Hi,
I have a 8 GB pen drive, where i am planning to install scientific linux. I need guidelines and help to partition this 8GB drive. I will be using it for programming java with the help of eclipse IDE.

So after the installation SC Linux, i will install JDK and Eclipse IDE only. Please help me at the earliest.

With only 8GB of space, I would install just a 500MB swap partition and the rest as root. This will give you 7.5GB for the root partition, which should be enough as long as you do not install lots of data on the home folder.
If you plan to install data, then perhaps you could mount a partition on the internal hard drive under media to store your data.

500MB swap on a USB Memory? Dont think its a good Idea.
I would simply start the live CD and it should automatically suggest a partition (probably with a menu USB install).
Or install it with unetbootin ? (use of the full size)

Thanks for the suggestions. I would go with 500MB of Swap and rest for root. So i don't need to have /boot partition correct?

You don't want your system swapping to a slow pen drive, for performance reasons. So I'd configure minimal swap, and then add more physical memory to your computer so you can (for the most part) alleviate the need for frequent swapping. How much memory does your computer currently have?

For a pen drive installation, everything should just go under /root. No need for seperate partitions for the various filesystems.

There are other considerations beyond partition types and sizes, such as if the drive will take partitions at all. Some do not. I personally don't worry about partitioning USB drives, and certainly not swap space as that would probably just wear out the drive. You do not need a /boot partition.

You seem to want it bootable, which means you need to know about the target machine and if it's a UEFI machine, which will determine your filesystem and bootloader. There is also the target CPU architecture to consider. (x86, x86_64, ARM, whatever)

Another idea is to track down a copy of Qemu (or similar) which will run in the host OS and load your Linux in that. I like to do that, as well as make the stick bootable. If you set it up right, they can both use the same kernel.

You will probably also want some outside storage to back up on. Anything from FTP to Dropbox would work.

Basically, I would put "just enough" on the USB drive to make it functional, and do the rest online.