AdvOL Student Seminars and Defences
Asma Paracha, December 12, 2017, 15:30-16:00, ITB 201
Speaker:   Asma Paracha

Title:  Lyndon factors and periodicities in strings
 
AdvOL Optimization Seminars
Alexander Rosa, December 12, 2017, 16:30-17:30, ITB 201
Speaker:   Alexander Rosa
Department of Mathematics & Statistics
McMaster University

Title:  Reaction graphs of combinatorial configurations
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Fields Institute Industrial Optimization Seminar, November 14, 2017
Speakers:   Christopher Swartz (McMaster University)
Jesus Flores-Carrillo (Praxair)

On the first Tuesday of each month, the Industrial Optimization Seminar is held at the Fields Institute. See the seminar series website for further information.
 
Home arrow Seminars arrow Invited seminars arrow Sabine Peres, October 20, 2015, 16:30-17:30, ITB 201
Friday, 24 November 2017
 
 
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Sabine Peres, October 20, 2015, 16:30-17:30, ITB 201
Speaker:   Sabine Peres
Laboratoire de Recherche en Informatique
Université Paris-Sud

Title:   SAT-based metabolics pathways analysis

Elementary flux modes (EFMs) are commonly accepted tools for metabolic network analysis under steady state conditions. They can be defined as the smallest sub-networks enabling the metabolic system to operate in steady state with all irreversible reactions proceeding in the appropriate direction. However, when networks are complex, the number of EFMs quickly leads to a combinatorial explosion, preventing from drawing even simple conclusions from their analysis. Since the concept of EFMs analysis, there has been an important and ongoing effort to develop more efficient algorithms during the last two decades. However, these methods share a common bottleneck: they enumerate all the EFMs which make the computation impossible when the metabolic network is large and only few works try to search only EFMs with specific properties. As we will show in this paper, enumerating all the EFMs is not necessary in many cases and it is possible to directly query the network instead with an appropriate tool. For ensuring a good query time, we will rely on a state of the art SAT solver, working on a propositional encoding of EFMs, and enriched with a simple SMT-like solver ensuring EFMs consistency with stoichiometric constraints. We illustrate our new framework by providing experimental evidences of almost immediate answer times on a non trivial EFMs network.
 
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