title: Object-oriented biological system integration: a SARS coronavirus example.
abstract: BACKGROUND
  The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary.
  
  
  RESULTS
  By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems.
  
  
  BACKGROUND
  A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm
authors.affiliation: Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon Street, PO Box 250835, Charleston, SC 29425, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Shegogue
authors.forename: W Jim
authors.initials: WJ
authors.lastname: Zheng
mesh_terms: D000818:Animals; D003198:Computer Simulation; D006801:Humans; D008954:Models, Biological; D045473:Severe acute respiratory syndrome-related coronavirus / Q000472:pathogenicity* / Q000502:physiology*; D045169:Severe Acute Respiratory Syndrome / Q000821:virology*; D049490:Systems Biology / Q000379:methods*; D018511:Systems Integration; D014764:Viral Proteins / Q000378:metabolism*
chemical_list: D014764:Viral Proteins
references.citation: Proteomics. 2004 Feb;4(2):492-504
references.pmid: 14760722
references.citation: J Biol Chem. 2004 Jan 16;279(3):1637-42
references.pmid: 14561748
references.citation: Nature. 2003 Nov 27;426(6965):450-4
references.pmid: 14647384
references.citation: Nat Genet. 2000 May;25(1):25-9
references.pmid: 10802651
references.citation: Virology. 1994 Aug 1;202(2):1018-23
references.pmid: 8030202
references.citation: FEBS Lett. 2003 Nov 20;554(3):257-63
references.pmid: 14623076
references.citation: J Virol. 2004 Jul;78(13):6723-34
references.pmid: 15194747
references.citation: In Silico Biol. 2003;3(1-2):215-27
references.pmid: 12762857
references.citation: Bioinformatics. 2003 Mar 1;19(4):524-31
references.pmid: 12611808
references.citation: Adv Virus Res. 1997;48:1-100
references.pmid: 9233431
references.citation: Bioinformatics. 2002 Jun;18(6):825-37
references.pmid: 12075018
references.citation: Mol Biol Cell. 1999 Aug;10(8):2703-34
references.pmid: 10436023
references.citation: Prog Biophys Mol Biol. 2004 Nov;86(3):379-406
references.pmid: 15302205
references.citation: Biochem Biophys Res Commun. 2003 Dec 26;312(4):1159-64
references.pmid: 14651994
references.citation: Bioinformatics. 2001 Nov;17(11):1053-7
references.pmid: 11724734
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D3-22
references.pmid: 14681349
references.citation: Brief Bioinform. 2002 Mar;3(1):32-44
references.pmid: 12002222
references.citation: Biochemistry. 1986 Mar 25;25(6):1335-9
references.pmid: 3008826
references.citation: Science. 2002 Mar 1;295(5560):1664-9
references.pmid: 11872830
references.citation: Brief Bioinform. 2002 Jun;3(2):166-80
references.pmid: 12139436
references.citation: Science. 2003 May 30;300(5624):1394-9
references.pmid: 12730500
references.citation: Bioinformatics. 2005 Feb 1;21(3):415-7
references.pmid: 15353449
references.citation: Annu Rev Genomics Hum Genet. 2001;2:343-72
references.pmid: 11701654
references.citation: J Virol. 2004 Jul;78(14):7311-8
references.pmid: 15220404
references.citation: Biosystems. 2004 Jul;75(1-3):3-14
references.pmid: 15245800