes of interactions between system components. Statistical significance is estimated using the method of surrogate data with Monte Carlo probabilities

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

Not applicabl

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

We present the Systems Biology Markup Language (SBML) SBML Level 2 Version 2, a model representation formalism for systems biology. SBML is oriented towards describing systems of biochemical reactions of the sort common in research on a number of topics, including cell signaling pathways, metabolic pathways, biochemical reactions, gene regulation, and many others. SBML is defined in a neutral fashion with respect to programming languages and software encoding; however, it is primarily oriented towards allowing models to be encoded using XML, the eXtensible Markup Language (Bosak and Bray, 1999; Bray et al., 2000). This document contains many examples of SBML models written in XML, as well as the text of an XML Schema (Biron and Malhotra, 2000; Fallside, 2000; Thompson et al., 2000) that defines SBML Level 2 Version 2. A downloadable copy of the XML Schema and other related documents and software are also available from the SBML project web site, http://sbml.org/. The SBML project is not an attempt to define a universal language for representing quantitative models. The rapidly evolving views of biological function, coupled with the vigorous rates at which new computational techniques and individual tools are being developed today, are incompatible with a one-size-fits-all idea of a universal language. A more realistic alternative is to acknowledge the diversity of approaches and methods being explored by different software tool developers, and seek a common intermediate format—a lingua franca—enabling communication of the most essential aspects of the models. The definition of the model description language presented here does not specify how programs should communicate or read/write SBML. We assume that for a simulation program to communicate a model encoded in SBML, the program will have to translate its internal data structures to and from SBML, use a suitable transmission medium and protocol, etc., but these issues are outside of the scope of this document

The ERATO Systems Biology Workbench: Architectural Evolution

Systems biology researchers make use of a large number of different software packages for computational modeling and analysis as well as data manipulation and visualization. To help developers easily provide the ability for their applications to communicate with other tools, we have developed a simple, open-source, application integration framework, the ERATO Systems Biology Workbench (SBW). In this paper, we discuss the architecture of SBW, focusing on our motivations for various design decisions including the choice of the message-oriented communications infrastructure