Eucalyptus Systems, which supports an open source platform for companies that want the benefits of cloud computing on their own infrastructure, has raised $5.5 million in a first round of funding led by Benchmark Capital.

Eucalyptus came from research at the University of California, Santa Barbara, where the company’s chief technology officer Rich Wolski was a computer scientist. Companies can use Eucalyptus to create a private cloud on their infrastructure, an internal environment for cloud applications that doesn’t face the normal concerns of security and being locked in to another company’s platform (which come with “public” cloud computing, such as running applications on Amazon’s or Google’s infrastructure). Even more significant, companies can then connect those private clouds with public ones like Amazon’s.

Why would someone do that? Wolski says there are three main cases where this sort of “hybrid cloud,” where companies move applications and data seamlessly from their infrastructure to a public cloud and back again, is particularly useful.

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The first is when the location of the data determines where you run an application, such as an application that analyzes customer data, some of which is stored online, some of which is stored on the company’s infrastructure. The second is when it doesn’t make sense to run an application in a homogenous environment, for example when it’s easier to build and test it in the private cloud, then move it onto public infrastructure once you’re ready for wider adoption. And the third is in cases when a company wants a backup, so the application stays up even when Amazon fails, or when the company’s own servers fail.

To be more specific, Wolski says one (unidentified) company was able to land a government contract by using Eucalyptus to do some computing on their infrastructure (addressing security concerns) and some on Amazon’s (lowering the cost).

Since launching the Eucalyptus platform last year, it has already been downloaded 14,000 times. It’s used by other cloud infrastructure companies such as Benchmark-backed RightScale. And it also provides the underlying technology for the Ubuntu Enterprise Cloud, an offering that’s now shipping with every version of the popular Ubuntu distribution of the Linux operating system.

With the funding from Benchmark (one of the leading cloud computing venture investors), Eucalyptus is now spinning off from an academic, open source project into a commercial business. Competitors include 3tera and Globus Nimbus. Wolski says the initial plan is to offer services and consultation at first, and eventually to start selling add-on products too. BV Capital also participated in the funding.

Here are the slides from Eucalyptus’ presentation at the Under the Radar conference last week.