SurreyFBA software

The constrained based modeling (CBM) of genome scale metabolic networks (GSMNs) allows prediction of metabolic capabilities of the cell from repertoire of enzymes implied by genome annotation and information about media conditions. The computer simulations of global cell metabolism in CBM framework are ideal for rational design of metabolism in synthetic biology approach to industrial biotechnology, identification of metabolic vulnerabilities of bacterial pathogens and investigation of metabolic states of healthy, aging and diseased human tissues. The success of CBM methodology gave raise to vast array of computational protocols for simulation of metabolic capabilities, nutrient consumption dynamics in batch cultures, and design of mutant strains. Moreover, the CBM offered fundamentally new approach to analysis of omics data. Our SurreyFBA software makes CBM methods available through Graphics User Interface. The stand-alone command line version, ideal for development of bioinformatics pipelines is also available.

Software distributions:

  • Download SurreyFBA-1.32 with JyMet (Gevorgyan, Bushell, Avignone-Rossa, Kierzek, Bioinformatics. 2011, 27:433-434.) [PubMed])
  • Download SurreyFBA2 with JyMet2 - SurreyFBA2 (manuscript in preparation) has been implemented by Huihai Wu with contributions from Albert Gevorgyan and Wataru Mori. New features include methods for analysis of -omics data in the context of GSMNs, linear inhibitor constraints, interface to QSSPN and network layout editor.
  • Simulocyte - under development. This version will implement full network editor with 3D visualisation and our novel QSSPN algorithm.

Tutorials:

People:

  • Huihai Wu,  h.wu@surrey.ac.uk (SurreyFBA2 development, SurreyFBA and JyMet contact)
  • Mehdi Khoury, m.khoury@surrey.ac.uk (Simulocyte development)
  • Andrzej Kierzek, a.kierzek@surrey.ac.uk (project leader)

Funding:

BBSRC grant: "SurreyFBA: Interactive tool for computer simulations of genome scale metabolic networks” PI: Andrzej Kierzek. Co-applicants: Johnjoe McFadden, Nick Plant, Claudio Avignone-Rossa