Do genome-scale models need exact solvers or clearer standards?

被引：36

作者：

Ebrahim, Ali ^{[1
]}

Almaas, Eivind ^{[2
]}

Bauer, Eugen ^{[3
]}

Bordbar, Aarash ^{[4
]}

Burgard, Anthony P. ^{[5
]}

Chang, Roger L. ^{[6
]}

Draeger, Andreas ^{[1
,7
]}

Famili, Iman ^{[8
]}

Feist, Adam M. ^{[1
]}

Fleming, Ronan M. T. ^{[3
]}

Fong, Stephen S. ^{[9
]}

Hatzimanikatis, Vassily ^{[10
]}

Herrgard, Markus J. ^{[11
]}

Holder, Allen ^{[12
]}

Hucka, Michael ^{[13
]}

Hyduke, Daniel ^{[14
]}

Jamshidi, Neema ^{[15
,16
]}

Lee, Sang Yup ^{[11
,17
]}

Le Novere, Nicolas ^{[18
]}

Lerman, Joshua A. ^{[1
]}

Lewis, Nathan E. ^{[19
]}

Ma, Ding ^{[20
]}

Mahadevan, Radhakrishnan ^{[21
]}

Maranas, Costas ^{[22
]}

Nagarajan, Harish ^{[5
]}

Navid, Ali ^{[23
]}

Nielsen, Jens ^{[11
,24
]}

Nielsen, Lars K. ^{[25
]}

Nogales, Juan ^{[26
]}

Noronha, Alberto ^{[3
]}

Pal, Csaba ^{[27
]}

Palsson, Bernhard O. ^{[1
]}

Papin, Jason A. ^{[28
]}

Patil, Kiran R. ^{[29
]}

Price, Nathan D. ^{[30
]}

Reed, Jennifer L. ^{[31
]}

Saunders, Michael

Senger, Ryan S. ^{[32
]}

Sonnenschein, Nikolaus ^{[11
]}

Sun, Yuekai ^{[33
]}

Thiele, Ines ^{[3
]}

机构：

[1] Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA

[2] Norwegian Univ Sci & Technol, Dept Biotechnol, N-7034 Trondheim, Norway

[3] Univ Luxembourg, Luxembourg Ctr Syst Biomed, Belval, Luxembourg

[4] Sinopia Biosci Inc, San Diego, CA USA

[5] Genomat Inc, San Diego, CA USA

[6] Harvard Univ, Sch Med, Dept Syst Biol, Boston, MA 02115 USA

[7] Univ Tubingen, Ctr Bioinformat Tuebingen ZBIT, Tubingen, Germany

[8] Intrexon Inc, San Diego, CA USA

[9] Virginia Commonwealth Univ, Dept Chem & Life Sci Engn, Richmond, VA USA

[10] Ecole Polytechn Fed Lausanne, Lab Computat Syst Biotechnol, Lausanne, Switzerland

[11] Tech Univ Denmark, Novo Nordisk Fdn Ctr Biosustainabil, DK-2800 Lyngby, Denmark

[12] Rose Hulman Inst Technol, Dept Math, Terre Haute, IN 47803 USA

[13] CALTECH, Dept Comp & Math Sci, Pasadena, CA 91125 USA

[14] Utah State Univ, Dept Biol Engn, Logan, UT 84322 USA

[15] Univ Calif Los Angeles, Dept Radiol, Los Angeles, CA USA

[16] Univ Calif San Diego, Inst Engn Med, San Diego, CA 92103 USA

[17] Korea Adv Inst Sci & Technol, Dept Chem & Biomol Engn, BK21 Plus Program, Daejeon 305701, South Korea

[18] Babraham Inst, Cambridge, England

[19] Univ Calif San Diego, Dept Pediat, San Diego, CA 92103 USA

[20] Stanford Univ, Dept Management Sci & Engn, Stanford, CA 94305 USA

[21] Univ Toronto, Dept Chem Engn & Appl Chem, Toronto, ON, Canada

[22] Penn State Univ, Dept Chem Engn, University Pk, PA 16802 USA

[23] Lawrence Livermore Natl Lab, Biosci & Biotechnol Div, Livermore, CA USA

[24] Chalmers Univ Technol, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden

[25] Univ Queensland, AIBN, Brisbane, Qld, Australia

[26] CSIC, Ctr Invest Biol, Dept Environm Biol, Madrid, Spain

[27] Biol Res Ctr, Synthet & Syst Biol Unit, H-6701 Szeged, Hungary

[28] Univ Virginia, Dept Biomed Engn, Charlottesville, VA USA

[29] European Mol Biol Lab, D-69012 Heidelberg, Germany

[30] Inst Syst Biol, Seattle, WA USA

[31] Univ Wisconsin, Dept Chem & Biol Engn, Madison, WI USA

[32] Virginia Tech, Dept Biol Syst Engn, Blacksburg, VA USA

[33] Stanford Univ, Inst Computat & Math Engn, Stanford, CA 94305 USA

来源：

MOLECULAR SYSTEMS BIOLOGY | 2015年 / 11卷 / 10期

基金：

英国生物技术与生命科学研究理事会;

关键词：

CONSTRAINT-BASED MODELS; TOOLBOX;

D O I：

10.15252/msb.20156157

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Recent results obtained by Chindelevitch et al (2014) are challenged by Ebrahim et al, illustrating several issues in the reproducibility of computational biology methods.[graphic not available: see fulltext]

引用

页数：3

共 12 条

[1] Exact solutions to linear programming problems [J].

Applegate, David L. ;

Cook, William ;

Dash, Sanjeeb ;

Espinoza, Daniel G. .

OPERATIONS RESEARCH LETTERS, 2007, 35 (06) :693-699

[2] Constraint-based models predict metabolic and associated cellular functions [J].

Bordbar, Aarash ;

Monk, Jonathan M. ;

King, Zachary A. ;

Palsson, Bernhard O. .

NATURE REVIEWS GENETICS, 2014, 15 (02) :107-120

[3] An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models [J].

Chindelevitch, Leonid ;

Trigg, Jason ;

Regev, Aviv ;

Berger, Bonnie .

NATURE COMMUNICATIONS, 2014, 5

[4]

Drager Andreas, 2014, Front Bioeng Biotechnol, V2, P61, DOI 10.3389/fbioe.2014.00061

[5]

Joyner D., 2012, ACM COMMUN COMPUT AL, V45, P225, DOI [10.1145/2110170.2110185, DOI 10.1145/2110170.2110185]

[6] Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans [J].

Kumar, Vinay Satish ;

Ferry, James G. ;

Maranas, Costas D. .

BMC SYSTEMS BIOLOGY, 2011, 5

[7] Systems metabolic engineering of Escherichia coli for L-threonine production [J].

Lee, Kwang Ho ;

Park, Jin Hwan ;

Kim, Tae Yong ;

Kim, Hyun Uk ;

Lee, Sang Yup .

MOLECULAR SYSTEMS BIOLOGY, 2007, 3 (1)

[8] Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli [J].

McCloskey, Douglas ;

Palsson, Bernhard O. ;

Feist, Adam M. .

MOLECULAR SYSTEMS BIOLOGY, 2013, 9

[9] What is flux balance analysis? [J].

Orth, Jeffrey D. ;

Thiele, Ines ;

Palsson, Bernhard O. .

NATURE BIOTECHNOLOGY, 2010, 28 (03) :245-248

[10] Critical assessment of genome-scale metabolic networks: the need for a unified standard [J].

Ravikrishnan, Aarthi ;

Raman, Karthik .

BRIEFINGS IN BIOINFORMATICS, 2015, 16 (06) :1057-1068

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