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There is a growing need for next-generation science gateways to increase the accessibility of data sets and cloud computing resources using latest technologies. Most science gateways today are built for specific purposes with pre-defined workflows, user interfaces, and fixed computing resources. There is a need to modernize them with middleware that can provide ‘plug in’ support to programmatically increase their extensibility and scalability to meet users’ growing needs. In this paper, we propose a novel middleware that can be integrated into science gate ways using a “bring-your-own” plug-in management approach. This approach features microservice architectures to decouple applications, and allows users (i.e., administrators, developers, researchers) to customize and incorporate domain-specific components in an existing science gateway. We detail the application programming interfaces in our middleware for creation of end-to end pipelines with diverse infrastructure, customized processes, detailed monitoring and flexible programmability for a scientific domain. We also demonstrate via a OnTimeRecommend case study on how our “bring-your-own” approach can be seamlessly integrated by a science gateway administrator/developer using a web application.