In April 2015, a symposium was held on how to improve the reproducibility of biomedical research. It was attended by scientists from research institutions, funding bodies and scientific journals. A report summarizing the symposium was published in November of last year. A very readable document, the report discusses various factors that contribute to poor reproducibility, as well as various recommendations
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In the last post, we learned to use the Python input() function to ask users to enter some information. Rather than sequentially prompting a user to enter information, we can have a user enter any relevent information when the program is run. Asking the user to input values when calling our program from the command line The command line is
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When we create a Python program or script, we sometimes need additional information. This information might be details from the experiments (e.g., subject age, amplifier settings, etc), or it might be an answer to a specific question (e.g., “Accept trial? Y or N”). When you need to ask the user of your code a question, you need their input, you
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In the previous lesson we merged the changes we made on our bug_fix_#001 branch into our master branch. Because the bug is now fixed, we have no need to keep the associated branch active. In this lesson we will learn how to close an active branch, as well as start a new, slightly more complicated example using branches. Closing an
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In light of recent depressing posts on the reproducibility crisis and the natural selection of bad science, I thought it worthwhile to revisit why we actually try to do good science, despite the pressures to compromise, and what qualities good scientists possess. Some time ago, the cell biologist Martin Schwartz wrote an interesting and honest essay on why, for sincere
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In the previous post, we created a branch called bug_fix_#001 and learned to make this our current branch using the git checkout <branch name> command. Once on this branch we made a change to one of our files (simulating a bug fix) and committed the change. By looking at the content of the changed file and our Git log, we
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Scientifically Sound 