PseudoCell: A collaborative network forin silicoprediction of regulatory pathways

Abstract

ABSTRACTWe introduce PseudoCell, an open-source regulatory network and simulation tool implemented in Java for the analysis of biological network dynamics. PseudoCell provides a customizable and scalable regulatory network of 572 cellular and molecular elements. Based on a systemic perspective, the PseudoCell tool implements a set of computational methods for asynchronous logical model simulation, including the definition of perturbations in constant or pulsatile frequency, as well as knockout emulation. The current version also provides a framework for exporting users’ modifications from the network to an online database, as well as importing updated versions. Finally, we validate our results withex vivoexperiments and demonstrate thatin silicodata generated with PseudoCell can qualitatively reproduce expected findings in the face of increasing stimuli with eotaxin-1 (CCL11) in human peripheral blood mononuclear cells.