Standards and Tools for Model Exchange and Analysis in Systems Biology

This work is about standards in systems biology and about support for these standards in systems biology software tools. The work is divided into three sections. The first section describes an extension to the systems biology markup language (SBML) for the storage of graphical information on biochemical reaction networks. In the first part it explains the history of the extension, what it is about and what it can be used for and in the second part it details implementations of the extension in the form of several different software tools. The second section of this work deals with the Systems Biology Markup Language (SBML) standard and the different aspects of its support in the COPASI software tool. COPASI is a tool for the simulation and analysis of biochemical reaction networks and it uses SBML files as an exchange format for these reaction network models. This section highlights the different aspects of the implementation of the SBML standard as well as the extension to the SBML standard that is described in the first section of this work. Additionally this section describes how the functionality of COPASI, which is written in the C++ programming language, has been made available to developers using other programming languages like Java or Python and how this functionality is used in different systems biology computer programs around the world. The third section of this thesis discusses methods for the normalization and comparison of mathematical expressions and the implementation of these methods in the form of a computer program. This program is used to analyze the mathematical expressions in all models of the current release of the BioModels database. At several occasions in this text, it is demonstrated how the methods and tools described in these three sections can make a valuable contribution to research in systems biology

SBML Level 3 package: Render, Version 1, Release 1

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). This document describes the SBML Level 3 Render package that complements the SBML Level 3 Layout package and provides a means of capturing the precise rendering of the elements in a diagram. The SBML Level 3 Render package provides a flexible approach to rendering that is independent of both the underlying SBML model and the Layout information. There can be one block of render information that applies to all layouts or an additional block for each layout. Many of the elements used in the current render specification are based on corresponding elements from the SVG specification. This allows us to easily convert a combination of layout information and render information into a SVG drawing

SBML layout and render news

This presentation gives a short overview on the layout and render extension to SBML and on recent software updates we did that support those two extensions

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded