Academia on bocklund.io

Why Jupyter Notebooks Won't Replace Academic Papers

Sun, 29 Jul 2018 00:00:00 -0400

Recently there has been some buzz around Jupyter Notebooks in science, especially in light of the LIGO team sharing their detection and analysis of gravitational waves in Jupyter Notebooks. Others have claimed that Jupyter Notebooks will render traditional academic journal articles obsolete. The notebook or literate programming format improves on the reproducibility and disseminating of scientific work, however several key factors limit the notebook as a way to communicate science. In the article, I'll touch on these issues and explain why I believe that the current model of sharing computational science is here to stay.

Atomate - reproducible computational materials science workflows in Python

Sat, 05 Aug 2017 00:00:00 -0400

If you've done any computational work on a high-performance computing system, odds are you are very familiar with shell scripting and running code in at least 3 different languages that was passed down through the years. You know the theory of how it all works, but can never find the time to weed through, organize and update someone else's FORTRAN code (that was out of date when it was written in 2002) to use the latest techniques. Atomate aims to solve these problems by leveraging the community developed materials science tools and analyses in pymatgen and the workflow management/database creation of FireWorks to document and allow for easy execution of community standardized and easily customizable workflows managed and written using Python.

Getting Papers Remotely

Thu, 06 Jul 2017 00:00:00 -0400

Whether you are at home or traveling to a conference, it can be helpful to have access to all of the literature online that you would have at your institution. This article covers some easy and practical ways to connect to your institution's library easily. Some of these techniques work on any website, and others are for Google Scholar, or with the Alfred app for the Mac. The examples here are specifically for connecting to the Penn State library, but the methods are general enough to work at many or all institutions.