Hello,
I am new to Linux, I have been asked to install Red Hat Enterprise 5.1 on a Dell server:
quad 2.5GHz, 8GB ram, 2 x 500GB hard drives.
Using the Dell setup cd I'm asked to configure the partitions, What would be a good partitioning scheme to get the most out of this setup.

This machine will be used as a web server, running the following apps:

(1) PAUP
(2) BLAST
(3) JAVA
(4) PERL 5.10.0
(5) Python
(6) APACHE
(7) egroupware
(8) MySql
(9) Matlab
(10) R
(11) MUSCLE
(12) Mr.Bayes
(13) Hyphy
(14) Modeller
(15) Jmol
(16) HMMER
(17) Autodock 4.2
(18) VMD
(19) Artemis

My plan was to just take the defaults, though it occurs to me that may not be the best use of space.

Any recommendations would be greatly appreciated.

Thanks
JT

Just FYI, 5.4 just came out, so you might want to run 'yum update' after the OS install and before any apps install, just to get up to date with patches etc.
As for disk space, it depends how much space you need. You could RAID1 (mirror), but what happens if one breaks...
You'd get twice as much space by treating them as separate disks.
If this system uses a lot of data, maybe you could have OS + App code on one, data files on the other.
In either case you'll need a robust backup soln.

Your partitioning scheme depends on how the system is used.

I don't like the standard setup of most distro's where MySQL and webpages are in /var; /var is not intended for that in my opinion.
So I move webpages to /home/whateveruser_that_is_responsible and databases to a dedicated partion/disk that I mount under e.g. /databases; you can also opt to use a special directory in /home (e.g. /home/databases) to store the databases which has the advantage that you don't have the problem that there is still plenty of space on one partition while the other one is full.
Just a thought