scholarly journals Integer Programming-Based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model

PLoS ONE ◽  
2014 ◽  
Vol 9 (3) ◽  
pp. e92637 ◽  
Author(s):  
Wei Lu ◽  
Takeyuki Tamura ◽  
Jiangning Song ◽  
Tatsuya Akutsu
2012 ◽  
pp. 774-791
Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.


Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.


Author(s):  
Takeyuki Tamura ◽  
Kazuhiro Takemoto ◽  
Tatsuya Akutsu

In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results.


2015 ◽  
Vol 22 (2) ◽  
pp. 85-110 ◽  
Author(s):  
Wei Lu ◽  
Takeyuki Tamura ◽  
Jiangning Song ◽  
Tatsuya Akutsu

Author(s):  
Fransiskus Lauson Matondang ◽  
Rosnani Ginting

PT XYZ sering mengalami keterlambatan waktu karena dalam setiap keterlambatan yang dilakukan selalu ada penalty yang diberikan kepada perusahaan dan hal ini mengakibatkan tambahan biaya , oleh karena itu hal ini harus dihindari dengan membuat penjadwalan yang efisien, dalam hal ini dilakukanlah perbaikan dengan meminimisasi waktu penyelesaian maksimum Cmax pada mesin paralel yang berpola aliran flowshop (dan tidak boleh dilakukan interupsi yang dilakukan pada pekerjaan yang sedang diproses, untuk melakukan pekerjaan lainnya, satu lintasan hanya memproduksi satu produk dan hanya satu produk juga yang dikerjakan secara langsung. Waktu penyelesaian yang berbeda dari setiap mesin dengan pengerjaannya juga adalah masalah yang dihadapi untuk menjadikan mesin mesin ini sesuai menjadi satu penjadwalan yang terintegrasi dengan metode integer programming yang membuat penjadwalan dengan konsep riset operasi dengan metode pendekatan 0-1 utuk menjadi lebih efisien lagi , dihasilkan minimisasi keterlambatan total penyelesaian order dengan 42,28 menit lebih baik dari sebelumnya.   PT XYZ often experiences time delays because in every delay made there is always a penalty given to the company and this results in additional costs, therefore this must be avoided by making efficient scheduling, in this case repairs are carried out by minimizing the maximum completion time of Cmax on parallel machines that are patterned with flowshop flow (and no interruptions should be carried out on the work being processed, to do other work, one track only produces one product and only one product is directly worked. Different completion times of each machine with the workmanship is also the problem faced to make this machine suitable to be one scheduling integrated with integer programming methods that makes scheduling with the operational research concept with the 0-1 approach method to be more efficient, resulting in minimization of the delay in the total settlement of orders with 42.28 minutes was better than before.


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