메뉴 건너뛰기




Volumn 12, Issue , 2011, Pages

FASIMU: Flexible software for flux-balance computation series in large metabolic networks

Author keywords

[No Author keywords available]

Indexed keywords

COMMERCIAL SOLVERS; COMPUTATIONAL TOOLS; FLUX MINIMIZATIONS; GNU PUBLIC LICENSE; LINEAR OPTIMIZATION; OPEN SOURCE PROJECTS; OPTIMIZATION PROGRAMS; THERMODYNAMIC FEASIBILITY;

EID: 78651553577     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-28     Document Type: Article
Times cited : (54)

References (47)
  • 1
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • 10.1038/84379, 11175725
    • Edwards JS, Ibarra RU, Palsson BO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 2001, 19(2):125-130. 10.1038/84379, 11175725.
    • (2001) Nat Biotechnol , vol.19 , Issue.2 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 2
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • 10.1016/j.jtbi.2007.12.008, 18249414
    • Schuster S, Pfeiffer T, Fell DA. Is maximization of molar yield in metabolic networks favoured by evolution?. J Theor Biol 2008, 252(3):497-504. 10.1016/j.jtbi.2007.12.008, 18249414.
    • (2008) J Theor Biol , vol.252 , Issue.3 , pp. 497-504
    • Schuster, S.1    Pfeiffer, T.2    Fell, D.A.3
  • 3
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • 10.1038/msb4100162, 1949037, 17625511
    • Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007, 3:119. 10.1038/msb4100162, 1949037, 17625511.
    • (2007) Mol Syst Biol , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 4
    • 33845238737 scopus 로고    scopus 로고
    • Systematic assignment of thermodynamic constraints in metabolic network models
    • 1664590, 17123434
    • Kümmel A, Panke S, Heinemann M. Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics 2006, 7:512. 1664590, 17123434.
    • (2006) BMC Bioinformatics , vol.7 , pp. 512
    • Kümmel, A.1    Panke, S.2    Heinemann, M.3
  • 5
    • 73849090293 scopus 로고    scopus 로고
    • Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology
    • 10.1002/biot.200900234, 19946878
    • Milne CB, Kim PJ, Eddy JA, Price ND. Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology. Biotechnol J 2009, 4(12):1653-1670. 10.1002/biot.200900234, 19946878.
    • (2009) Biotechnol J , vol.4 , Issue.12 , pp. 1653-1670
    • Milne, C.B.1    Kim, P.J.2    Eddy, J.A.3    Price, N.D.4
  • 7
    • 34347258175 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
    • 10.1038/nprot.2007.99, 17406635
    • Becker SA, Feist AM, Mo ML, Hannum G, Palsson B, Herrgård MJ. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2007, 2(3):727-738. 10.1038/nprot.2007.99, 17406635.
    • (2007) Nat Protoc , vol.2 , Issue.3 , pp. 727-738
    • Becker, S.A.1    Feist, A.M.2    Mo, M.L.3    Hannum, G.4    Palsson, B.5    Herrgård, M.J.6
  • 8
    • 0003876171 scopus 로고    scopus 로고
    • MATLAB - The Language Of Technical Computing
    • [The MathWorks, Inc]
    • MATLAB - The Language Of Technical Computing. [The MathWorks, Inc]., http://www.mathworks.com/products/matlab/
  • 9
    • 84874758859 scopus 로고    scopus 로고
    • TOMLAB is a general purpose development and modeling environment in Matlab for research, teaching and practical solution of optimization problems
    • [Tomlab support and development. Västerås Technology Park, Trefasgatan 4, SE-721 30 Västerås, Sweden]
    • TOMLAB is a general purpose development and modeling environment in Matlab for research, teaching and practical solution of optimization problems. [Tomlab support and development. Västerås Technology Park, Trefasgatan 4, SE-721 30 Västerås, Sweden]., http://tomopt.com/tomlab
  • 11
    • 47649105109 scopus 로고    scopus 로고
    • The Systems Biology Research Tool: evolvable open-source software
    • 10.1186/1752-0509-2-55, 2446383, 18588708
