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  ProteoLens
  SafMap
  Visualization
  Data Mining

We develop computer software tools, and also collect or recommend tools useful for large-scale data management, data integration, data analysis, data mining, and information visualization. (more external link will be added)

ProteoLens: A Visual Network Data Mining Tool

ProteoLens is a freely downloadable, powerful visual network data mining platform developed by our group. It is especially developed for biological network visual exploration, annotation, and data mining purposes; but it can also be used to support any type of networks including social networks and computer communication networks. It has build-in Robust Relational Database Engine support (Oracle 10g DBMS and PostgreSQL 8.x). A user can directly query the data stored in your database using Oracle SQL or PostgreSQL, and immediately visualize the network display results. It support Standard GML file format. A user can import and manipulate any network data using standard GML file formats in addition to structured data stored in the relational databases. It supports Flexible Annotation Data Mapping. A user can use SQL queries to specify and store"associations" between nodes/edges and node annotation/edge annotation. These associations can be used to visually annotate large displayed networks using node/edge shape, size, weight, color, and text. This is much more powerful than any custom-built annotation user-interfaces for complex visual network analysis. The tool also supports Multiple Network Layout Choices. The tool comes with the same professional graph layout engine optimized for relational data. Several different types of layout such as organic and hierachical methods can be configured. It supports Session and File Sharing. Analysis sessions can be saved for later retrieval. Network files can also be saved as layout files or image files for sharing.

Download site: http://bio.informatics.iupui.edu/proteolens/

SafMap: A Sequence Alignment and Feature Mapping Tool

This simple tool allows user to enter any popular gene identifiers (e.g., Locus ID, GI number, or gene description) and it will show a mapping of all annotated sequence features derived from NCBI's in a JavaApplot in the web browser.

Access site: http://bio.informatics.iupui.edu/service/safmap.shtm