Science gateways have been widely utilized by a large number of user communities to simplify access to complex distributed computing infrastructures. While science gateways are still becoming increasingly popular and the number of user communities is growing, the fast and efficient creation of new science gateways and the flexibility to deploy these gateways on-demand on heterogeneous computational resources, remain a challenge. Additionally, the increase in the number of users, especially with very different backgrounds, requires intuitive embedded e-learning tools that support all stakeholders to find related learning material and to guide the learning process. This paper introduces a novel science gateway framework that addresses these challenges. The framework supports the creation, publication, selection, and deployment of cloud-based reference architectures that can be automatically instantiated and executed even by nontechnical users. The framework also incorporates a knowledge repository exchange and learning module that provides embedded e-learning support. To demonstrate the feasibility of the proposed solution, two scientific case studies are presented based on the requirements of the plasmasphere, ionosphere, and thermosphere research communities.