The Winnower | Open source publishing to boost your career

"When I started my PhD I was rather naïve about the workings of academia, never mind open science. This is my story on how I learned that open science, and in my case open source publishing, can not only fast-track science itself but actively stimulate collaboration, maximize impact, and in the process boost your career. The topic of my PhD (2006-2012 TCD) was the creation of an experimental and computational framework to study the biomechanical properties of human soft tissue (relevant to the improvement of car safety through simulations of tissue injury during crashes). The basic set of tools I required involved visualization, image processing, 3D modeling, and computational analysis. For each it seemed separate commercial and closed source software was available requiring specific licenses and license servers. Some software was simply not within budget, while others only operated on specific sites on campus and only if enough shared licenses happened to be available. In addition, to perform all the steps I required, I had to manually export/import files between packages. The inefficiency of this process and the costs associated with the commercial licenses frustrated me. It was also frustrating that I could not see how these systems worked under the hood. I wanted to understand and validate the software components and expand their capabilities, automate them, and integrate them into a single efficient pipeline. I therefore set out to create a dedicated toolbox within the programming environment MATLAB capable of performing all steps in a clear and transparent way (see visual examples in Figure 1) ..."