Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks v

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 environ...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Jacek Sroka, Lukasz Bieniasz-Krzywiec, Szymon Gwozdz, Dariusz Leniowski, Jakub Lacki, Mateusz Markowski, Claudio Avignone-Rossa, Michael E. Bushell, Johnjoe McFadden, Andrzej M. Kierzek
• Keywords: Biometrics, BMCBI 2011, Disease Syndromes, Genetic Polymorphism, Variability Analysis