Within the project different models shall be developed and documented, to those belong models of the wnt pathway. Different models shall be developed for different objectives and complex phenomena like the interaction between different pathways shall be explored. One focus of interest will be spatial processes. The concrete models will be developed in close cooperation with projects in FSI and FSII as it shall help evaluating the methods that are developed in these projects. Also this project will help to answer questions that are raised in projects in FSIII. In addition, the different phases of the systems biology life cycle shall be analyzed and means that help a better integration between wet-lab and dry-lab experiments shall be developed, e.g., in the area of parameter estimation, or model validation. 

Status

The work is currently based on the modelling and simulation framework JAMES II, which is permanently extended to meet the challenges arising out of this project. Ongoing work is, e.g., the integration of further efficient algorithms and data structures for efficient simulations, the integration of sequential and parallel optimization algorithms for model parameter optimization, the integration of mechanisms for model validation, the integration of additional modelling languages to ease the creation of models, on reliable modelling and simulation experiments, on general flexible, scalable and reusable architectures for these, on automizing parts of the modelling and simulation workflow, workflows for modelling and simulation, and on quality issues in modelling and simulation software products.

Currently we are focusing on a better integration of technology for dry-lab experiments - a prerequisite for the integration of wet- and dry-lab technology.

Recent diploma/master theses

• Arvid Schwecke (2007): Parameteroptimierung und Sensitivitätsanalyse in James II. - Diplomarbeit, Universität Rostock.
• Stefan Leye (2008): Grid-Inspired Simulation of Computationally Intensive Models. - Diplomarbeit, Universität Rostock.
• Sebastian Lieske (2008): Aggregation verteilter Simulationsdaten. - Diplomarbeit, Universität Rostock.

• Peter Sievert (2008): Parallele Optimierung von Simulationsmodellen. - Diplomarbeit, Universität Rostock.
• Yvonne Oertel (2009): ExML - ein Austauschformat für valide Experimentbeschreibungen zum Austausch zwischen verschiedenen Simulationssystemen. - Diplomarbeit, Universität Rostock.
• Alexander Steiniger (2009): Web-basiertes visuelles Monitoring von James II Simulationen. - Diplomarbeit, Universität Rostock.
• Enrico Seib (2010): Arbeitsabläufe in der Modellierung und Simulation. Masterarbeit, Universität Rostock.
• Running (-2011): Model-checking of models in JAMES II by using LoLA. Bachelorarbeit, Universität Rostock
  
• Running (-2011): The integration of software to compute BioPEPA models in JAMES II. Bachelorarbeit, Universität Rostock / University of Edinburgh