Department of Bioinformatics - BiGCaT 1 Bioclipse-OpenTox: Interactive Predictive Toxicology Egon Willighagen, @egonwillighagen Dept. of Bioinformatics - BiGCaT - Maastricht University orcid.org/0000-0001-7542-0286 ACS New Orleans, 9 April 2013, #ACSNola #DrugDisco
Bioclipse-OpenTox is a platform developed for the interactive prediction of toxicity-related properties or organic molecules. Integrating two independent projects, it enables toxicity prediction based on the analysis of chemical structures, and visualization the substructure contributions to the toxicity prediction. OpenTox is a semantic web framework, based on web services, which supports open data exchange and toxicology model building and validation. Bioclipse is used to provide user-friendly solution for graphical interaction and visualisations, as well as scripting for workflow needs. It was recently extended to dynamically discover computational algorithms exposed via the OpenTox servers, acting as a registry of available computational toxicology services on the OpenTox network. We further show how predictions from multiple services can be simultaneously evaluated while editing substructures new compounds.
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Hardy, B. et al. JChemInf 2010 2(1):1-29.Jeliazkova, N et al. JChemInf 2011 3:18.
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Thus: Bioclipse-OpenTox
Willighagen, EL et al. BMC Res Notes 2011 4(1):487.
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Application #1: decision support
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Application #2: descriptor calculation
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Application #3: scripting
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Managers: the vital organs of Bioclipse
Some theory● Make sure that things happen● They provide all domain-related functionality● All Bioclipse GUI is using managers in the background● Takes care of threading (background processes)● They are plugged into the system● Bioclipse dynamically discovers managers when booted● Extend the JavaScript Console (also Groovy)Spjuth, O., Alvarsson, J., Berg, A., Eklund, M., Kuhn, S., Mäsak, C., Torrance, G., Wagener, J., Willighagen, E. L., Steinbeck, C., Wikberg, J. E., Dec. 2009. Bioclipse 2: A scriptable integration platform for the life sciences. BMC Bioinformatics 10 (1), 397+.
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Managers can be combined ...var alkanesIUPACNames = ["methane", "ethane", "propane", "butane"];