Journal Article

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Kuperstein, Inna, Zinovyev, Andrei, Viara, Eric, Barillot, Emmanuel, Calzone, Laurence, Pook, Stuart, Cohen, David PA

2013

Overview

Background Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

• Publisher: BioMed Central,BioMed Central Ltd
• Subject: Algorithms / Analysis / Biochemistry, Molecular Biology / Bioinformatics / Biomedical and Life Sciences / Blogging / Cellular and Medical Topics / Computational Biology - methods / Computational Biology/Bioinformatics / Computer Science / Genomics / Internet / Life Sciences / Macromolecular Substances - metabolism / Methods / Molecular biology / Physiological / Quantitative Methods / Simulation and Modeling / Software / software and technology / Systems Biology