BioInfoCallboratory: Towards an Agent- Assisted Web-Based Collaboration Environment for Bioinformatics

Yan Chen1, Yi-Ping Phoebe Chen2, Queensland University of Technology;, Queensland University of Technology

The discovery 50 years ago of the structure of DNA was due to international cooperation. Such collaboration between researchers in biology and later in bioinformatics has continued to today with the completed mapping of human genome with contributions from more than five countries. The goal of BioInfoCallboratory is to provide an effective agent assisted web-based environment for collaborations in Bioinformatics research communities. An agent is an autonomous and goal-directed process, with many agents work interactively and collaboratively towards a common goal. This agent assisted web based environment consists of three types of agents: 1) Referral Agents for matchmaking; 2) Data Retrieval Agents for internet-spanning gene expression data and/or DNA microarray data mining roaming distributed genome databases in many different web sites; 3) Event Agents that react to events on behalf of a human researcher in the collaborative environment. The referral agents try to match up biologists with similar interests by mining and examining the query records and web access logs of different researchers. The tasks of data retrieval agents are to optimally organize gene expression data and/or DNA microarray data which resides in multiple genome databases spanning over the internet for quick search. Depending on different interests and search-patterns the same bioinformatics data source may be reorganized to be distributed in a grid computing structure for better and faster access. Event agents provide a virtual presence for each biological researcher in the collaborative environment. They alert researchers when an interest event occurs for example: new gene information has been added to the database; a collaborating peer has become “on-line”; or a new gene sequence has been discovered by other agents. Through multiple agent interaction, BioInfoCallboratory provides a set of sophisticated interactions that are necessary in bioinformatics, such as: matchmaking, internet spanning data retrieval, and event alert. These sets of agent assisted interactions will effectively facilitate useful collaborations among researchers in BioInfoCallboratory.