DocumentCode :
1991283
Title :
XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes
Author :
Blinov, Michael L. ; Moraru, Ion I.
Author_Institution :
Univ. of Connecticut Health Center, Farmington
fYear :
2007
fDate :
14-17 Oct. 2007
Firstpage :
987
Lastpage :
994
Abstract :
Multi-state molecules and multi-component complexes are commonly involved in cellular signaling. Accounting for molecules that have multiple potential states, such as a protein that may be phosphorylated on multiple residues, and molecules that combine to form heterogeneous complexes located among multiple compartments, generates an effect of combinatorial complexity. Models involving relatively few signaling molecules can include thousands of distinct chemical species. Several software tools (StochSim, BioNetGen) are already available to deal with combinatorial complexity. Such tools need information standards if models are to be shared, jointly evaluated and developed. Here we discuss XML conventions that can be adopted for modeling biochemical reaction networks described by user-specified reaction rules. These could form a basis for possible future extensions of the Systems Biology Markup Language (SBML).
Keywords :
XML; biochemistry; biology computing; macromolecules; molecular biophysics; proteins; XML encoding; biochemical reaction networks; cellular signaling; combinatorial complexity; heterogeneous complexes; multi-component molecular complexes; multi-state molecules; multiple potential states; multiple residues; phosphorylation; protein; rule-based modeling; software tools; systems biology markup language; user-specified reaction rules; Amino acids; Biological system modeling; Chemicals; Communication system signaling; Encoding; Markup languages; Proteins; Software tools; Systems biology; XML; SBML; XML; mashine-readable description; mathematical model; molecular interaction networks; multi-component complexes; rule-based;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on
Conference_Location :
Boston, MA
Print_ISBN :
978-1-4244-1509-0
Type :
conf
DOI :
10.1109/BIBE.2007.4375678
Filename :
4375678
Link To Document :
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