Various bioinformatics tools for biological data processing have been developed and most of them are available in public. Most bioinformatics works are carried out by a composite application of those tools. Several integration approaches have been proposed for easy use of the tools. This paper proposes a new multi agent system to integrate bioinformatics tools in the perspective of workflow since the composite applications of tools can be regarded as workflows. For the easy integration, the proposed system employs wrapper agents for existing tools, uses XML-based messages in the inter-agent communication, and agents are supposed to extract necessary information from the received messages. This allows new tools to be easily added on the integration framework. The proposed method allows various control structures in workflow definition and provides the progress monitoring capability of the on-going workflows. In particular, agents in this system have the rule-based architecture which allows the defined rule set to be a special role agent. This feature provides fast and flexible agent development to aid in managing the complexity of bioinformatics application. This system has been partially implemented and has been proven to be a viable implementation for workflow-based bioinformatics tool integration.