title: Acorn: a grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface.
abstract: BACKGROUND
  Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment.
  
  
  RESULTS
  Here, we present Acorn, an open source (GNU GPL) grid computing system for constraint-based simulations of genome scale metabolic reaction networks within an interactive web environment. The grid-based architecture allows efficient execution of computationally intensive, iterative protocols such as Flux Variability Analysis, which can be readily scaled up as the numbers of models (and users) increase. The web interface uses AJAX, which facilitates efficient model browsing and other search functions, and intuitive implementation of appropriate simulation conditions. Research groups can install Acorn locally and create user accounts. Users can also import models in the familiar SBML format and link reaction formulas to major functional genomics portals of choice. Selected models and simulation results can be shared between different users and made publically available. Users can construct pathway map layouts and import them into the server using a desktop editor integrated within the system. Pathway maps are then used to visualise numerical results within the web environment. To illustrate these features we have deployed Acorn and created a web server allowing constraint based simulations of the genome scale metabolic reaction networks of E. coli, S. cerevisiae and M. tuberculosis.
  
  
  CONCLUSIONS
  Acorn is a free software package, which can be installed by research groups to create a web based environment for computer simulations of genome scale metabolic reaction networks. It facilitates shared access to models and creation of publicly available constraint based modelling resources.
authors: Institute of Informatics University of Warsaw, Poland.
authors: Jacek
authors: J
authors: Sroka
authors: Lukasz
authors: L
authors: Bieniasz-Krzywiec
authors: Szymon
authors: S
authors: Gwóźdź
authors: Dariusz
authors: D
authors: Leniowski
authors: Jakub
authors: J
authors: Lącki
authors: Mateusz
authors: M
authors: Markowski
authors: Claudio
authors: C
authors: Avignone-Rossa
authors: Michael E
authors: ME
authors: Bushell
authors: Johnjoe
authors: J
authors: McFadden
authors: Andrzej M
authors: AM
authors: Kierzek
references: Nat Rev Microbiol. 2004 Nov;2(11):886-97
references: 15494745
references: Genome Res. 2005 Jun;15(6):820-9
references: 15930493
references: Genome Biol. 2007;8(5):R89
references: 17521419
references: J Bacteriol. 2008 Apr;190(8):2790-803
references: 18192387
references: Plant Physiol. 2009 Nov;151(3):1570-81
references: 19755544
references: Mol Syst Biol. 2010 Sep 7;6:411
references: 20823849
references: BMC Bioinformatics. 2010 Apr 29;11:213
references: 20426874
references: Microbiology (Reading). 2002 Oct;148(Pt 10):2967-2973
references: 12368430
references: Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82
references: 17267599
references: Mol Syst Biol. 2007;3:121
references: 17593909
references: Bioinformatics. 2009 Nov 1;25(21):2850-2
references: 19689960
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D355-60
references: 19880382
references: Bioinformatics. 2009 Aug 1;25(15):1987-8
references: 19420054
references: BMC Microbiol. 2005 Mar 07;5:8
references: 15752426
references: J Biol Chem. 2007 Sep 28;282(39):28791-28799
references: 17573341
references: Genome Res. 2004 Jul;14(7):1298-309
references: 15197165
references: Microb Cell Fact. 2010 Jul 01;9:50
references: 20594333
references: Metab Eng. 2003 Oct;5(4):264-76
references: 14642354
references: Mol Syst Biol. 2010 Sep 7;6:401
references: 20823844
references: Bioinformatics. 2003 Mar 1;19(4):524-31
references: 12611808
references: Brief Bioinform. 2010 Jan;11(1):40-79
references: 19955237
references: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W144-9
references: 20483918