We constructed a a comprehensive influenza A virus (IAV) replication and host response pathway map. The FluMap map was constructed by manual curation with the literature as well as various pathway databases such as Reactome, KEGG and Panther Pathway database. This is the open commnuity resource to understand the mechanisms of influenza A viral replication and the host responses.
CTen is an enrichment algorithm to identify changes in the cell-type demographics of in vivo tissue samples. While a large variety of cell types are included, CTen may best be suited for immunology studies- allowing researchers to relate genes expression to changes in immune cell population due to immune cell migration as well as cell death and cell proliferation.
CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks. Networks are drawn based on the process diagram, with graphical notation system proposed by Kitano which is compliant to Systems Biology Graphical Notation (SBGN), and are stored using the Systems Biology Markup Language (SBML), a standard for representing models of biochemical and gene-regulatory networks. Networks are able to link with simulation and other analysis packages through Systems Biology Workbench (SBW). CellDesigner is being developed by our collaborator, the Systems Biology Institute (SBI).
Payao aims to enable a community to work on the same models simultaneously, insert tags to the specific parts of the model, exchange comments, record the discussions and eventually update the models accurately and concurrently. Payao reads the models in SBML(Systems Biology Markup Language) format, displays them with CellDesigner, a process diagram editor which complies the SBGN (Systems Biology Graphical Notation), and provides an interface for adding tags and comments to the models for the community members. Payao is being developed by SBI and OIST.
iPathways+ (iPathways Plus) is the online pathway model repository and visualizer developed by SBI and OIST. FluMap is provided via iPathways+ system.
The protein similarity network (PSIN) is a protein network in which the proteins are connected only if their sequences are similar. The PSIN covers 17,410 proteins connected by 1,749,273 edges.
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