Systems Biology Colloquium

This is a series of invited colloquiual lectures provided by top researchers in the field of systems biology, theoretical and computational biology, bioinformatics and related fields of applied mathematics and computer science. The series is prepared in collaboration with Global Change Research Centre AS CR as a part of the ESF co-funded project CyanoTeam. The project is associated with an international network CyanoNetwork.

Lectures run irregularly during the academic year with respect to the time schedule provided on this web page. Each of the lectures will be announced at least one week in advance.

Next presentation

TITLE: Exploring Chemical Transformation Space

Christoph Flamm

  • When: Wednesday 14th of November 2012, 14:00
  • Where: Faculty of Informatics MU, Botanick√° 68a, lecture room C416
  • Who: doc. Dr. Christoph Flamm (associated professor at Institute of Theoretical Chemistry, University of Vienna)

[ Research Profile ]


Although (bio)chemical reaction networks have been under intensive study during the last decades, a general theoretical formalism capturing both the algebraic and the energetic properties of the underlying chemistry is still missing.

The structural change of molecules during chemical reactions can conveniently be modeled as graph rewrite, if the participating molecules are treated as edge and vertex labeled graphs. The graph grammar approach to chemical transformation captures nicely the algebraic structure of chemical transformation i.e. the fact that reacting molecules yield novel molecules while retaining the possibility to assign physico-chemical properties to the molecules via the arsenal of chemoinformatics methods.

With a constructive method to expand arbitrary chemical transformation space at hand, the focus of interest shifts to the question of finding sub network with particular properties, e.g. exhibiting auto-catalytic behavior, in these spaces. The problem of finding such sub networks can be formulated as a network flow problem on the underlying hyper-graph which can be solved using integer linear programming techniques.


[1] Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler (2012) Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete. J Sys Chem 3:1 (doi:10.1186/1759-2208-3-1)

Upcoming talks

Next speaker is planned to be Vashti Galpin, Ph.D., a well-acclaimed computer scientist from University of Edinburgh with many experiences in application of process algebras to systems biology. The talk is planned for February/March 2013.

Please check this page for updates.

Passed talks

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