If you have been paying attention to the scientific tabloids (if there is such a thing), the headlines would continually be filled with claims that modern science is having a crisis of confidence. In big bold letters, tabloids would announce there is a REPRODUCIBILITY CRISIS in science. But is all this due to a handful of grumpy scientists who got
Read more
The computer age has seen many advances in science, including how scientists analyse data and report results. While some tools are complex and make it difficult for other scientists to understand exactly what steps were followed, other tools strive to increase the transparency and reproducibility of research. iPython and Jupyter notebooks A new and exciting tool is the electronic notebook.
Read more
I am assuming you have followed the first and second tutorial in this short series. You should now have a list variable called refs2 in your Python console. If you inspected the first item in refs2 list, you will notice that it specifies the journal, volume and page information for the first reference. 1 ‘1. J Neurosci. 2015 Dec 9;35(49):16159-70.
Read more
In the previous post, I explained how I recently had to sort through PubMed references to extract email addresses. As part of the tutorial, I had you download a sample text file containing 14 references, and we read the content of this file in Python. We are now going to continue cleaning the references to have them in a standardized
Read more
My colleagues and I recently needed to identify all the PubMed references on a given topic and locate email addresses of the corresponding authors. The good news is that the Author information section of PubMed references contains one or more email addresses approximately half of the time. This meant that I could automate the extraction of these email addresses by
Read more
In the previous post you learned about Git branches. Specifically, you learned about how branches could be used to make changes or additions to files in secret. The original versions of the files that are presentable (manuscripts, thesis, etc) or functional (computer programs) remain available as you make your changes on a branch. The beauty of this approach is that
Read more
Scientifically Sound 