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Hiroyuki Nakamura (Keio University, Kanagawa, Japan)
Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. However, biological network data is usually huge, complex, and it exists in various data formats. Therefore, it requires a huge amount of work for bioinformaticians to analyze network data, writing scripts that parse flat files from the interaction database. To address this situation, we developed eXpanda, an integrated platform for network analysis and visualization. It was implemented as Perl module, to help researchers parsing, analyzing and visualizing biological networks. We have continued developing eXpanda, and here we present eXpanda version 2.0. Our main purpose of this update is to improve functions for visualizing biological networks. We added many layout algorithms and improved function related to graphics, including Systems Biology Graphical Notation (SBGN) support. Furthermore, we worked on usability of eXpanda, and added "eXpanda flow", which allow non-programmer researchers to easily create analysis procedure on web interface.