This question gets a little complicated so please bear with me.
So we have a new custom designed desktop which we will be mostly a dedicated machine for scientific computations in FORTRAN and MATLAB. The IT initially installed Windows 7 on it and gave it to us. Our preferred OS is Ubuntu. The second choice is Fedora but we won't go there unless we absolutely have to and if someone here can give us good arguments that Fedora makes things mentioned below easier than Ubuntu.
If we were to just reformat the entire drive and install Ubuntu, things are easy but my adviser makes a good case that we should keep Windows too in addition to ubuntu.
First question, are there any good replacements for microsoft office in a linux environment? I know about open office of course and have even used it but if I receive a complicated .doc form or something and open it in open office, boxes/tables/text/spaces/margins are messed up and misaligned. Same happens in power point. In addition, if I prepare documents in open office (document or a presentation) it is messed up when opened in microsoft office. So what is the "best" replacement for office for linux? If this question has no good answer, then we have to keep windows.
Keeping windows, I was just going to repartition the hard drive, give windows a tiny bit of space and have ubuntu on the rest. But then there is the problem of sharing files between the two. So then I thought about having a tiny partition for windows, a decent chunk for ubuntu, and the largest one for documents.
What is a good file system for my documents partition which will be stable in the long run and both windows and ubuntu can read and write to easily? Note some files will be quite large like giant text files containing the output from a long simulation. Should I use NTFS or ext3 or what? Windows can't use ext3, right? But how good is ubuntu with NTFS? There won't be any read/write/checksum errors/issues? And what about FAT32? Any better alternatives I don't know about?
Any recommendations for a good free partitioning/formatting utility? I won't be able to format the entire drive. Windows is already on it and we want to keep it without removing it and reinstalling it. So I'll just shrink windows partition, repartition the rest into two more, then format the other two appropriately. There is only one physical drive involved in all this.
Now is the complicated part, given two partitions on the same physical hard drive, one with windows and one with ubuntu, is there any way for me to have some sort of a virtual machine which can mount another physical partition on the same physical HD? For example, if I am logged onto ubuntu and I have some figures I need to add into and modify a powerpoint, I want to be able to start a VM in ubuntu, mount my (physical) windows partition and use powerpoint. Is there anything for ubuntu that can do this like VMWare or something? Preferably free? What about the other way if I want to use ubuntu quickly while logged into windows?
Given question 3, will there be any licensing issues when mounting windows on a VM from a physical partition? We only have a single license and I imagine the MAC address will change when mounting windows to a virtual drive so will windows ask us to put in the license info again or something?
I know too many questions but they are all related. Just trying to plan carefully to build this machine in the least complicated way that can do everything we need and make sure it lasts a long time. I put this all here together so that the bigger picture can be seen by all and perhaps a better suggestion/strategy will be offered.
FYI, I am a fairly advanced computer user, as you can tell, not afraid to partition/reformat drives but I am rather inexperienced with linux so don't be afraid to go into detail if necessary.