Data-driven research is increasingly ubiquitous and data itself is a defining asset for researchers, particularly in the computational social sciences and humanities. Entire careers and research communities are built around valuable, proprietary or sensitive datasets. However, many existing computation resources fail to support secure and cost-effective storage of data while also enabling secure and flexible analysis of the data. To address these needs we present CLOUD KOTTA, a cloud-based architecture for the secure management and analysis of social science data. CLOUD KOTTA leverages reliable, secure, and scalable cloud resources to deliver capabilities to users, and removes the need for users to manage complicated infrastructure. CLOUD KOTTA implements automated, cost-aware models for efficiently provisioning tiered storage and automatically scaled compute resources. CLOUD KOTTA has been used in production for several months and currently manages approximately 10TB of data and has been used to process more than 5TB of data with over 75,000 CPU hours. It has been used for a broad variety of text analysis workflows, matrix factorization, and various machine learning algorithms, and more broadly, it supports fast, secure and cost-effective research.