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I have an existing windows installation with important applications. I want to take advantage of unix tools and OS environment of Ubuntu. What would be the best way for me to 'overlay' Ubuntu on top of existing windows environment? - I need to run both OS and use the windows apps everyday (the windows apps are computationally intensive like Matlab--i'll migrate these apps to use the linux version one by one once I see the setup is better for the way I work) - I would like to have ubuntu to see the windows file system (Windows XP, windows Vista, windows 7 for three diff computers) - I would like to retain maximum performance for both OS - I want to safely implement this change and be able to reverse this without too much trouble.

I know about Wubi but want a more permanent solution. I'm thinking repartitioning and installing Ubuntu,.. then from there start something like Zen to 'boot' into windows to run my windows app.. while being able to do things like search thru the windows file system from Ubuntu..

Can you please help with details/links on how to do this satisfying the constraints above? Thanks for your help.

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If I understand correctly, you need to run Ubuntu and Windows at the same time?

If that's the case, then I would recommend that you install VirtualBox. It is a free software virtualization solution that's available for Windows, Linux, OS X and Solaris. It's quite user friendly and efficient.

Since Virtualbox can run on all those platforms, you can choose which to have as a main operating system. In your case, I think I'd recommend running Ubuntu in the virtual machine, because it's far easier to convert to a "real" install later. It's also usually much faster as a virtualized guest than Windows is. I'd then try to use Ubuntu as much as possible, converting tools as you're able to, and then – when you feel ready – move the Ubuntu system onto the host itself as a normal install. That's very easy, and you'll find many documents describing how.

An advantage of running Ubuntu as the host is that you can run the Windows desktop as a seemless workspace, which means it'll be more comfortable if you need to switch between them frequently. If you decide to convert the Windows install, check your licenses first.

If you use Windows XP, then converting is extremely difficult. Windows 7 is said to be easier, but I haven't tried it myself. After spending three days converting a simple XP system, I've tried very hard to avoid ever having to do it again.

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Depending on your system specifiations, you can:

Dual boot Your best bet in terms of performance etc on both OSes is to set up a dual boot system ( How to dual boot windows 7 and ubuntu? ). This will allow you to use both Ubuntu and Windows, but you'll have to reboot each time you want to use the other OS.

Virtualization You mentioned that you are using MatLab on Windows, so maybe this isn't for you, but you can install one OS inside a virtual machine (VM) using virtualization software (e.g., Virtualbox). This is great if you need to use both OSes simultaneously but you won't get the best performance if you are running intensive tasks, and you will want to have good hardware and lots of RAM in your computer so can can allocate as many resources as you need to to the virtual machine.

Wubi As you mentioned, Wubi is another option too. See What's the difference between Wubi and a regular installation?

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Virtual Box. Simple and easy. Install Vbox on Windows and use it to install Ubuntu. You can even use the seamless mode of Vbox and it looks pretty cool

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