There are many restrictions which may prevent software from being installed, such as software licenses or the ability to be installed within a Linux Operating Environment. That being said, there are many applications that could be installed and you are encouraged to ask the question "can my required software be installed on the HPC facilities". As there are many cases where the answer will be yes.
The HPC facility is designed to allows user access to large storage systems which are located near significant computing resources. This is designed to assist in the running of simulations and programs. Therefore, users are expected to upload require data files and execute HPC programs. Once the data is no longer required, it should be removed from the HPC facilities. It is suggested to look at the "Data tools" section for more permanent storage options.
Yes. If you have your HPC account mapped (see here for instructions), you can edit your files directly. It should be noted when using some windows tools, the files are saved as "windows format files", rather than "unix format files". This is a particular issue for PBS submission scripts. It is suggested to use an alternative text file editor, such as metapad - http://liquidninja.com/metapad/. This "notepad" replacement has many additional features, including saving the file in unix format. This program is also superior for opening output files as well.
"gedit" is a good program for editing text files, such as PBS "submission" scripts, program code and program output. To use gedit, simply open a terminal session and execute the command