Life/Time/Task Management

• GNU Emacs Org-mode (all platforms) (http://orgmode.org) is an Emacs mode for keeping notes, maintaining ToDo lists, and doing project planning with a fast and effective plain-text system (GNU Emacs is a text editor --- see below under Text Editors). Org-mode develops organizational tasks around NOTES files that contain information about projects as plain text. Visibility cycling and structure editing help to work with the tree. Tables are easily created with a built-in table editor. Org-mode supports ToDo items, deadlines, time stamps, and scheduling. It dynamically compiles entries into an agenda. Plain text URL-like links connect to websites, emails, and any files related to the projects. For printing and sharing of notes, an Org-mode file can be exported as a structured ASCII file, HTML, and LaTeX.
  
  I use Org-mode to implement David Allen’s Getting Things Done (GTD) approach and Stephen Covey’s The 7 Habits of Highly Effective People. Whereas the 7 Habits helps one develop a personal mission statement to align long term goals with one’s values and priorities, the GTD approach provides the operational details for "getting things done." The irony of the 7 Habits approach is that one becomes overwhelmed trying to accomplish many worthwhile and fulfilling endeavors. Hence, the need for the GTD approach. Price = $0.
  
  Org-mode is right for you if you regularly use a text editor and you're willing to learn GNU Emacs. If this is not for you, then try Task Coach (all platforms) or OmniFocus (Mac OS).
  
  
  
  
  
• Task Coach (all platforms) (http://www.taskcoach.org) is a simple open source todo manager to manage personal tasks and todo lists. If you don't use Emacs, try Task Coach. Price = $0.

Computer Operating Systems

• Ubuntu Linux (http://www.ubuntu.com) is an open source operating system based on Debian Linux, and is the clear choice if you want excellent functionality, reliability, and security at an affordable price. You can convert your old MS Windows computer to Ubuntu Linux, or purchase a computer with it pre-installed (e.g., System76). Linux is an affordable alternative to Mac OS (also Linux-like). For the average workplace and home, Ubuntu Linux will have everything you need (including hundreds of free software solutions). For a limited budget, Ubuntu Linux is the clear choice.
  
  At home, we have four Ubuntu Linux computers and one MacBook Pro. I have transitioned all my professional work from Mac OS to Ubuntu Linux; it is much easier to access and maintain all the open source software I use in my work (R, GNU Emacs, Texlive LaTeX, OpenOffice.org, TaskJuggler, GIMP, pdfjam, pdf2swf, etc.)
  
  Here is a screenshot of Ubuntu Linux on System76 computer. On the left upper corner is GNU Emacs running AUCTeX; Gmail on the right upper corner; and Terminal on the lower right corner. The desktop background comes from Mac OS Snow Leopard.
  
  
  
  
  

• Mac OS X (http://www.apple.com/) is an alternative choice if you want the functionality, reliability and security of Linux combined with the user-friendliness of Macs! After many years of dissatisfaction with Windows, I had switched to the Mac OS, and I have never looked back. Mac OS X is a derivative from the FreeBSD operating system (originally from UC Berkeley!) with lots of open source (free) tools/software (although not as many as Linux). If you are comfortable with Macs you are one step away from moving up to Linux.
  

Integrated Office Suite

• OpenOffice.org (all platforms) (http://www.openoffice.org) is a free, open source, Microsoft Office-compatible and cross-platform (Windows, Linux, Solaris, and Mac OS) productivity software suite that includes a word-processor, spreadsheet, presentation program, and relational database, comparable to Microsoft Office's Word, Excel, PowerPoint, and Access. OpenOffice can read and output these MS Office files (I have not used MS Office products since 1997). It also includes editors for HTML, drawing, and math equations. OpenOffice exports to many formats, including Portable Document Format (PDF) and LaTeX. OpenOffice.org operates very well in the Windows OS. OpenOffice.org output is of the highest professional quality and gives you the most flexibility in making your work available to the widest audience worldwide. OpenOffice.org is available in many languages and is the fastest growing office applications suite worldwide. Price = $0.
  

Web Browsers

• Mozilla Firefox (all platforms) (http://www.mozilla.com), an open-source stand-alone web browser, designed for standards-compliance, performance and portability. Firefox is an award winning preview of next generation browsing technology from mozilla.org. Firefox empowers you to accomplish your online activities faster, more safely and efficiently than any other browser, period. Built with Tab browsing, popup blocking and a number of other seamless innovations, Firefox stands out ahead. Price = $0.

Web Authoring and Collaboration

• Google Groups, Docs, Sites, Apps, Gmail, etc. (http://www.google.com) is a set of freely available web applications that enable collaborative document and web authoring at a very high level of quality and functionality. I used Google Sites to develop this web site. We use Google Docs to prepare our research and training grants. Price = $0.

Epidemiologic Programming

• R (all platforms) (http://www.r-project.org) is an open source programming language for statistical computing and graphics - my favorite! Better programming language than S-Plus, Stata, SPSS, SAS. Price = $0. If you are new to R, check out my manual Applied Epidemiology Using R. Also check out epitools, our R package for epidemiology. Price = $0.
  
  Read about R in the New York Times.
  
  
• Stata (all platforms) (http://www.stata.com) is a user-friendly, yet powerful proprietary statistical package with excellent documentation. I used Stata extensively in graduate school but eventually switched to R (better programming language and graphics). Stata is not cheap, but once you buy it, its yours---no ongoing licensing fee (like SAS). Stata now has a R-like matrix programming language called 'mata'. If you are not satisfied with R, Stata should meet your needs. Price = $1500 (commercial) vs. $900 (academic).
  
