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The R2 update includes other new features in the SB Messaging adapter, the HL7 Accelerator and more, which are listed on this MSDN page. BizTalk Server 2013 R2 can run in the cloud in a virtual machine on Windows Server and/or connect to the cloud in a variety of ways, including via Azure BizTalk Services. Azure BizTalk Services allows users to build enterprise application integration (EAI), EDI (electronic data interchange) and B2B (business-to-business) apps and services on Azure.

The cloud is disrupting all aspects of information technology and one area undergoing significant change is that of integration. Traditionally, integration has been either on-premises system to system EAI or B2B, today, many systems that companies wish to integrate with are well beyond the corporate firewall, often SaaS-based, API-centric providers handling everything from sales leads to invoicing, email and social media. Microsoft BizTalk Server 2016 allows customers to integrate disparate applications and heterogeneous data to deliver solutions such as payment processing, supply chain management, business-to-business EDI, real-time decision making, and reporting.