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Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods

Vitor Vieira, Paulo Maia, Isabel Rocha, Miguel Rocha
2017 Interdisciplinary Sciences Computational Life Sciences  
Keywords Constraint-based modeling · Metabolic engineering · Pathway analysis · Minimal cut sets · Strain optimization Abbreviations List of Enzymes ACOAH Acetyl-CoA hydrolase ATPS atp synthase G6PDH Glucose  ...  Recently, MCSEnumerator has extended the scale of these methods, namely regarding enumeration of minimal cut sets, now able to handle GSMMs.  ...  Acknowledgements The authors thank the project "DeYeastLibrary-Designer yeast strain library optimized for metabolic engineering applications", Ref.  ... 
doi:10.1007/s12539-017-0218-7 pmid:28238112 fatcat:6yfi4pqmvzecfgmtb2ot55azoi

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

Steffen Klamt, Radhakrishnan Mahadevan, Axel von Kamp
2020 BMC Bioinformatics  
Background The concept of minimal cut sets (MCS) has become an important mathematical framework for analyzing and (re)designing metabolic networks.  ...  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).  ...  The funding bodies did not play any role in the design or development of this study, in the analysis and interpretation of data, or in the writing of this manuscript.  ... 
doi:10.1186/s12859-020-03837-3 pmid:33167871 fatcat:oe3kpjjhcjat3h7nib4icizdoe

Design Space Exploration via Answer Set Programming Modulo Theories [article]

Philipp Wanko
2019 arXiv   pre-print
As a result, for the first time, we proposed a sophisticated methodology that allows for the direct integration of multi-objective optimization of non-linear objectives into ASP.  ...  My research aims at developing systems that help the designer express the complex design problem in a declarative way and explore the design space to obtain divers sets of solutions with desirable properties  ...  Hence, we developed three different exploration strategies calculating the Pareto set in an anytime fashion.  ... 
arXiv:1905.05248v1 fatcat:qhqhlihgy5bz5pe5b2sz4xozlq

A solver-aided language for test input generation

Talia Ringer, Dan Grossman, Daniel Schwartz-Narbonne, Serdar Tasiran
2017 Proceedings of the ACM on Programming Languages  
Developing a small but useful set of inputs for tests is challenging. We show that a domain-specific language backed by a constraint solver can help the programmer with this process.  ...  The solver can generate a set of test inputs and guarantee that each input is different from other inputs in a way that is useful for testing.  ...  ACKNOWLEDGMENTS We thank Emina Torlak for help with our contributions to Rosette. We thank Nikolaj Bjorner for prompt fixes to bugs in the development version of Z3.  ... 
doi:10.1145/3133915 dblp:journals/pacmpl/RingerGST17 fatcat:w3bggqy4x5btvb5tcxapgzp57a

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

Axel von Kamp, Steffen Klamt, Costas D. Maranas
2014 PLoS Computational Biology  
In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal) provide an exhaustive enumeration approach.  ...  Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still  ...  Acknowledgments We are grateful to Oliver Hä dicke for valuable hints and discussions. Author Contributions Analyzed the data: AVK SK. Wrote the paper: AVK SK. Designed the study: SK.  ... 
doi:10.1371/journal.pcbi.1003378 pmid:24391481 pmcid:PMC3879096 fatcat:6zn7wf27k5fppae6xmcuk5d7fe

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets

Philipp Schneider, Axel von Kamp, Steffen Klamt, Kiran Raosaheb Patil
2020 PLoS Computational Biology  
The concept of minimal cut sets (MCS) provides a flexible framework for analyzing properties of metabolic networks and for computing metabolic intervention strategies.  ...  In particular, we present a set of novel compression rules for GPR associations, which effectively speedup the computation of gene-based MCS by a factor of up to one order of magnitude.  ...  Acknowledgments We thank Elad Noor for providing thermodynamic data for the iML1515 E. coli model used for the characterization of the MCS.  ... 
doi:10.1371/journal.pcbi.1008110 pmid:32716928 fatcat:rt5eyc54mbh3xard6t3pvrwaxe

SCIL — Symbolic Constraints in Integer Linear Programming [chapter]

Ernst Althaus, Alexander Bockmayr, Matthias Elf, Michael Jünger, Thomas Kasper, Kurt Mehlhorn
2002 Lecture Notes in Computer Science  
SCIL introduces symbolic constraints into branch-and-cut-and-price algorithms for integer linear programs.  ...  Symbolic constraints are known from constraint programming and contribute signi cantly to the expressive p o wer, ease of use, and e ciency of constraint programs.  ...  The success of the system strongly depends on the quality of the symbolic constraints in the library.  ... 
doi:10.1007/3-540-45749-6_11 fatcat:nxav3bgfbrb5nd4dwatsogfonu

Logic, Optimization, and Constraint Programming

John N. Hooker
2002 INFORMS journal on computing  
It traces the history of logic-based methods in optimization and the development of constraint programming in artificial intelligence.  ...  It sketches the intellectual background for recent efforts at integration.  ...  Some more specific research projects might also be mentioned. • Combine integrated modeling and decomposition into a single framework. • Develop a repertory of useful global constraints for each of several  ... 
doi:10.1287/ijoc. fatcat:22kiqfcqqvfcppogsgbd5xqj2y

