Bridging the gaps in systems biology

M. Cvijovic, J. Almquist, J. Hagmar, S. Hohmann, H.-M. Kaltenbach, E. Klipp, M. Krantz, P. Mendes, S. Nelander, J. Nielsen, A. Pagnani, N. Przulj, A. Raue, J. Stelling, S. Stoma, F. Tobin, J.A.H. Wodke, R. Zecchina, M. Jirstrand. Molecular Genetics and Genomics, 2014, 289(5), 727-734.

Systems biology aims at creating mathematical models, i.e. computational reconstructions of biological systems and processes that will result in a new level of understanding – the elucidation of the basic and presumably conserved “design” and “engineering” principles of bio-molecular systems. Thus systems biology will move biology from a phenomenological to a predictive science. Mathematical modeling of biological networks and processes has already greatly improved our understanding of many cellular processes. However, given the massive amount of qualitative and quantitative data currently produced and number of burning questions in health care and biotechnology needed to be solved, is still in its early phases. The field requires novel approaches for abstraction, for modeling bioprocesses that follow different biochemical and biophysical rules, and for combining different modules into larger models that still allow realistic simulation with the computational power available today. We have identified and discussed currently most prominent problems in systems biology: (i) How to bridge different scales of modelling abstraction, (ii) How to bridge the gap between topological and mechanistic modelling, and (iii) How to bridge the wet and dry lab gap. The future success of systems biology largely depends on bridging the recognized gaps.

Authors and Affiliations

  • Marija Cvijovic, Chalmers University of Technology and University of Gothenburg, Sweden
  • Joachim Almquist, Fraunhofer-Chalmers Centre, Sweden
  • Jonas Hagmar, Fraunhofer-Chalmers Centre, Sweden
  • Stefan Hohmann, University of Gothenburg, Sweden
  • Hans-Michael Kaltenbach, ETH, Switzerland
  • Edda Klipp, Humboldt University, Germany
  • Marcus Krantz, Humboldt University, Germany
  • Pedro Mendes, Manchester University, UK
  • Sven Nelander, Uppsala Univeristy, Sweden
  • Jens Nielsen, Chalmers University of Technology, Sweden
  • Andrea Pagnani, Politecnico di Torino, Italy
  • Natasa Przulj, Imperial College, UK
  • Andreas Raue, University of Freiburg, Germany
  • Jörg Stelling, ETH, Switzerland
  • Szymon Stoma, INRIA, France
  • Frank Tobin, Tobin Consulting LLC, USA
  • Judith A. H. Wodke, Humboldt University, Germany
  • Riccardo Zecchina, Politecnico di Torino, Italy
  • Mats Jirstrand, Fraunhofer-Chalmers Centre, Sweden

Photo credits: Nic McPhee