Elastra, a company that helps manage applications in the Internet cloud, has raised $12 million in new funding.

This is Elastra’s second venture round, and it was led by Bay Partners, with Amazon.com and existing investor Hummer Winblad Venture Partners also participating. Amazon’s backing is particularly impressive, since its Elastic Compute Cloud (EC2) makes Amazon one of the most important companies to cloud computing in general, and to Elastra in particular, since the San Francisco startup hosts applications on Amazon’s EC2 service.

The last few months have seen a number of significant cloud computing announcements, including the launch of Google App Engine, which allows developers to build and deploy their applications using Google’s infrastructure. On the investing side, Benchmark Capital invested $4.5 million in Elastra competitor RightScale, open source cloud company 10gen raised $1.5 million from Union Square Ventures and Benchmark and Amazon both contributed to a $15 million second round for Engine Yard, which hosts apps built using the Ruby on Rails framework.

Chief executive Kiril Sheynkman says Elastra’s offering is unique because it can manage individual applications, rather than virtual appliances (i.e. an entire virtual machine), and because it manages applications across private and public Internet clouds. Since its launch in March, Elastra has signed up more than 40 paying customers, and some of the new funding will go toward expanding that customer base.

Elastra raised $2.6 million a year ago.

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