    • Wright J, Wagner A. The Systems Biology Research Tool: evolvable open-source software. BMC Syst Biol 2008, 2:55. 10.1186/1752-0509-2-55, 2446383, 18588708.
    • (2008) BMC Syst Biol , vol.2 , pp. 55
    • Wright, J.1    Wagner, A.2
  • 12
    • 0346250869 scopus 로고    scopus 로고
    • BioSPICE: access to the most current computational tools for biologists
    • 10.1089/153623103322637715, 14683613
    • Garvey TD, Lincoln P, Pedersen CJ, Martin D, Johnson M. BioSPICE: access to the most current computational tools for biologists. OMICS 2003, 7(4):411-420. 10.1089/153623103322637715, 14683613.
    • (2003) OMICS , vol.7 , Issue.4 , pp. 411-420
    • Garvey, T.D.1    Lincoln, P.2    Pedersen, C.J.3    Martin, D.4    Johnson, M.5
  • 13
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • 137552, 12415116
    • Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 2002, 99(23):15112-15117. 137552, 12415116.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.23 , pp. 15112-15117
    • Segrè, D.1    Vitkup, D.2    Church, G.M.3
  • 15
    • 42549159856 scopus 로고    scopus 로고
    • AnNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
    • 10.1186/1471-2105-9-199, 2375130, 18416814
    • Zamboni N, Kümmel A, Heinemann M. anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics 2008, 9:199. 10.1186/1471-2105-9-199, 2375130, 18416814.
    • (2008) BMC Bioinformatics , vol.9 , pp. 199
    • Zamboni, N.1    Kümmel, A.2    Heinemann, M.3
  • 16
    • 48549085591 scopus 로고    scopus 로고
    • Pruning genome-scale metabolic models to consistent ad functionem networks
    • full_text, 18546498
    • Hoffmann S, Hoppe A, Holzhütter HG. Pruning genome-scale metabolic models to consistent ad functionem networks. Genome Inform 2007, 18:308-319. full_text, 18546498.
    • (2007) Genome Inform , vol.18 , pp. 308-319
    • Hoffmann, S.1    Hoppe, A.2    Holzhütter, H.G.3
  • 17
    • 36248990302 scopus 로고    scopus 로고
    • Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks
    • 10.1186/1752-0509-1-23, 1903363, 17543097
    • Hoppe A, Hoffmann S, Holzhütter HG. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst Biol 2007, 1:23. 10.1186/1752-0509-1-23, 1903363, 17543097.
    • (2007) BMC Syst Biol , vol.1 , pp. 23
    • Hoppe, A.1    Hoffmann, S.2    Holzhütter, H.G.3
  • 18
    • 51349092391 scopus 로고    scopus 로고
    • Network-based prediction of human tissue-specific metabolism
    • 10.1038/nbt.1487, 18711341
    • Shlomi T, Cabili MN, Herrgård MJ, Palsson B, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008, 26(9):1003-1010. 10.1038/nbt.1487, 18711341.
    • (2008) Nat Biotechnol , vol.26 , Issue.9 , pp. 1003-1010
    • Shlomi, T.1    Cabili, M.N.2    Herrgård, M.J.3    Palsson, B.4    Ruppin, E.5
  • 19
    • 77956456621 scopus 로고    scopus 로고
    • Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis
    • [Accepted], 10.1186/1752-0509-4-120, 2941759, 20807400
    • Huthmacher C, Hoppe A, Bulik S, Holzhütter HG. Antimalarial drug targets in Plasmodium falciparum predicted by stage-specific metabolic network analysis. BMC Syst Biol 2010, 4(120). [Accepted], 10.1186/1752-0509-4-120, 2941759, 20807400.
    • (2010) BMC Syst Biol , vol.4 , Issue.120
    • Huthmacher, C.1    Hoppe, A.2    Bulik, S.3    Holzhütter, H.G.4
  • 20
    • 84871320661 scopus 로고    scopus 로고
    • IBM ILOG CPLEX - High-performance mathematical programming engine
    • IBM ILOG CPLEX - High-performance mathematical programming engine. , http://www.ibm.com/software/integration/optimization/cplex
  • 21
    • 84888282669 scopus 로고    scopus 로고
    • LINDO Systems - Optimization Software: Integer Programming, Linear Programming, Nonlinear Programming, Global Optimization
    • LINDO Systems - Optimization Software: Integer Programming, Linear Programming, Nonlinear Programming, Global Optimization. , http://www.lindo.com
