Favorite Free / Open-Source Software

Word processing
Presentation slides and handouts
Powerdot package in LaTeX
Presentation graphics
PSTricks package in LaTeX; R
Scientific posters
Sciposter package in LaTeX
Report preparation
Sweave package in R and LaTeX
Statistical analysis
General programming
Bibliography management
BibDesk (works with LaTeX)
PDF comments and markup
Text editing
Web browsing
Web page creation
Digital audio recording
Digital image manipulation
Make sheet music
File encryption
GNU Privacy Guard (GPG)
Database management
MySQL and Sequel Pro


    LaTeX is a general-purpose document preparation system.  It is used worldwide and is open-source, public-domain software that is available for most computer platforms.

    LaTeX can be thought of as a programmable word processor.  Although I do have a current copy of Microsoft Office, I prefer LaTeX for almost all document preparation.  A relatively small core program provides basic functionality for writing simple documents, such as letters or memos.  LaTeX excels at formatting tables, mathematical notation, and inclusion of graphics, among other tasks, and it produces beautiful, professional-quality products.  (Many scientific books nowadays are bound photo-reproductions of LaTeX output.)  Hundreds of add-on "packages" are available, many of them contributed by users, to extend LaTeX's capabilities for more specialized purposes.  Examples are packages for computer slide presentations, graphics of all kinds, questionnaires, web pages, reports with content incorporated automatically from a statistics package, brochures, music scores, calendars, side-by-side dual-language manuscripts, and so on.  Like LaTeX itself, the add-on packages are freely downloadable from the Comprehensive TeX Archive Network (CTAN) website, which has mirror sites worldwide.

    As a Macintosh user, I use the standard MacTeX installation, which includes all of the basic required software plus most of the packages on CTAN.

     Although what-you-see-is-what-you-get (WYSIWYG) variants of LaTeX are available, I myself prefer a standard version that takes a plain-text ASCII file as input and produces a PDF file as output.  The plain-text input file contains both the document content and embedded LaTeX mark-up commands that specify the desired formatting.  On the Macintosh, I use the front-end program TeXShop, also free, which has a built-in editor to create input files.  TeXShop provides easy ways to compile the plain-text input file to a finished PDF file that can be viewed and printed within TeXShop itself.

    I use several LaTeX packages heavily:


    Yes, R--just one letter.  R is both a statistics package and a programming language.  R is the main software that I use for data analysis and the main computer language in which I write programs.  It is an open-source, public-domain descendant of S (an earlier open-source programming language) and a close relative of S-plus (a commercial product).

    As a statistics package, R is comparable in functionality to Stata, SAS, and SPSS although it has difficulty with very large databases.  Like Stata, SAS, and LaTeX, R is vastly expandable through hundreds of "packages," many of them user-contributed, that are designed to do various specialized tasks and analysis.

    As a programming language, R incorporates many convenient and powerful features, including graphics commands to create figures, text-processing functions, date manipulation, database storage and retrieval, and interfacing with LaTeX and HTML documents.  An R program handles many administrative tasks for EPI 512-513, including assignment of students to groups, generating random call-on lists, supporting preparation of customized feedback after exams, and grading.  In the past, I have used R for entirely non-statistical projects, including creation of a PDF slide show of fine-arts images as a supplement to art historian Giorgio Vasari's Lives of the Artists.

Other software

    Other programs that I use regularly and can personally recommend are described briefly below.  All are in the public domain and are freely downloadable via the Internet.
BibDesk, TextWrangler, Skim, and Sequel Pro are available for Mac OS X only.  Audacity, SeaMonkey, Gimp, LilyPond, GPG, and MySQL are available for several platforms.

Last modified: 10/1/2012