Modelling, parameter identification, and simulation play an important rôle in Systems Biology. In recent years, various software packages have been established for scientific use in both licencing types, open source as well as commercial. Many of these codes are based on inefficient and mathematically outdated algorithms. By introducing the package BioPARKIN recently developed at ZIB, we want to improve this situation significantly. The development of the software BioPARKIN involves long standing mathematical ideas that, however, have not yet entered the field of Systems Biology, as well as new ideas and tools that are particularly important for the analysis of the dynamics of biological networks. BioPARKIN originates from the package PARKIN, written by P.Deuflhard and U.Nowak, that has been applied successfully for parameter identification in physical chemistry for many years.
The thesis deals with the implementation and application of out-of-the-box tools in linear and mixed integer programming. It documents the lessons learned and conclusions drawn from five years of implementing, maintaining, extending, and using several computer codes to solve real-life industrial problems. By means of several examples it is demonstrated how to apply algebraic modeling languages to rapidly devise mathematical models of real-world problems. It is shown that today's MIP solvers are capable of solving the resulting mixed integer programs, leading to an approach that delivers results very quickly. Even though, problems are tackled that not long ago required the implementation of specialized branch-and-cut algorithms. In the first part of the thesis the modeling language Zimpl is introduced. Chapter 2 contains a complete description of the language. In the subsequent chapter details of the implementation are described. Both theoretical and practical considerations are discussed. Aspects of software engineering, error prevention, and detection are addressed. In the second part several real-world projects are examined that employed the methodology and the tools developed in the first part. Chapter 4 presents three projects from the telecommunication industry dealing with facility location problems. Chapter 5 characterizes questions that arise in UMTS planning. Problems, models, and solutions are discussed. Special emphasis is put on the dependency of the precision of the input data and the results. Possible reasons for unexpected and undesirable solutions are explained. Finally, the Steiner tree packing problem in graphs, a well-known hard combinatorial problem, is revisited. A formerly known, but not yet used model is applied to combine switchbox wire routing and via minimization. All instances known from the literature are solved by this approach, as are some newly generated bigger problem instances.