By a News Reporter-Staff News Editor at Information Technology Newsweekly -- Research findings on Bioinformatics are discussed in a new report. According to news reporting originating in Hinxton, United Kingdom, by VerticalNews journalists, research stated, "Logic modeling is a useful tool to study signal transduction across multiple pathways. Logic models can be generated by training a network containing the prior knowledge to phospho-proteomics data."
The news reporters obtained a quote from the research from European Molecular Biology Laboratory, "The training can be performed using stochastic optimization procedures, but these are unable to guarantee a global optima or to report the complete family of feasible models. This, however, is essential to provide precise insight in the mechanisms underlaying signal transduction and generate reliable predictions. We propose the use of Answer Set Programming to explore exhaustively the space of feasible logic models. Toward this end, we have developed caspo, an open-source Python package that provides a powerful platform to learn and characterize logic models by leveraging the rich modeling language and solving technologies of Answer Set Programming. We illustrate the usefulness of caspo by revisiting a model of pro-growth and inflammatory pathways in liver cells. We show that, if experimental error is taken into account, there are thousands (11 700) of models compatible with the data. Despite the large number, we can extract structural features from the models, such as links that are always (or never) present or modules that appear in a mutual exclusive fashion. To further characterize this family of models, we investigate the input-output behavior of the models. We find 91 behaviors across the 11 700 models and we suggest new experiments to discriminate among them."
According to the news reporters, the research concluded: "Our results underscore the importance of characterizing in a global and exhaustive manner the family of feasible models, with important implications for experimental design."
For more information on this research see: Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics, 2013;29(18):2320-2326. Bioinformatics can be contacted at: Oxford Univ Press, Great Clarendon St, Oxford OX2 6DP, England. (Oxford University Press - www.oup.com/; Bioinformatics - bioinformatics.oxfordjournals.org)
Our news correspondents report that additional information may be obtained by contacting C. Guziolowski, European Mol Biol Lab, European Bioinformat Inst, Hinxton CB10 1SD, United Kingdom. Additional authors for this research include S. Videla, F. Eduati, S. Thiele, T. Cokelaer, A. Siegel and J. Saez-Rodriguez.
Keywords for this news article include: Europe, Hinxton, United Kingdom, Bioinformatics
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