Biological systems models taken to the next level
The goal of systems biology is to predict biological phenomena through the use of computational and mathematical modelling. To calculate the effects of cellular functions, highly detailed computer models are constructed to identify trends, while mathematical models precisely calculate the interactions of components to predict system behaviour. A key aspect, these models need to reflect real-world conditions by incorporating physico-chemical constraints to make them diagnostically conclusive. However, genome-scale development of holistic, detailed, and reliable computer models incorporating physico-chemical constraints can only be achieved using precise automated methods. The EU-funded project AMBICON (Automated multi-level modelling of biological systems considering physico-chemical constraints), an international collaboration project between the University of California, San Diego, in the United States and the University of Tübingen, Germany, addressed this challenge. The aim was to develop new computational methods that can model biological systems at all levels. Project partners identified and solved the limitations of existing model representation standards and developed a new method to allow researchers to identify potential bacterial transcription factors for targeted experiments. A new model-based approach also showed that it is possible to calculate the minimal protein equipment of bacterial cells. In addition, scientists prepared personalised blood models across multiple cell types. Contributions were made to a new visualisation method for metabolic networks as well as the extensively updated and improved open source knowledge-base of models called BiGG Models. Finally, the outcomes of this project were not only published in scientific articles, but also through social media such as blog posts, Twitter, Facebook, and YouTube as well as international workshops and conferences. The AMBICON methodology will permit entire cellular systems to be simulated, thereby providing major benefits for the biotechnological production of medication and the development of personalised medicine.
Keywords
Cells, physico-chemical constraints, systems biology, models, AMBICON