  
• SAS --- NOT!!! For data analysis and graphics, SAS makes no economical sense: there are too many lower cost alternatives. SAS's strength is in the efficient management of large data. If your focus, like me, is on data analysis and graphics, don't waste your (or your employer's) money. The money you save not paying SAS licensing fees can be put towards advanced trainings and specialized software when you truly need it.
  

Text Editors

• GNU Emacs (all platforms) (http://www.gnu.org/software/emacs/) is an open source, extensible, and powerful text editor. Absolutely the best! My clear favorite for R programming, editing (text, HTML), and preparing technical documents using LaTeX. For Mac OS, I recommend Carbon Emacs that comes packaged with AUCTeX, Emacs Speaks Statistics (ESS), and much more. Also consider Aquamacs Emacs --- an easy-to-use, Mac-style Emacs for Mac OS X. For Windows OS, I recommend the Emacs/AUCTeX bundle; however, you will need to add ESS. For Ubuntu Linux, I prefer 'emacs-snapshot-gtk' which is available from the package manager. Price = $0.
  
  Emacs uses an initialization file in the user's directory called .emacs (/Users/mydir/.emacs in Mac OS; or /home/mydir/.emacs in Linux). Here is my .emacs file if you find this helpful.
  
  Here is a desktop screenshot of GNU Emacs running Emacs Speaks Statistics (ESS) and R (left), and an R plot (right)
  
  
  

Portable Document Format (PDF) manipulation

Photo & Image Editor

• GIMP (all platforms) (http://www.gimp.org/) is the GNU Image Manipulation Program. It is an open source program for such tasks as photo retouching, image composition, and image authoring. I use the GIMP primarily for cropping and rescaling images, converting images (e.g., TIFF to EPS, etc.), and creating images for the Web (e.g., PNG). This is the only image (including photos) editing software you will ever need. Price = $0.
  
  
• ImageMagick (all platforms) (http://www.imagemagick.org/) is an open source software suite to create, edit, and compose bitmap images. It can read, convert and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to translate, flip, mirror, rotate, scale, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves. The functionality of ImageMagick is typically utilized from the command line. Price = $0.

Professional Typesetting

• LaTeX (all platforms) (http://www.latex-project.org/) is a high-quality typesetting system, with features designed for the production of technical and scientific documentation, especially that involving mathematical notation. LaTeX is the de facto standard for the communication and publication of scientific documents. For Ubuntu Linux, just install Texlive using the package manager. For Mac OS, I recommend the MacTeX Texlive distribution. For Windows OS, I recommend the MiKTeX distribution. Price = $0.
  
  If you are new to LaTeX, see my tutorial LaTeX for Public Health and Medicine.
  
  
• AUCTeX (http://www.gnu.org/software/auctex/) AUCTeX is an open source, extensible package for writing and formatting TeX files in GNU Emacs. It supports many different TeX macro packages. AUCTeX includes preview-latex which makes LaTeX a tightly integrated component of your editing workflow by visualizing selected source chunks (such as single formulas or graphics) directly as images in the source buffer. AUCTeX makes creating LaTeX documents easier, fun, and error-free. Price = $0.

Slide Presentations

• Beamer class (LaTeX) (all platforms) (http://latex-beamer.sourceforge.net/) is a LaTeX class for creating high-quality, professional slides. The Wiki site is very informative with a gallery of available presentation themes. Here is a recent slide presentation I created using Beamer (using Cal Berkekey colors!). View slides in a PDF viewer (e.g., GSview, Mac OS Preview, or Adobe Acrobat Reader). To view slide presentation use the "Full Screen" mode. Enjoy! Price = $0.
  
  
• OpenOffice Impress (see above): Better than Microsoft PowerPoint.
  

Bibliography Management

• JabRef (all platforms) (http://jabref.sourceforge.net/) is an open source bibliography reference manager. The native file format used by JabRef is BibTeX, the standard LaTeX bibliography format. JabRef runs on the Java VM (version 1.4.2 or greater), and should work equally well on Windows, Linux and Mac OS X. I use JabRef to search PubMed (http://www.pubmed.org), and import and manage references. As a bibliography manager, JabRef is clearly superior to EndNote. If you don't use LaTeX and/or BibTeX, you don't need JabRef. Price = $0.
  
  
  
  
  
  
• OpenOffice.org Bibliographic Project. OpenOffice.org 3.X will have a new bibliographic package. This is great news! For details visit http://bibliographic.openoffice.org/.

Project Management

• TaskJuggler (Linux) (http://www.taskjuggler.org) is a modern and powerful, open source project management tool. Its new approach to project planing and tracking is more flexible and superior to the commonly used Gantt chart editing tools. It covers the complete spectrum of project management tasks from the first idea to the completion of the project. It assists you during project scoping, resource assignment, cost and revenue planing, risk and communication management. Your PM work is done in a built-in or external text editor. For those not comfortable with working in a text editor see Gnome Planner below. Price = $0.
  
  
  
  
  
• Gnome Planner (Linux) (http://live.gnome.org/Planner) is a modern and user-friendly, open source project management tool similar to Microsoft Project. Price = $0.
  
  
  

Relational Database Systems

• OpenOffice.org BASE (all platforms) (http://www.openoffice.org/product/base.html), new to Version 2, enables you to manipulate database data seamlessly within OpenOffice.org. Create and modify tables, forms, queries, and reports, either using your own database or BASE’s own built-in HSQL database engine. BASE offers a choice of using Wizards, Design Views, or SQL Views for beginners, intermediate, and advanced users. Price = $0.
  
  
• PostgreSQL (all platforms) (http://www.postgresql.org/), a powerful, open source relational database system. It has more than 15 years of active development and a proven architecture that has earned it a strong reputation for reliability, data integrity, and correctness. It runs on all major operating systems, including Linux, UNIX derivatives, andWindows. Price = $0.