scholarly journals Genome-scale strain designs based on regulatory minimal cut sets

2015 ◽  
Vol 31 (17) ◽  
pp. 2844-2851 ◽  
Author(s):  
Radhakrishnan Mahadevan ◽  
Axel von Kamp ◽  
Steffen Klamt
Keyword(s):  
Minimal Cut Sets ◽  
Minimal Cut ◽  
Genome Scale

scholarly journals Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Steffen Klamt ◽  
Radhakrishnan Mahadevan ◽  
Axel von Kamp
Keyword(s):  
Metabolic Networks ◽  
Dual System ◽  
Mixed Integer ◽  
Mathematical Framework ◽  
Stoichiometric Matrix ◽  
Farkas Lemma ◽  
Minimal Cut Sets ◽  
Minimal Cut ◽  
General Importance ◽  
Genome Scale

Abstract Background The concept of minimal cut sets (MCS) has become an important mathematical framework for analyzing and (re)designing metabolic networks. However, the calculation of MCS in genome-scale metabolic models is a complex computational problem. The development of duality-based algorithms in the last years allowed the enumeration of thousands of MCS in genome-scale networks by solving mixed-integer linear problems (MILP). A recent advancement in this field was the introduction of the MCS2 approach. In contrast to the Farkas-lemma-based dual system used in earlier studies, the MCS2 approach employs a more condensed representation of the dual system based on the nullspace of the stoichiometric matrix, which, due to its reduced dimension, holds promise to further enhance MCS computations. Results In this work, we introduce several new variants and modifications of duality-based MCS algorithms and benchmark their effects on the overall performance. As one major result, we generalize the original MCS2 approach (which was limited to blocking the operation of certain target reactions) to the most general case of MCS computations with arbitrary target and desired regions. Building upon these developments, we introduce a new MILP variant which allows maximal flexibility in the formulation of MCS problems and fully leverages the reduced size of the nullspace-based dual system. With a comprehensive set of benchmarks, we show that the MILP with the nullspace-based dual system outperforms the MILP with the Farkas-lemma-based dual system speeding up MCS computation with an averaged factor of approximately 2.5. We furthermore present several simplifications in the formulation of constraints, mainly related to binary variables, which further enhance the performance of MCS-related MILP. However, the benchmarks also reveal that some highly condensed formulations of constraints, especially on reversible reactions, may lead to worse behavior when compared to variants with a larger number of (more explicit) constraints and involved variables. Conclusions Our results further enhance the algorithmic toolbox for MCS calculations and are of general importance for theoretical developments as well as for practical applications of the MCS framework.

Computing irreversible minimal cut sets in genome-scale metabolic networks via flux cone projection

2018 ◽  
Vol 35 (15) ◽  
pp. 2618-2625 ◽  
Author(s):  
Annika Röhl ◽  
Tanguy Riou ◽  
Alexander Bockmayr
Keyword(s):  
Metabolic Networks ◽  
Supplementary Information ◽  
Oriented Matroid ◽  
Matroid Theory ◽  
Supplementary Data ◽  
Large Genome ◽  
Minimal Cut Sets ◽  
Minimal Cut ◽  
Genome Scale ◽  
Target Reaction

Abstract Motivation Minimal cut sets (MCSs) for metabolic networks are sets of reactions which, if they are removed from the network, prevent a target reaction from carrying flux. To compute MCSs different methods exist, which may fail to find sufficiently many MCSs for larger genome-scale networks. Results Here we introduce irreversible minimal cut sets (iMCSs). These are MCSs that consist of irreversible reactions only. The advantage of iMCSs is that they can be computed by projecting the flux cone of the metabolic network on the set of irreversible reactions, which usually leads to a smaller cone. Using oriented matroid theory, we show how the projected cone can be computed efficiently and how this can be applied to find iMCSs even in large genome-scale networks. Availability and implementation Software is freely available at https://sourceforge.net/projects/irreversibleminimalcutsets/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Minimal cut sets with time dependencies analysis

2013 ◽  
Vol 17 (2) ◽  
pp. 219
Author(s):  
Paweł Skrobanek
Keyword(s):  
Minimal Cut Sets ◽  
Minimal Cut ◽  
Time Dependencies

FTAe – Fault Tree Analysis in Microsoft Excel

2014 ◽  
Vol 889-890 ◽  
pp. 591-594
Author(s):  
Richard Kuracina ◽  
Denis Šandor ◽  
Karol Balog
Keyword(s):  
Fault Tree ◽  
Fault Tree Analysis ◽  
Software Tool ◽  
Short Description ◽  
Microsoft Excel ◽  
Tree Analysis ◽  
Minimal Cut Sets ◽  
Minimal Cut ◽  
Cut Set

FTAe is software tool for Fault Tree Analysis in Microsoft Excel. This paper is focused on short description of created FTAe. A brief description of Fault Tree Analysis is in the first part of paper. The Structure, Logic and Minimal Cut Sets in Fault Tree analysis is described too. Next part of this paper is focused on the choice of algorithm for cut set calculation and brief description of structure of FTAe. Finally, advantages of FTAe software in Microsoft Excel are described in conclusions.

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