Favorite Free / Open-Source Software

Word processing	LaTeX
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	R
General programming	R, Julia
Bibliography management	BibDesk (works with LaTeX)
Text editing	BBEdit, Visual Studio Code
Web page creation	SeaMonkey
Digital audio recording	Audacity
Digital image manipulation	Photoscape, Gimp
Make sheet music	LilyPond
File encryption	GNU Privacy Guard (GPG)
Database management	SQLite
Password management	Bitwarden

LaTeX

    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 an older 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 regularly:

Powerdot makes computer slide presentations. All of my lectures in EPI 512-513 and other scientific presentations use slides made with Powerdot. The presentation content is created as a plain-text file, using LaTeX mark-up commands to specify what material goes on which slide in what format. That file is then compiled into a PDF file that can be projected using the standard Adobe Reader program. The results look very similar to PowerPoint slides (which most viewers assume they are). Exploiting the programmability of LaTeX, I created a set of Powerdot add-on commands to facilitate making various common kinds of slides, such as a set of bullet points centered on the slide that appear one at a time, a figure on the left and a sequence of bullet points on the right, a centered figure that fills the slide, a series of related figures that progressively add features, and others. A nice feature of Powerdot is that the same plain-text input file that is used to make slides can also be compiled into a PDF handout. All of the slide content is included in the handout, but in a more compact format. Additional information, such as citations and a reference list, or an appendix, can appear only in the handout.

Within Powerdot presentations, hyperlinks can be inserted to allow skipping from the current slide to any other slide, with or without returning to the original slide afterward. This feature provides the flexibility to skip certain slides gracefully if time is short, or to re-visit a certain key slide from anywhere in the presentation. The hyperlinks also function as such in the PDF handout.

Slides in Powerdot can be prepared using any of various styles that are included with the package, or the user can create a new custom style. I developed a very simple style, paintings, that is now included with the Powerdot package itself.
PSTricks creates graphics. Instead of drawing shapes with a mouse or trackpad and then saving the finished picture, one programs PSTricks to draw the figure. PSTricks defines LaTeX commands that offer access to the rich graphical features of the PostScript page-description language. PSTricks is very powerful and has its own suite of sub-packages to make special kinds of figures, such as chemical compounds, barcodes, tree diagrams, maps, pictures of mathematical functions, and so on. A sub-package that I use extensively is pst-nodes, which allows the user to create "nodes" of various sorts (such as a box containing text) and to connect the nodes with arrows, line segments, curves, etc. State/transition diagrams and diagrams of study designs can be produced in this manner. Although it is a bit odd at first not to see what the resulting figure actually looks like until the commands are compiled, the results are almost always better than I could have drawn by hand, and they are easy to re-use and customize.
Sweave marries LaTeX and the R programming language (see below). Technically an R package, Sweave allows LaTeX documents to include placeholder mark-up commands that are later replaced with information provided by R. For example, the LaTeX document could be a report that summarizes a set of analysis results on a certain project. In its initial state, the report might include an introduction, methods section, table "shells", and a discussion, but without actual numerical results in the tables. The table "shells" specify only the format of tables that will contain the results (e.g. table title, number of columns, format of each column, column titles, etc.) but contain a placeholder command rather than actual numbers as the table body. The LaTeX document is then processed through R. R performs the statistical analyses as usual, then replaces the placeholders in the document with the numerical results. The augmented document is then compiled by LaTeX in the usual manner to produce the finished report. If new data come in, or there are minor revisions to the analysis protocol, the report can simply be run through R again to insert updated results; the report itself need not be re-written. Sweave is at the heart of a program that I wrote to generate an extensive set of monthly data quality reports at the National Alzheimer's Coordinating Center.
Sciposter creates scientific posters in LaTeX. It can automatically distribute text material to fill several columns, provides easy ways to incorporate tables and figures, and allows fonts, colors, and overall poster layout to be customized at will.

R

    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 less suitable for analysis of really huge datasets (millions of records). Like Stata, SAS, and LaTeX, R is vastly expandable through thousands of "packages," many of them user-contributed, that are designed to do various specialized tasks and forms of 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. I often use 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 for the Mac that I use regularly and can personally recommend are described briefly below. All are in the public domain and are freely downloadable over the Internet.

BibDesk manages bibliographic data for LaTeX documents. BibDesk can download citation data directly from PubMed, organize the data in libraries to user specifications, and create custom bibliographies. LaTeX itself uses a companion program, BibTeX, to provide functionality similar to the commercial product EndNote.
BBEdit is a general-purpose text editor that I like for writing LaTeX files, plain-text documents, and R programs.
Visual Studio Code (a.k.a. VS Code) is a text editor that I find very convenient for programming Visual Studio Code's appearance and functionality can be extensively customized. I recently switched to Visual Studio Code after several years of using Atom, an essentially similar text editor created by GitHub (which is now part of Microsoft, which created Visual Studio Code). Visual Studio Code is even easier to customize, and it is faster than Atom. Extensions are readily available for writing LaTeX files, Julia code, and many other languages. One drawback is that it is not easy to print hard copies of text files from Visual Studio Code; for that purpose, I open the same file in BBEdit, an older free text editor that does support printing.
Audacity is a digital sound recorder and editor. Audacity can also post-process the recordings to remove extraneous content or noise and to convert the recording to MP3 format for website posting.
SeaMonkey is a web browser that can also be used to create and edit web pages. This web page and others on my website were created using SeaMonkey.
Photoscape is a user-friendly editor for jpg-files that can crop, rotate, change brightness/contrast levels, adjust color balance, add text and graphics, and much more. It can also be used just as a photo viewer. Gimp is an even more powerful (but more complex) open-source digital image manipulation program.
LilyPond engraves (typesets) music, generating professional-quality sheet music. Input is a text file, using a simple musical notation; output is a PDF file of sheet music. LilyPond can be used for simple tunes but can also handle long and complex pieces, up to and including entire symphonies and oratorios.
GNU Privacy Guard encrypts and decrypts files or e-mail messages using the Pretty Good Privacy (PGP) encryption system. It uses public and private keypairs and requires a passphrase for decryption. On the Mac, it can be called up using the Services function and applied to any file, or it can be invoked by other programs, such as R.
SQLite is a compact but still very capable SQL data management system that is useful for many small to medium-sized database tasks. SQLite is already present in modern Macs because Mac OS X and many software packages use it. DB Browser for SQLite is a free stand-alone "front end" for SQLite on Macs, and SQLite Manager is a free browser add-on that provides access to SQLite databases through a web brower. The R package RSQLite facilitates using SQLite in R programs.
Bitwarden is a free password manager for Mac OS X and several other platforms. It stores passwords and other associated information in an encrypted file that is compatible with KeePass, MacPass, KeeWeb, and other password managers. It can be set up easily to insert usernames and passwords into many web pages on command with a simple keystroke.
Julia is a relatively new programming language, first publicly released in 2012 by a team of language developers at MIT. I find Julia's syntax to be more elegant than any other language I have used, making it a fun language in which to write programs. Unlike R or Python, Julia code is compiled to native machine code, which typically runs much faster. For that reason, Julia is especially well-suited for applications that involve a lot of number-crunching, such as complex simulations or processing of very large files. But it can also be used as a general programming language. I have used it to write several useful programs on the Mac, including one to organize and annotate >15,000 images in my own photo collection.

Last modified: 2024-03-19