  The proliferation of sensor technologies and advancements in data collection
methods have enabled the accumulation of very large amounts of data.
Increasingly, these datasets are considered for scientific research. However,
the design of the system architecture to achieve high performance in terms of
parallelization, query processing time, aggregation of heterogeneous data types
(e.g., time series, images, structured data, among others), and difficulty in
reproducing scientific research remain a major challenge. This is specifically
true for health sciences research, where the systems must be i) easy to use
with the flexibility to manipulate data at the most granular level, ii)
agnostic of programming language kernel, iii) scalable, and iv) compliant with
the HIPAA privacy law. In this paper, we review the existing literature for
such big data systems for scientific research in health sciences and identify
the gaps of the current system landscape. We propose a novel architecture for
software-hardware-data ecosystem using open source technologies such as Apache
Hadoop, Kubernetes and JupyterHub in a distributed environment. We also
evaluate the system using a large clinical data set of 69M patients.
