Novel methods for constraint-based modelling with the COBRA Toolbox

Wednesday, August 30, 2017 -
10:00am to 11:00am
The FUNG Auditorium
Ronan M. T. Fleming

Luxembourg Centre for Systems Biomedicine, University of Luxembourg

Novel methods for constraint-based modelling with the COBRA Toolbox


COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for the integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain design, experimental design, network visualisation and network integration of cheminformatic, metabolomic, transcriptomic, proteomic and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and non-linear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This talk discusses how some of these novel methods have and will enable advances in constraint-based modelling in a wide variety of molecular systems biology scenarios.


Dr. Fleming received his PhD in Systems Biology from the National University of Ireland, Galway. His dissertation focused on the analysis of transcriptomic data in E. coli using empirical mode decomposition a mathematical exploration of the physico-chemical basis of constraint-based modeling. Dr. Fleming leads the Systems Biochemistry Group, an interdisciplinary research group of mathematical, computational and experimental biologists. The fundamental interest is to develop scalable mathematical and numerical analysis techniques that increase the predictive fidelity of biomolecular network models, by incorporating physicochemical constraints, motivated by optimality principles. Their applied interest is in the aetiopathogenesis and amelioration of Parkinson’s disease. Dr. Fleming is also an Adjunct Assistant Professor in the Division of Analytical Biosciences, Leiden Academic Centre for Drug Research at the University of Leiden, The Netherlands.