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

Molecular Systems Biology

Volumn 11, Issue 10, 2015, Pages

  Ebrahim, Ali ^a   Almaas, Eivind ^b   Bauer, Eugen ^c   Bordbar, Aarash ^d   Burgard, Anthony P ^e   Chang, Roger L ^f   Dräger, Andreas ^a,g   Famili, Iman ^h   Feist, Adam M ^a   Fleming, Ronan M T ^c   Fong, Stephen S ⁱ   Hatzimanikatis, Vassily ^j   Holder, Allen ^l   Hucka, Michael ^m   Hyduke, Daniel ⁿ   Jamshidi, Neema ^o,p,q   Lee, Sang Yup ^k   Le Novère, Nicolas ^r   Lerman, Joshua A ^a   Lewis, Nathan E ^s   Ma, Ding ^t   Mahadevan, Radhakrishnan ^u   Maranas, Costas ^v   Nagarajan, Harish ^e   Navid, Ali ^w   Nielsen, Jens ^k,x   Nielsen, Lars K ^y   Nogales, Juan ^z   Noronha, Alberto ^c   Pal, Csaba ^aa   Palsson, Bernhard O ^a   Papin, Jason A ^ab   Patil, Kiran R ^ac   Price, Nathan D ^ad   Reed, Jennifer L ^ae   Saunders, Michael ^t   Senger, Ryan S ^af   Sonnenschein, Nikolaus ^k   Sun, Yuekai ^t   Thiele, Ines ^c   more..

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^c UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^d Sinopia Biosciences   (United States)

^e GENOMATICA INC   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

^g UNIVERSITY OF TÜBINGEN   (Germany)

^h INTREXON CORPORATION   (United States)

ⁱ Virginia Commonwealth University   (United States)

^j EPFL   (Switzerland)

^k Chalmers University of Technology   (Denmark)

^l ROSE HULMAN INSTITUTE OF TECHNOLOGY   (United States)

^m CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

ⁿ Utah State University   (United States)

^o UNIVERSITY OF CALIFORNIA   (United States)

^p UNIVERSITY OF CALIFORNIA   (United States)

^q Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^r BABRAHAM INSTITUTE   (United Kingdom)

^s UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^t Stanford University   (United States)

^u UNIVERSITY OF TORONTO   (Canada)

^v The Pennsylvania State University   (United States)

^w LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^x CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^y UNIVERSITY OF QUEENSLAND   (Australia)

^z CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^aa INSTITUTE OF BIOCHEMISTRY   (Hungary)

^ab University of Virginia   (United States)

^ac EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^ad INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^ae University of Wisconsin Madison   (United States)

^af State University   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

BIOMASS PRODUCTION; CELL GROWTH; GENE SEQUENCE; GENETIC MODEL; GENOME; GENOME SCALE MODEL; GROWTH RATE; LETTER; PRIORITY JOURNAL; REPRODUCIBILITY; STANDARD; THERMODYNAMICS; BIOLOGICAL MODEL;

GENOME; MODELS, BIOLOGICAL; THERMODYNAMICS;

EID: 84945933008     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20156157     Document Type: Letter

References (12)

1. Applegate DL, Cook W, Dash S, Espinoza DG, (2007) Exact solutions to linear programming problems. Oper Res Lett 35: 693-699
2. Bordbar A, Monk JM, King ZA, Palsson BO, (2014) Constraint-based models predict metabolic and associated cellular functions. Nat Rev Genet 15: 107-120
3. Chindelevitch L, Trigg J, Regev A, Berger B, (2014) An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models. Nat Commun 5: 4893
4. Dräger A, Palsson BØ, (2014) Improving collaboration by standardization efforts in systems biology. Front Bioeng Biotechnol 2: 61
5. Joyner D, Čertík O, Meurer A, Granger BE, (2012) Open source computer algebra systems: SymPy. ACM Commun Comput Algebra 45: 225-234
6. Lee KH, Park JH, Kim TY, Kim HU, Lee SY, (2007) Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol 3: 149
7. McCloskey D, Palsson BØ, Feist AM, (2013) Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli. Mol Syst Biol 9: 661
8. Orth JD, Thiele I, Palsson BØ, (2010) What is flux balance analysis? Nat Biotechnol 28: 245-248
9. Ravikrishnan A, Raman K, (2015) Critical assessment of genome-scale metabolic networks: the need for a unified standard. Brief Bioinform doi: 10.1093/bib/bbv003
10. Satish Kumar V, Ferry JG, Maranas CD, (2011) Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans. BMC Syst Biol 5: 28
11. Schellenberger J, Lewis NE, Palsson BØ, (2011a) Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J 100: 544-553
12. Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson BØ, (2011b) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6: 1290-1307