Dan J. Bower

Tools of the Trade

I am a strong advocate for open-source (and to some degree, freeware) software. Fortunately, in my day-to-day research I am largely able to steer clear from proprietary software. Even the occasional Microsoft Excel spreadsheet from a geochemist can be elegantly handled by OpenOffice (and then returned in OpenDocument Format).

There is always inertia in migrating to an open-source mentality but you will discover software that is often more robust, faster, more versatile and customisable than the proprietary equivalents. In this corner of my website I pay tribute to the communities that continue to develop, maintain and support open-source software projects, particularly those pertinent to academic research.

Here are my tools of the trade (in alphabetical order):

Computational Infrastructure for Geodynamics (CIG) (http://www.geodynamics.org/)

Coming soon ...

Generic Mapping Tools (GMT) (http://www.soest.hawaii.edu/gmt/)

Coming soon ...

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

Coming soon ...

LaTeX and BibTeX (http://www.latex-project.org/ and http://www.bibtex.org/)

With elementary scripting ability you can produce staggeringly beautiful and well-rendered documents (even presentations with the beamer class) in LaTeX whilst BibTeX robustly creates your bibliography from a database of entries. The fundamental ethos is that content and style are separate components of the document and thus can easily be isolated from one another. This freedom allows an author to produce, for example, a journal article using a particular style file from the publisher, and then later changing just the style file (i.e. one line of the script) to merge the textual content into a thesis. I hardly dare imagine how long this would take using the dreaded WYSIMOLWY (What You See Is More Or Less What You Get) combination of Microsoft Word and EndNote.

Linux

Arguably the most visible example of open-source software and the operating system of choice for workstations and supercomputers. I personally prefer the usability of Ubuntu but there are other great Linux distributions available.

Paraview (http://www.paraview.org/)

Robust visualisation software package for bringing VTK files to life. Ideal for making 3-D eye candy for your latest grant proposal or Science journal cover.

Python (http://www.python.org/)

The workhorse for my scripting to predominantly pre and post-process datasets. Wraps the Generic Mapping Tools (GMT) binaries beautifully and provides a great framework for dealing with VTK files through the Visualization Toolkit (VTK) python bindings. Along with the NumPy, SciPy, and matplotlib packages you will never again be required to have an internet connection and battle with the rest of an academic campus for MATLAB licenses.

Subversion (svn) (http://subversion.apache.org/)

Coming soon ...

Vim (http://www.vim.org/)

Every computational scientist has their text editor of choice and over the years I have largely settled on Vim because it is so ubiquitous. One day I should examine emacs more carefully, but for the time being at least my editing needs are fully satisfied by Vim.

Visualization Toolkit (VTK) (http://www.vtk.org/)

VTK and the associated python bindings provide a set of convenient functions to read/write/edit VTK files which can then be visualized using software such as Paraview.