Minimal cut sets in a metabolic network are elementary modes in a dual network

Kathrin Ballerstein, Axel von Kamp, Steffen Klamt, Utz-Uwe Haus
2011 Computer applications in the biosciences : CABIOS  
Motivation: Elementary Modes (EMs) and Minimal Cut Sets (MCSs) provide important techniques for metabolic network modeling.  ...  We introduce a duality framework for metabolic networks where the enumeration of MCSs in the original network is reduced to identifying the EMs in a dual network.  ...  ACKNOWLEDGMENT Funding: This work was partially supported by the German Federal Ministry of Education and Research (FORSYS-Center MaCS) and the Ministry of Education and Research of Saxony-Anhalt (Research  ... 
doi:10.1093/bioinformatics/btr674 pmid:22190691 fatcat:65cuwawignc5fevukhtd5tmsjq

Comparison of pathway analysis and constraint-based methods for cell factory design

Vítor Vieira, Paulo Maia, Miguel Rocha, Isabel Rocha
2019 BMC Bioinformatics  
To this end, we devised a pipeline including enumeration of strategies from evolutionary algorithms (EA) and minimal cut sets (MCS), filtering and flux analysis of predicted mutants to optimize the production  ...  Minimal cut sets are particularly interesting since their definition allows searching for intervention strategies that impose strong growth-coupling phenotypes, and are not subject to optimality bias when  ...  Acknowledgements The authors thank Paulo Vilaça for helpful discussions regarding constraintbased modelling methods and Hugo Giesteira for the assistance in integrating the minimal cut set enumeration  ... 
doi:10.1186/s12859-019-2934-y fatcat:hnkpupduxreppldxdzn6zyx2su

Integrated crew scheduling and roster problem for trainmasters of passenger railway transportation

Dung-Ying Lin, Meng-Rung Tsai
2019 IEEE Access  
In this paper, we propose a formulation to integrate these two critical sub-problems and develop a branch-and-price-and-cut algorithm and a depth-first search-based algorithm to solve the composite problem  ...  This type of observation can only be accurately characterized when these two sub-problems are considered in an integrated manner.  ...  Finally, the rostering rules have more impact than the scheduling rules in the planning process, which is an observation that can only be made within an integrated framework.  ... 
doi:10.1109/access.2019.2900028 fatcat:2peeo52sibbuhkd3x2qxkk22om

Integrated approach for security of electricity supply analysis

Gerd H. Kjølle, Oddbjørn Gjerde
2010 International Journal of Systems Assurance Engineering and Management  
The integrated methodology is under development in an ongoing research project focusing the power system reliability analysis, making it possible to take the risk of extraordinary events into account.  ...  This paper describes an integrated approach for security of electricity supply analysis, by the integration of power system reliability analysis with the power market analysis.  ...  The reliability model is based on summation of contributions from the critical contingencies (min. cut-sets).  ... 
doi:10.1007/s13198-010-0014-9 fatcat:eiocc77cubhfjljrxd5vrjnaea

Answer Set Programming for Computing Constraints-Based Elementary Flux Modes: Application to Escherichia coli Core Metabolism

Maxime Mahout, Ross P. Carlson, Sabine Peres
2020 Processes  
Traditionally, EFMs are computed by the double description method, an efficient algorithm based on matrix calculation; however, only a few constraints can be integrated into this computation.  ...  We present aspefm, a hybrid computational tool based on Answer Set Programming (ASP) and Linear Programming (LP) that permits the computation of EFMs while implementing many different types of constraints  ...  An overview of the framework is presented in Figure 3 .  ... 
doi:10.3390/pr8121649 fatcat:zis664lpbrbxvbtfd7df6zl6nu

Logic-based MultiObjective Optimization for Restoration Planning [chapter]

Jing Gong, Earl E. Lee, John E. Mitchell, William A. Wallace
2009 Springer Optimization and Its Applications  
After a disruption in an interconnected set of systems, it is necessary to restore service.  ...  The speed at which a useful set of points on the efficient frontier can be determined should allow the integration of the determination of the tasks to be performed with the evaluation of the various costs  ...  Acknowledgments This research is supported by NSF grant CMS 0301661, Decision Technologies for Managing Critical Infrastructure Interdependencies  ... 
doi:10.1007/978-0-387-88617-6_11 fatcat:ademieo3sfcndig37cxfwwpyde

Automatic robust convex programming

Johan Löfberg
2012 Optimization Methods and Software  
This paper presents the robust optimization framework in the modeling language YALMIP, which carries out robust modeling and uncertainty elimination automatically, and allows the user to concentrate on  ...  While introducing the software package, a brief summary of robust optimization is given, as well as some comments on modeling and tractability of complex convex uncertain optimization problems.  ...  An important feature of this relaxation, compared to more advanced schemes using recent developments in convex optimization based relaxations of polynomial problems, such as sum-of-squares and moment relaxations  ... 
doi:10.1080/10556788.2010.517532 fatcat:4uvmsmjuejflzc6xxidjmkeikq
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