  • 22
    • 84870583176 scopus 로고    scopus 로고
    • GLPK (GNU Linear Programming Kit)
    • GLPK (GNU Linear Programming Kit). , http://www.gnu.org/software/glpk/
  • 23
    • 0242483744 scopus 로고    scopus 로고
    • Lp_solve - a Mixed Integer Linear Programming (MILP) solver
    • lp_solve - a Mixed Integer Linear Programming (MILP) solver. , http://lpsolve.sourceforge.net/
  • 24
    • 84888278179 scopus 로고    scopus 로고
    • GNU Awk
    • GNU Awk. , http://www.gnu.org/software/gawk/
  • 25
    • 84888284279 scopus 로고    scopus 로고
    • Bash, the GNU Project's Bourne Again SHell, a complete implementation of the IEEE POSIX and Open Group shell specification
    • Bash, the GNU Project's Bourne Again SHell, a complete implementation of the IEEE POSIX and Open Group shell specification. , http://www.gnu.org/software/bash/
  • 27
    • 70349581497 scopus 로고    scopus 로고
    • Cytoscape: a community-based framework for network modeling
    • full_text, 19597788
    • Killcoyne S, Carter GW, Smith J, Boyle J. Cytoscape: a community-based framework for network modeling. Methods Mol Biol 2009, 563:219-239. full_text, 19597788.
    • (2009) Methods Mol Biol , vol.563 , pp. 219-239
    • Killcoyne, S.1    Carter, G.W.2    Smith, J.3    Boyle, J.4
  • 28
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • 10.1186/1752-0509-1-2, 1847467, 17408509
    • Klamt S, Saez-Rodriguez J, Gilles ED. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 2007, 1:2. 10.1186/1752-0509-1-2, 1847467, 17408509.
    • (2007) BMC Syst Biol , vol.1 , pp. 2
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3
  • 29
    • 3242795003 scopus 로고    scopus 로고
    • The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
    • Holzhütter HG. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur J Biochem 2004, 271(14):2905-2922.
    • (2004) Eur J Biochem , vol.271 , Issue.14 , pp. 2905-2922
    • Holzhütter, H.G.1
  • 30
    • 32044470064 scopus 로고    scopus 로고
    • The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies
    • Holzhütter HG. The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies. Biosystems 2006, 83(2-3):98-107.
    • (2006) Biosystems , vol.83 , Issue.2-3 , pp. 98-107
    • Holzhütter, H.G.1
  • 31
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • 10.1073/pnas.0406346102, 1140402, 15897462
    • Shlomi T, Berkman O, Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 2005, 102(21):7695-7700. 10.1073/pnas.0406346102, 1140402, 15897462.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.21 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 32
    • 0035812464 scopus 로고    scopus 로고
    • Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
    • 10.1002/bit.1127, 11427938
    • Burgard AP, Maranas CD. Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol Bioeng 2001, 74(5):364-375. 10.1002/bit.1127, 11427938.
    • (2001) Biotechnol Bioeng , vol.74 , Issue.5 , pp. 364-375
    • Burgard, A.P.1    Maranas, C.D.2
  • 33
    • 4644220226 scopus 로고    scopus 로고
    • Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states
    • 10.1101/gr.2546004, 515326, 15342562
    • Reed JL, Palsson B. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res 2004, 14(9):1797-1805. 10.1101/gr.2546004, 515326, 15342562.
    • (2004) Genome Res , vol.14 , Issue.9 , pp. 1797-1805
    • Reed, J.L.1    Palsson, B.2
  • 34
    • 34247094270 scopus 로고    scopus 로고
    • An interval approach for dealing with flux distributions and elementary modes activity patterns
    • 10.1016/j.jtbi.2006.12.029, 17292923
    • Llaneras F, Picó J. An interval approach for dealing with flux distributions and elementary modes activity patterns. J Theor Biol 2007, 246(2):290-308. 10.1016/j.jtbi.2006.12.029, 17292923.
    • (2007) J Theor Biol , vol.246 , Issue.2 , pp. 290-308
