Mats Jirstrand

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We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well(More)
Many problems in control theory can be formulated as formulae in the first-order theory of real closed fields. In this paper we investigate some of the expressive power of this theory. We consider dynamical systems described by polynomial differential equations subjected to constraints on control and system variables and show how to formulate questions in(More)
Technical reports from the Automatic Control group in Linkk oping are available by anonymous ftp at the address This report is contained in the compressed postscript le Abstract A method for computing invariant sets of piecewise aane systems is presented. The method is based on convex optimization techniques and linear(More)
Many substances are hepatotoxic due to their ability to cause intrahepatic cholestasis. Therefore, there is a high demand for in vitro systems for the identification of cholestatic properties of new compounds. Primary hepatocytes cultivated in collagen sandwich cultures are known to establish bile canaliculi which enclose secreted biliary components.(More)
An increasing number of industrial bioprocesses capitalize on living cells by using them as cell factories that convert sugars into chemicals. These processes range from the production of bulk chemicals in yeasts and bacteria to the synthesis of therapeutic proteins in mammalian cell lines. One of the tools in the continuous search for improved performance(More)
In this paper we consider the problem of estimating parameters in ordinary differential equations given discrete time experimental data. The impact of going from an ordinary to a stochastic differential equation setting is investigated as a tool to overcome the problem of local minima in the objective function. Using two different models, it is demonstrated(More)
Systems biology models tend to become large since biological systems often consist of complex networks of interacting components, and since the models usually are developed to reflect various mechanistic assumptions of those networks. Nevertheless, not all aspects of the model are equally interesting in a given setting, and normally there are parts that can(More)
MathModelica is an integrated interactive development environment for advanced system modeling and simulation. The environment integrates Modelica-based modeling and simulation with graphic design, advanced scripting facilities, integration of program code, test cases, graphics, documentation, mathematical type setting, and symbolic formula manipulation(More)
Inclusion of stochastic differential equations in mixed effects models provides means to quantify and distinguish three sources of variability in data. In addition to the two commonly encountered sources, measurement error and interindividual variability, we also consider uncertainty in the dynamical model itself. To this end, we extend the ordinary(More)
LINKÖPING Technical reports from the Automatic Control group in Linkk oping are available as UNIX-compressed Postscript les by anonymous ftp at the address Abstract We consider the problem of moving the system state between different equilibrium points. For systems whose linearizations are exponentially stable along a curve(More)