Welcome to FOSS!

Here are my recommendations for software solutions that might increase your productivity, improve your product quality, and save you tons of time and money. My philosophy is to use software that is high quality, reliable, secure, multi-platform, and cost-effective. Your feedback and suggestions are welcome. Enjoy…

Life / Time / Task Management

Org-mode (http://orgmode.org)

Org-mode 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.

Task Coach (http://www.taskcoach.org)

Task Coach 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)

Ubuntu Linux 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 very 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.

Here is a screenshot of Ubuntu Linux on a 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 (http://www.apple.com)

Mac OS X is an alternative choice if you want the functionality, reliability and security of Linux combined with the popularity 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 nearly as many as Linux). If you are comfortable with Macs you are one step away from moving up to Linux. (Personally, I find Ubuntu Linux much more user-friendly that Macs.)

Integrated Office Suite

LibreOffice (http://www.libreoffice.org)

LibreOffice 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. LibreOffice exports to many formats, including Portable Document Format (PDF) and LaTeX. LibreOffice.org output is of the highest professional quality and gives you the most flexibility in making your work available to the widest audience worldwide. At home, we only have and use LibreOffice. Price = $0.

Web Browsers

Google Chrome (http://www.google.com/chrome)

Google Chrome is a web browser designed for speed, simplicity, security and much more: search, chat, email, shop, bank, read the news, watch videos online, etc.Price = $0.

Mozilla Firefox (http://www.mozilla.com)

Mozilla Firefox is an open-source 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, pop-up blocking and a number of other seamless innovations, Firefox stands out ahead. Price = $0.

Epidemiologic Programming

R (http://www.r-project.org)

R 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 (http://www.stata.com) — proprietary but excellent

Stata 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 – proprietary

— 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 sets. 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 (http://www.gnu.org/software/emacs)

GNU 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 the modified Emacs for Mac OS X 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 the Emacs meta package which is available from the package manager. Price = $0.

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 Toolkit (http://www.pdfhacks.com/pdftk)

pdftk is a command line program to merge, delete, burst, rotate pages from PDF documents — and much more! Please do not purchase expensive PDF manipulation software!

Photo & Image Editors

GIMP (http://www.gimp.org)

GIMP is the GNU Image Manipulation Program. It is an open source program for such tasks as photo retouching, image composition, and image authoring similar to Adobe Photoshop. 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 (http://inkscape.org)

Inkscape is an open source 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.Price = $0.

ImageMagick (http://www.imagemagick.org)

ImageMagick 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 (http://www.latex-project.org)

LaTeX 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.

Bibliography Management

JabRef (http://jabref.sourceforge.net)

JabRef 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, and should work equally well on Windows, Linux and Mac OS X. I use JabRef to search PubMed, 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.

Slide Presentations

LibreOffice Impress (http://www.libreoffice.org/features/impress)

Impress is a truly outstanding tool for creating effective multimedia presentations. Your presentations can be enhanced with 2D and 3D clip art, special effects and transition styles, animations, and high-impact drawing tools. Master pages simplify the task of preparing your materials. And you can save even more time by downloading templates from the LibreOffice template repository. You can also open Microsoft PowerPoint files, and save your work in PowerPoint format for people still locked into Microsoft products. Alternatively, you can use the built-in exporter to create Flash (.swf) versions of your presentations.

Beamer (https://bitbucket.org/rivanvx/beamer/wiki/Home)

Beamer is a LaTeX class for creating presentations that are held using a projector, but it can also be used to create transparency slides. Preparing presentations with Beamer is different from preparing them with WYSWYG programs like LibreOffice’s Impress, Apple’s Keynote, or KOffice’s KPresenter. A Beamer presentation is created like any other LaTeX document: It has a preamble and a body, the body contains \sections and \subsections, the different slides (called frames in Beamer) are put in environments, they are structured using itemize and enumerate environments, and so on. The obvious disadvantage of this approach is that you have to know LaTeX in order to use Beamer. The advantage is that if you know LaTeX, you can use your knowledge of LaTeX also when creating a presentation, not only when writing papers. Here is a gallery of Beamer themes. Price = $0.

Web Scientific Publishing and Blogging

WordPress using Annotum Theme (http://annotum.org)

Annotum is a hosted theme on WordPress.com, and a free theme on WordPress.org. This is the result of many months of hard work by many people at Google, PLoS, NLM, Automattic, and Crowd Favorite. Get started using this fantastic new tool to author and publish beautiful, peer-reviewed scholarly articles and journals. For example, medepi.com runs (for free) at medepi.wordpress.com, and I have chosen the Annotum Sans theme. To start blogging just start a free account at www.wordpress.com, then select the Annotum or other theme.

Project Management

jxProject (http://www.jxproject.com) — free but not FOSS

jxProject is a free project management software. You can install jxProject on all of your computers at no cost. You’ll also be able to share your project plans with anyone that has access to the Internet, because everyone on the Internet can access and install jxProject. Windows, Linux and Solaris are supported platforms and many Mac OS X users have reported great success using jxProject. Price = $0.

RationalPlan (http://www.rationalplan.com) — proprietary but affordable

RationalPlan is a powerful project management software designed to help both project managers and teams to create consistent project plans, allocate resources and analyze workload, track work progress, estimate projects’ costs and manage budgets. Whether your applications are in the area of construction, engineering, services and consulting, software development or any other business field, RationalPlan can help you to complete your projects on time and within budget. RationalPlan is a great alternative to Microsoft Project with some extra-features like multi-project management. It offers you the most important capabilities of a good project management software while being able to operate on various platforms starting with Windows, Mac OS X, Linux and all other Java enabled platforms.

Relational Database Management Systems

LibreOffice Base (http://www.libreoffice.org/features/base)

Base is a full-featured desktop database front end, designed to meet the needs of a broad array of users, for all kinds of usages, such as: keeping track of collections of objects;maintaining customer information databases; maintaining student grade and curriculum databases; storing survey information and experimentation data; storing population and census data; producing monthly financial reports in companies and organizations managing audit, quality assurance and production data. Price = $0.

THE END!