Photons, photosynthesis, and high-performance computing: Challenges, progress, and promise of modeling metabolism in green algae

Journal of Physics: Conference Series

Volumn 125, Issue , 2008, Pages

  Chang, C H ^a   Graf, P ^a   Alber, D M ^a   Kim, K ^a   Murray, G ^b   Posewitz, M ^b   Seibert, M ^a  

^a NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

^b Department of Geology and Geological Engineering   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 65549159599     PISSN: 17426588     EISSN: 17426596     Source Type: Conference Proceeding    
DOI: 10.1088/1742-6596/125/1/012048     Document Type: Article

References (33)

1. Schulze-Kremer S 2002 In Silico Biol. 2 0017
2. Consortium T G O 2000 Nat. Genet. 25 25-9
3. Degtyarenko K, de Matos P, Ennis M, Hastings J, Zbinden M, McNaught A, Alcntara R, Darsow M, Guedj M and Ashburner M 2008 Nucl. Acids Res. 36 D344-D350
4. Beckett D (ed) 2004 RDF/XML Syntax Specification (Revised) Resource Description Framework (RDF) (W3C)
5. Powell A and Johnston P 2003 Guidelines for implementing Dublin Core in XML Tech. rep. Dublin Core Metadata Initiative
6. Hucka M, Finney A, Sauro H M, Bolouri H, Doyle J C, Kitano H, Arkin A P, Bornstein B J, Bray D, Cornish-Bowden A, Cuellar A A, Dronov S, Gilles E D, Ginkel M, Gor V, Goryanin I I, Hedley W J, Hodgman T C, Hofmeyr J H, Hunter P J, Juty N S, Kasberger J L, Kremling A, Kummer U, Le Novère N, Loew L M, Lucio D, Mendes P, Minch E, Mjolsness E D, Nakayama Y, Nelson M R, Nielsen P F, Sakurada T, Schaff J C, Shapiro B E, Shimizu T S, Spence H D, Stelling J, Takahashi K, Tomita M, Wagner J and Wang J 2003 Bioinformatics 19 524-531
7. Bornstein B J, Keating S M, Jouraku A and Hucka M 2008 Bioinformatics 24 880-1
8. Machné R, Finney A, Müller S, Lu J, Widder S and Flamm C 2006 Bioinformatics 22 1406-1407
9. Ausbrooks R, Buswell S, Carlisle D, Dalmas S, Devitt S, Diaz A, Froumentin M, Hunter R, Ion P, Kohlhase M, Miner R, Poppelier N, Smith B, Soiffer N, Sutor R and Watt S 2001 Mathematical markup language (MathML) Version 2.0 (2nd edn
10. Schulz M, Uhlendorf J, Klipp E and Liebermeister W 2006 Genome Informatics Ser. 17 62-71
11. Palsson B 2006 Syst. Biology: Properties Reconstructed Networks (New York: Cambridge Univ. Press)
12. Lee J M, Gianchandani E P and Papin J A 2007 Briefings Bioinformatics prov
13. Klipp E, Herwig R, Kowald A, Wierling C and Lehrach H 2005 Systems Biology in Practice: Concepts, Implementation and Application (Weinheim: Wiley-VCH)
14. Beard D A, Babson E, Curtis E and Qian H 2004 J. Theor. Biol. 228 327-33
15. Beard D A, Liang S d and Qian H 2002 Biophys. J. 83 79-86
16. Feist A M, Henry C S, Reed J L, Krummenacker M, Joyce A R, Karp P D, Broadbelt L J, Hatzimanikatis V and Palsson B 2007 Mol. Syst. Biol. 3 121
17. Jamshidi N and Palsson B 2007 BMC Syst. Biol. 1 26
18. Oh Y K, Palsson B, Park S M, Schilling C H and Mahadevan R 2007 J. Biol. Chem. 282 28791-9
19. Teusink B, Passarge J, Reijenga C A, Esgalhado E, van der Weijden C C, Schepper M, Walsh M C, Bakker B M, van Dam K, Westerhoff H V and Snoep J L 2000 Eur. J. Biochem. 267 5313-29
20. Segel I H 1975 Enzyme Kinetics (Wiley Wiley Classics Library, 1993 ed New York: John Wiley & Sons)
21. Beard D A 2005 PLoS Comput. Biol. 1 e36
22. Wu F, Yang F, Vinnakota K C and Beard D A 2007 J. Biol. Chem. 282 24525-37
23. Grima R and Schnell S 2006 Biophysical Chem. 124 1-10
24. Mulquiney P J and Kuchel P W 1999 Biochem. J. 342 581-96
25. Mus F, Dubini A, Seibert M, Posewitz M C and Grossman A R 2007 J. Biol. Chem. 282 25475-86
26. Drghici S 2003 Data Analysis Tools for DNA Microarrays (Boca Raton: Chapman & Hall/CRC) 25
27. Hindmarsh A C, Brown P N, Grant K E, Lee S L, Serban R, Shumaker D E and Woodward C S 2005 ACM Trans. Math. Softw. 31 363-396 ISSN 0098-3500
28. Benson S, McInnes L C, Moré J, Munson T and Sarich J 2007 TAO user manual (revision 1.9) Tech. Rep. ANL/MCS-TM-242 Mathematics and Computer Science Division, Argonne National Laboratory http://www.mcs.anl.gov/tao
29. Chang C, Alber D, Graf P, Kim K and Seibert M 2007 J. Phys.: Conference Ser. 78 012011
30. Alber D, Chang C, Graf P, Kim K and Seibert M 2008 in preparation
31. Berry S and Rumberg B 2000 Bioelectrochemistry 53 35-53
32. Zhu X G, de Sturler E and Long S P 2007 Plant Physiology 145 513-26 supplementary Information link included in Link to PDF field
33. Posewitz M C, Smolinski S L, Kanakagiri S, Melis A, Seibert M and Ghirardi M L 2004 Plant Cell 16 2151-2163