SYSINBIO

SYSINBIO - Systems Biology as a Driver for Industrial Biotechnology


Coordination and support action (EU Coordination Action - call FP7-KBBE-2007-1)


Partners:

Organisation Name Organisation Short Name Scientific Team Leader Town Country
Chalmers University of Technology CHALMERS
Jens NIELSEN
Lisbeth OLSSON
Gothenburg Sweden
Technical University of Denmark DTU
Anna Eliasson Lantz
Kiran Patil
Lyngby Denmark
Valtion teknillinen tutkimuskeskus VTT
Merja PENTTILÄ
Espoo Finland
Ecole Polytechnique Federale de Lausanne LPF
Vassily HATZIMANIKATIS
Lausanne Switzerland
University of Stuttgart US
Matthias REUSS
Martin SIEMANN-HERZBERG
Stuttgart Germany
Technische Universiteit Delft TUD
Jack PRONK
Joseph HEIJNEN
Delft The Netherlands
University of Milano Bicocca UMIMIB
Danillo PORRO
Milano Italy
University of Minho UM
Isabel ROCHA
Braga Portugal
Siegen University SU
Wolfgang WIECHERT
Siegen Germany
Swiss Federal Institute of Technology Zürich ETH
Matthias HEINEMANN
Uwe SAUER
Zürich Switzerland
Saarland University USAAR
Elmar HEINZLE
Christoph WITTMANN
Saarbrücken Germany
Lund University LU
Marie Gorwa GRAUSLUND
Bärbel HAHN-HÄGERDAL
Lund Sweden
Bogazici University BU
Betul KIRDAR
Istanbul Turkey
Fluxome Sciences FS
Jochen FÖRSTER
Lyngby Denmark
Novozymes NZ
Carsten HJORT
Bagsværd Denmark
Chr. Hansen CH
Hans van den BRINK
Hørsholm Denmark
Fraunhofer Chalmers Center FCC
Mats Jirstrand
Gothenburg Sweden
BASF BASF
Oskar ZELDER
Ludwigshafen Germany
DSM DSM
Hermann PEL
Delft The Netherlands
Degussa DEGUSSA
Ralf TAKORS
Künsebeck Germany
Metabolic Explorer METEX
Philippe SOUCAILLE
Saint-Beauzire France


Objectives

The overall goal of SYSINBIO is to coordinate research activities in the field of model driven metabolic engineering in Europe and according to the concept described above coordinate how systems biology can be used to improve the performance of metabolic model and further how mathematical models can be used for improved design of cell factories used in industrial biotechnology.

The overall goal is divided into 11 specific objectives that are dealt with in 11 workpackages that form the basis of the project:

  • Coordination of research efforts in the field of model guided metabolic engineering within Europe through organizing yearly meetings of leading European research groups working in this field. Furthermore, coordination will involve setting up a web-site that allows for easy exchange of information and interactions between the different groups (WP1).
  • Coordination of advanced education in the field of metabolic engineering in Europe. This will involve dedicated courses and workshops on mathematical modelling and metabolic engineering, and establishing advanced research training and student exchange between the involved laboratories in order to ensure further education of researchers in the multidisciplinary field of metabolic engineering (WP2).
  • Organizing an international conference with focus on the use of model guided metabolic engineering for development of efficient cell factories. The conference will ensure dissemination of new results generated by the participating research groups and further push forward the research field by bridging between academia and industry (WP3).
  • Coordination of the development of metabolic models and providing a database for existing models. Concepts and methods for setting up genome-scale metabolic models will be exchanged and developed. This will involve implementation and adaptation of existing platforms for setting up this kind of models, as well as defining efficient workflows for model generation (WP4).
  • Coordinating the development of dynamic models for design of metabolic engineering strategies. Concepts and methods for setting up and analyzing dynamic models will be exchanged and developed. Efficient workflows for setting up dynamic models of metabolic reaction networks including parameter estimation, model validation and discrimination, parameter estimation, and simulation will be exchanged and defined for different types of dynamic models (WP5).
  • Coordinating the development of novel simulation tools that allow the use of metabolic models for design of metabolic engineering strategies. Different algorithms for identification of metabolic engineering targets through the use of genome-scale metabolic models will be compared and evaluated, and based on the evaluation, general guidelines for the use of metabolic models for metabolic engineering will be specified (WP6).
  • Coordinating the integration of omics data with metabolic models in order to improve their predictive strength. Different concepts and methods for integration of "omics" data into metabolic models will be compared and evaluated leading to guidelines on how such data can be used for the reconstruction and evaluation of genome-scale metabolic models (WP7).
  • Coordinating the development of novel tools for 13C-based fluxomics (both experimental and computational tools). Different tools for fluxomics will be compared and evaluated, and guidelines for quantification of metabolic fluxes in microorganisms, during industrial fermentations, will be proposed (WP8).
  • Coordinating the development of novel tools for metabolomics. Different methods for sampling and analysis of key intracellular metabolites will be compared and evaluated, and guidelines for use of different analytical tools for the analysis of intracellular metabolites, in different industrially important microorganisms, will be set up (WP9).
  • Coordination of the use of statistical methods and metabolic models for upgrading the information content in "omics" data. Different methods and concepts will be evaluated for their ability to upgrade the information content in "omics" data, and in particularly it will be evaluated how this kind of data can be used to identify novel metabolic engineering targets (WP10).
  • Coordinating research activities on the use of DNA arrays, tiling DNA arrays and DNA sequencing for rapid identification of mutations that lead to improved phenotypic properties. The use of these different methods for mapping of mutations in strain lineages will be evaluated and new standards and concepts will be defined (WP11).