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Life Sciences companies are increasingly looking to cloud computing technologies to deal with the deluge of data that they are faced with. There is also increasing collaboration among various life sciences players in the pre-competitive areas of drug discovery and for that too cloud computing platforms are being looked at. Cloud computing has proven to be scalable and capable of meeting the computation needs in life sciences domain but a key inhibitor has been security concerns. This paper describes how to leverage a public cloud to build a scalable genome sequence search platform that will enable secure collaboration among multiple partners, some of the common security challenges associated with it and how to address them using several open source solutions. The paper also describes how to implement federated identity for applications on a public cloud so that stakeholders from multiple collaborating organizations can securely share information. This paper also describes solutions for ensuring security of data in transit and at rest for genome sequence data.