This work presents VANESA, a powerful and easy-to-use modeling software. The software application is laid out to support scientists from the natural sciences in the modeling and analysis of biological systems to better understand biological processes. Therefore, it combines different fields of research, such as information fusion, modeling, analysis, simulation, and network visualization, which are some of the most important areas in bioinformatics and systems

biology.

Using VANESA, scientists have the possibility to automatically reconstruct important biomedical systems with information from the databases KEGG, MINT, IntAct, HPRD, and BRENDA. Additionally, experimental results can be expanded with database information to better analyze the investigated elements and processes in an overall context. This results in biological models,

which enable scientists to focus on complex interactions and/or to investigate the role of individual components and processes within whole biological systems. Furthermore, users have the possibility to use graph theoretical approaches in VANESA to identify regulatory structures and significant actors within the modeled systems. These structures can then be further

investigated in the Petri net environment of VANESA for hypothesis generation and in silico experiments.

VANESA can be applied in many different life sciences, such as fundamental biology, theoretical biology, systems biology, biotechnology, and medical research, among others. The software application has already been proven useful in several biological and medical application cases, in which the provided features were applied to an increasing number of biochemical problems such as signal transduction, cellular rhythms and cell-to-cell communication, among others. Although it is primarily addressed to members of the laboratory, it can be used by any scientist. All interested people, who would like to use VANESA for their own research can download VANESA at http://vanesa.sf.net

or start it via Java web start. It is platform-independent and free-of-charge.