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This paper presents two bio-inspired methods addressing the problem of business process optimization. We provide a comparative approach for optimal business process flow selection and resource allocation using two of the most important bio-inspired meta-heuristics: Ant Colony Optimization and Bee Colony Optimization. Our approach does not use predefined rules for making the decisions when selecting the flow in the business process model. Given a business process, our approach starts from the business goal and reconstructs the optimal process flow by going backwards in the process in an iterative manner and solving everything that needs to be done for that goal to be completed. This reconstruction is realized by combining the bio-inspired algorithms with resource allocation strategies. The bio-inspired optimizations have been comparatively evaluated on a set of manufacturing scenarios.