Writing: LaTeX, Vim, Pandoc
LaTeX is a typesetting system, very popular among mathematicians due to its wide support of mathematical formulae. As opposed to the common approach “what you see is what you get” (WYSIWYG) kind of writing tools (such as word), in LaTeX the files are text files, and the formatting options are embed in the text. This means that the content and the style are separated, which saves me hours of tinkering with tables and whitespace. LaTeX also has a very consistent handling of intra-document references and bibliography, whereas Word usually sucks at this. Another advantage is the inline creation of scalable vector graphics, and the ability to use them. (https://www.latex-project.org/).
Vim is arguably the most powerful text editor ever created. Ubiquitous in any Linux system, it has been used for over 30 years and it is still the tool of choice for hard-core programmers. If your workflow involves heavy editing of text files (this includes data), I suggest you give it a try. It does takes a while to get used to it, but once you do, you become one being with the computer (http://www.vim.org/).
Pandoc is a simple command line application that allows for easy converting of text files between document formats: LaTeX, HTML, Markdown, Word and many more. It may come in handy for a thousand reasons (http://pandoc.org/).
File management: Git, Bash shell, sed & awk
Git is the best software for version control available. Also a command line tool, it is able to keep track of your work, create an automatic back-up in an external server, and revert it to previous versions if something goes wrong (https://git-scm.com/).
The bash shell is the most widely used command line, found in UNIX computers (Apple and Linux). In windows it can be obtained through applications like Cmder (http://cmder.net/). To explain it somehow, it’s like removing the limitations of interface-based operative systems, gaining access to a whole new world of automation. Commands like “sed” and “awk” for example, enable you to search for words inside documents, modify them, perform operations with them, export results to external files, and much more.
Graphics: SVG, inkscape, TikZ, Matplotlib, D3js
Scalable Vector Graphics (SVG), is a graphic format that allows you to maintain perfect resolution, no matter how much you zoom in, at minimum file size. Unlike bitmaps, where every dot in the picture has to be stored, in SVG the drawing is a set of equations that describe the image. This should be your preferred method to create plots and figures. Inkscape is the Photoshop equivalent of SVG, completely free (https://inkscape.org/es/). Another good option is TikZ, a LaTeX package for creating graphics programmatically in an intuitive manner (http://www.texample.net/tikz/).
For publication quality graphics, I recommend the plotting library of python, a popular programming language for scientific purposes. It allows you to create almost any kind of graphic, and customization is borderline infinite (https://matplotlib.org/index.html).
Data crunching: Python, R, Octave
Excel is usually the “go to” statistic tool for most people. I would need a book to explain all the reason why any programming language with scientific libraries and a decent interface (like any of the above), is far better in most tasks. Now, which one to choose really depends on your needs. Python is better suited for general purpose programming, data-science and system modelling (https://www.python.org/). R excels at statistics (https://www.r-project.org/), and Octave draws its strength by sharing the same syntax as MATLAB (https://www.gnu.org/software/octave/). You will have to research which one is more appropriate for your needs. If all of them can be used, I feel that Python is the one with most potential and reusability.
Presentations: beamer, Prezi, reveal.js
I admit that Power Point is an excellent tool when used properly. However, for some cases when you really need to shine, having better alternatives may come in handy. Beamer is the LaTeX package for creating presentations. A presentation with Beamer includes automatically updated progress bars and sections, compatibility with SVG, and all the magic and professionality of LaTeX (https://www.ctan.org/pkg/beamer).
Another option is Prezi. An online platform for presentations that gives you a gigantic canvas, and lets you fly through it as you present. It can look dazzling with the right topic, especially with touching histories, or when different parts of the presentation relate to a bigger, unifying part. Otherwise it can be a distracting rollercoaster (https://prezi.com/login/).
GIS: Quantum GIS
Finally, Quantum GIS, an open source GIS that comes with a Python console to create your own applications and automate your workflow. QGIS is part of Atkins innovation programme, state of the art in efficiency (https://www.qgis.org/es/site/index.html).
As you can see, there is a whole world of open source tools available. All of them are free, which means that you can install them anywhere, anytime. They are constantly being developed by a friendly community of users, and are fully customizable to your needs.
These tools require patience, time and dedication. But once you master them, trust me, you will never regret it.