Freeware How-To

or "Startup and Recovery for Your Computer at the BRC"

This page describes how to download and correctly install some freeware that grad students in Bioinformatics have found useful to have on their computers at the BRC or at home. These installation instructions should be clearer than those typically provided by the distributors of freeware code.

These instructions can be helpful if you are just starting your program at NC State, upgrading to newer versions of the software, or recovering from a virus or worm attack that required wiping your hard drive.

Links and installation guidance are offered for the freeware listed below. If you're installing WinEdt with plug-ins and macros, follow the recommended installation order described below under WinEdt and Associated Plug-Ins and Macros.

See the Software section for more links to data analysis, programming, and other web-based tools for research.

If this program is not installed already on your computer, you can download it from http://www.ncsu.edu/it/essentials/. It is recommended that you enable automatic updates of your virus definition files by going to File/Schedule Updates once the program is installed and setting the schedule to daily updates.

This is a personal firewall program that can help prevent problems of unauthorized users on your computer. It can be downloaded for free at http://www.zonelabs.com.

Download the current version at http://aspn.activestate.com/ASPN/Downloads/ActivePerl/Source.

R is a powerful language for statistical analysis that is basically a free version of S-plus with a command line interface. Its functionality increases with the use of the R plug-in for WinEdt. Download the binary rw1071.exe from http://lib.stat.cmu.edu/R/CRAN/.

Request current versions of these programs (free for school or home to NCSU students!) from the Software Services at http://www.ncsu.edu/it/sas. They will notify you by email when your cds are ready. Pick them up from Rm. 208 in the Hillsborough Building (2620 Hillsborough St.).

Having a revision control system is particularly useful once you start writing any articles you intend for publication or working on your dissertation, although you can use it for almost any type of file in order to keep backups of your revisions. This type of program allows you to easily go to any saved revision and compare the changes between any two revisions. You can then revert to a previous revision if it is preferable or even develop several versions in parallel. A free implementation of a revision control system called CS-RCS is available. It can be integrated into WinEdt as a plug-in for increased functionality (see below). Download from http://www.componentsoftware.com/products/rcs/.

This viewer will allow you to look at pdf files. Download the current version from http://www.adobe.com/products/acrobat/.

WinEdt can be used, among other things, as a text editor for Perl, R, LaTeX and HTML. (A plug-in for compiling C, C++ and Fortran is also available; see winedt.org for more information.) WinEdt has useful plug-ins for each of these types of tasks and different menus that will help you with context-dependent highlighting of syntax, easy compiling and running of scripts, nice ways to view the help documentation, easier management of multiple file projects, and short-cuts for remembering commands, particularly for LaTeX.

WinEdt also has a plug-in for the Revision Control System that is extremely helpful for writing your dissertation and papers for publication. Note that WinEdt is shareware, and you are asked to register for about $30 after a month free trial. This software is worth it – and rewarding the author for his work is reasonable. Those of us who paid for it four years ago haven’t looked back.

To install and run WinEdt, follow the installation order listed below. To run WinEdt, you must first install MikTex. It is useful to have Ghostscript, Ghostview and Adobe Acrobat Reader installed as well. Ghostscript must be installed before Ghostview.

If you plan to use WinEdt to write LaTeX documents, installing BibTex (and its required MUI package) can be very useful for managing bibliographies.

Installing the whole set of packages is described here, but it is possible to install just the parts that you are interested in and still have lots of functionality.

Note: To install a newer version of WinEdt over an older version, in WinEdt, choose Options/Configurations/Backup. Exit WinEdt, then run install. After the program is installed, go to Options/Configurations/Restore and this will restore all your settings.

Order of Installation for WinEdt with Plug-ins and Macros

Note: It is best to install Perl and R onto your computer before installing the WinEdt plugins for them.

1. MikTex
Download setup.exe from http://www.miktex.org. This is a wizard that will help you download the rest of the MikTex packages.
Install MikTex in C:/Program Files/MikTex.
2. Ghostscript
Download the current version .exe file from http://www.cs.wisc.edu/~ghost/.
3. Ghostview
This viewer will allow you to look at postscript files. Download the current version .exe file from http://www.cs.wisc.edu/~ghost/gsview.
4. WinEdt
Download the current version .exe file from http://www.winedt.com.
Once you install the plug-ins and macros listed here you should be able to switch from Perl to LaTeX configurations by choosing Options/Configuration and then choosing either Perl/Perl Editor or MikTex.
Currently to use R-winedt you must first open up R, but this may be changing with newer versions - see documentation.
5. Perl syntax highlighter and editor
Download WinEdt_PerlCC_NT.exe from http://www.winedt.org/Config/modes/perl.php.
Open WinEdt and from the menu bar choose Macros/Execute Macro/Browse and open install.edt.
6. R-winEdt
Download the current version .zip file from http://cran.r-project.org/contrib/extra/winedt/.
Use the Readme file there to figure out installation instructions.
7. MUI
Only install this if you plan to install BibTeX. Download mui.zip from http://www.winedt.org/Plugins/mui.php.
Run install.edt and install into the folder Plugins/MUI in your WinEdt directory. If this folder doesn’t exist, go ahead and create it.
8. BibTeX
Download bibMacros.zip from http://www.winedt.org/Config/menus/BibTeX.php.
Unzip this file into your WinEdt directory in the Macros/LaTeX folder. If this folder doesn’t exist, go ahead and create it.
9. Revision Control System integrated into WinEdt
After installing your Revision Control System (see above), download RCS.zip from http://www.winedt.org/Config/menus/RCS.php.
Unzip this package in the folder Config/RCS in your WinEdt directory. If the file doesn’t exist, go ahead and create it. Then open WinEdt, choose Options/Menu Setup/Append and choose RCS.dat.

CDs for Maple, Matlab, and PCTex (a text editor aimed at producing LaTeX files) are available from Stan Martin (help@statgen.ncsu.edu). His office is 1523 in the BRC. See the Software/Programming section for links to documentation for these programs.

Eos http://www.eos.ncsu.edu/software/ has some other free software for students and good general information about computing. Additionally, Windows Office, Windows XP OS, and S-plus are also available on CD from Stan Martin (help@statgen.ncsu.edu), or see him in his office (1523 in the BRC).