    • Llaneras, F.1    Picó, J.2
  • 35
    • 0032787428 scopus 로고    scopus 로고
    • Metabolic flux analysis: a powerful tool for monitoring tissue function
    • 10.1089/ten.1999.5.347, 10477857
    • Lee K, Berthiaume F, Stephanopoulos GN, Yarmush ML. Metabolic flux analysis: a powerful tool for monitoring tissue function. Tissue Eng 1999, 5(4):347-368. 10.1089/ten.1999.5.347, 10477857.
    • (1999) Tissue Eng , vol.5 , Issue.4 , pp. 347-368
    • Lee, K.1    Berthiaume, F.2    Stephanopoulos, G.N.3    Yarmush, M.L.4
  • 36
    • 52949144612 scopus 로고    scopus 로고
    • Detection of stoichiometric inconsistencies in biomolecular models
    • 10.1093/bioinformatics/btn425, 18697772
    • Gevorgyan A, Poolman MG, Fell DA. Detection of stoichiometric inconsistencies in biomolecular models. Bioinformatics 2008, 24(19):2245-2251. 10.1093/bioinformatics/btn425, 18697772.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2245-2251
    • Gevorgyan, A.1    Poolman, M.G.2    Fell, D.A.3
  • 38
    • 77956416570 scopus 로고    scopus 로고
    • FluxViz - Cytoscape Plug-in for Vizualisation of Flux Distributions in Networks
    • König M, Holzhütter HG. FluxViz - Cytoscape Plug-in for Vizualisation of Flux Distributions in Networks. Genome Informatics 2010, 24:96-103., http://sourceforge.net/projects/fluxvizplugin
    • (2010) Genome Informatics , vol.24 , pp. 96-103
    • König, M.1    Holzhütter, H.G.2
  • 40
    • 34447543690 scopus 로고    scopus 로고
    • METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks
    • 10.1186/1752-0509-1-5, 1839895, 17408512
    • Gille C, Hoffmann S, Holzhütter HG. METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks. BMC Syst Biol 2007, 1:5. 10.1186/1752-0509-1-5, 1839895, 17408512.
    • (2007) BMC Syst Biol , vol.1 , pp. 5
    • Gille, C.1    Hoffmann, S.2    Holzhütter, H.G.3
  • 42
    • 9444266171 scopus 로고    scopus 로고
    • CellDesigner: a process diagram editor for gene-regulatory and biochemical networks
    • Funahashi A, Tanimura N, Morohashi M, Kitano H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 2003, 1(5):159-162.
    • (2003) BIOSILICO , vol.1 , Issue.5 , pp. 159-162
    • Funahashi, A.1    Tanimura, N.2    Morohashi, M.3    Kitano, H.4
  • 43
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration
    • 10.1089/153623103322637670, 14683609
    • Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS 2003, 7(4):355-372. 10.1089/153623103322637670, 14683609.
    • (2003) OMICS , vol.7 , Issue.4 , pp. 355-372
    • Sauro, H.M.1    Hucka, M.2    Finney, A.3    Wellock, C.4    Bolouri, H.5    Doyle, J.6    Kitano, H.7
  • 44
    • 84870855544 scopus 로고    scopus 로고
    • Numerical Analysis Group, Science & Facilities Council
    • Numerical Analysis Group, Science & Facilities Council The HSL Mathematical Software Library Numerical Analysis Group, Science & Facilities Council., http://www.hsl.rl.ac.uk/
    • The HSL Mathematical Software Library
  • 45
    • 17544366029 scopus 로고    scopus 로고
    • Expa: a program for calculating extreme pathways in biochemical reaction networks
    • 10.1093/bioinformatics/bti228, 15613397
    • Bell SL, Palsson B. expa: a program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 2005, 21(8):1739-1740. 10.1093/bioinformatics/bti228, 15613397.
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1739-1740
    • Bell, S.L.1    Palsson, B.2
  • 46
  • 47
    • 33747856186 scopus 로고    scopus 로고
    • Metatool 5.0: fast and flexible elementary modes analysis
    • 10.1093/bioinformatics/btl267, 16731697
    • von Kamp A, Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 2006, 22(15):1930-1931. 10.1093/bioinformatics/btl267, 16731697.
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1930-1931
    • von Kamp, A.1    Schuster, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.