Software Solutions

Here are my recommendations for software solutions that might increase your productivity, improve your product quality, and save you time and money. My philosophy is to use software that is high quality, reliable, secure, multi-platform, and cost-effective. I also have a bias toward Free/Open Source Software (FOSS). FOSS not only saves you money, but also enables sharing and collaboration worldwide. Your feedback and suggestions are welcome. Enjoy...

Life/Time/Task Management

GNU Emacs Org-mode

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).

Task Coach

Task Coach (all platforms) (http://www.taskcoach.org) is a simple FOSS 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

Ubuntu Linux (http://www.ubuntu.com) is a FOSS 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

Mac OS X (www.apple.com) is an alternative choice if you want the functionality, reliability and security of Linux combined with the user-friendliness of Macs! Mac OS X is a derivative from the FreeBSD operating system (originally from UC Berkeley!) with many FOSS applications (although not as many as Linux). If you are comfortable with Macs you are one step away from moving up to Linux. Unfortunately, Apple's primary objective is to lock you into their ecosystem of hardware and software. This is most evident with their mobile devices and apps. I no longer purchase or use any Apple products, although I keep on old MacBook Pro at home. However, Mac OS still much better that MS Windows.

Online Backup and Synchronization

Dropbox

Dropbox.com (all platforms) (http://www.dropbox.com) provides an easy, secure and consolidated 2 GB free online backup, sync, sharing, access, and storage solution for Windows, Mac OS X, and Linux. Not only do I back up all my critical files, these files are synchronized across three computers (home, work, and laptop). I selected Dropbox because they provide five features (backup, sync, storage, access, and sharing) for all common operating systems, including Linux. The first 2 GBs are free forever. The synchronization feature is priceless!

Before selecting Dropbox I reviewed several online backup services. My primary criteria were online backup, encryption, synchronization, and Linux compatibility. I also incrementally backup my home computer nightly to an external hard drive using Linux's Grsync. For disaster recovery, it is important to backup off site---Dropbox fulfills this role.

Integrated Office Suite

OpenOffice.org

OpenOffice.org (all platforms) (http://www.openoffice.org) is a FOSS, 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.

Here is a screenshot of OpenOffice.org Writer (word processor) and Impress (slide presentation make). In Writer, notice the Styles & Formatting tool on the left. This powerful tool enables standard and customized global formatting using XML tags.

Web Browsers

Mozilla Firefox

Mozilla Firefox (all platforms) (http://www.mozilla.com), a FOSS 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.

Epidemiologic & Statistical Programming

R

R (all platforms) (http://www.r-project.org) is a FOSS environment for statistical computing and graphics -- my favorite! Better programming language than S-Plus, Stata, SPSS, SAS. R's strength is data analysis and graphics (not data management of large data sets). 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.

Read about R in the New York Times (here is follow up article).

Here is a screenshot of R running in the Mac OS X environment.

Text Editors

GNU Emacs

GNU Emacs (all platforms) (http://www.gnu.org/software/emacs) is a FOSS, 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

pdftk -- The PDF Tookkit

pdftk -- The PDF Tookkit (all platforms) (http://www.pdfhacks.com/pdftk/) to merge, delete, burst, rotate pages from PDF documents --- and much more! Please do not purchase expensive PDF manipulation software! Price = $0.

pdfjam

pdfjam (all platforms) (http://go.warwick.ac.uk/pdfjam) is a small collection of shell scripts which provide a simple interface to some of the functionality of the excellent pdfpages package for pdfLaTeX (see Professional Typesetting below). I use pdfjam to create PDF handouts for my LaTeX Beamer slide presentations (see Slide Presentations below). Price = $0.

Photo & Image Editing

GIMP

GIMP (all platforms) (http://www.gimp.org) is the GNU Image Manipulation Program. It is a FOSS 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.

Inkscape

Inkscape (all platforms) (http://www.inkscape.org) is a FOSS vector graphics editor, with capabilities similar to Illustrator, CorelDraw, or Xara X, using the W3C standard Scalable Vector Graphics (SVG) file format. Inkscape supports many advanced SVG features (markers, clones, alpha blending, etc.) and great care is taken in designing a streamlined interface. It is very easy to edit nodes, perform complex path operations, trace bitmaps and much more. We also aim to maintain a thriving user and developer community by using open, community-oriented development. Inkscape is shocking powerful! You will not be disappointed. Price = $0.

ImageMagick

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.

Video Editing & DVD Burning

coming soon

Professional Typesetting

LaTeX

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. And here are my LaTeX templates.

AUCTeX

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

LaTeX Beamer class

LaTeX Beamer class (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

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, and works equally well on Windows, Linux, and Mac OS. 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. I also use the JabRef OpenOffice.org plugin to create customizable bibliographies in OpenOffice.org. Price = $0.

Project Management

Gnome Planner

Gnome Planner (Linux) (http://live.gnome.org/Planner) is a modern and user-friendly, open source project management tool similar to Microsoft Project. If you are new to project management, this program is for you. Price = $0.

TaskJuggler

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.

Relational Database Systems

OpenOffice.org BASE

OpenOffice.org BASE (all platforms) (http://www.openoffice.org/product/base.html) 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.