Favorite Free / Open-Source Software

LaTeX

• 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

Other software

• 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.
  
  
• TextWrangler is a general-purpose text editor.  It has many convenient features, including sophisticated search and replace functions and text coloring for various languages (including, of course, LaTeX).
  
  
• Skim allows adding comments, highlighting, and other mark-up to any PDF document.  It can be used like the Track Changes features in Word when reading a PDF document.
  
  
• Audacity is a digital sound recorder and editor.  It has been used to make digital recordings of EPI 512-513 lectures.  Audacity can also post-process the recordings to remove extraneous pre- and post-lecture room noise or announcements 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.  My web pages were created using SeaMonkey.
  
  
• Gimp manipulates digital images, such as .jpg-files taken by digital cameras, roughly akin to Photoshop.  Gimp can crop, rotate, change brightness/contrast levels, adjust color balance, add text and graphics, and much more.
  
  
• 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.
  
  
• MySQL is a general-purpose database management system.  Sequel Pro is a free front-end to MySQL for Mac OS X.  MySQL works smoothly with R via the RMySQL package in R.