BioInfoCallboratory: Towards an Agent- Assisted Web-Based Collaboration Environment for Bioinformatics
Yan Chen1, Yi-Ping Phoebe Chen2
1y52.chen@student.qut.edu.au, Queensland University of Technology; 2p.chen@qut.edu.au, 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.