How frequently do you update your lab notebook? Do you have a notebook for working on the computer? What is the point of a lab notebook even? How dependent are you on tools that utilize a graphical user interface (GUI)? If you were asked to regenerate a figure from your last lab meeting, how long would it take? We will be using blog posts as a way to maintain an electronic lab notebook in conjunction with project-specific GitHub repositories for our bioinformatics analyses.

The Notebook

Technically speaking, a laboratory notebook is something of a legal document that the PI of each lab owns. The PI depends on the laboratory notebook in cases where there are concerns over methods and results. It is often seen as a safety measure like keeping the receipts from the past 5 years in case you get an audit. But these are all negative reasons to maintain a laboratory notebook and don’t explain why you - the researcher - should keep a good laboratory notebook.

Imagine you are the only investigator in the lab. Why would you want to maintain a notebook? It’s a document that contains the many fragments that you will hopefully compile into a paper or a presentation. Traditional bound, paper and pen notebooks are more dangerous than helpful for informatics projects and are probably past their prime for use with wet-lab experiments. How much would you have to be paid to write out, long hand, your commands and the output? That would suck and even worse, it would be highly prone to transcription errors. The beauty of a computational notebook is that the code, output, and text are all together. Furthermore, it is possible to incorporate multimedia including images, videos, plots, tables, links to raw data, etc. It becomes an organizational tool that works for you.

Collaboration

Perhaps the most undervalued role of the laboratory notebook is in collaboration. Someone once said that your best collaborator is you… in six months. I would add that the second most important collaborator is your PI now, but especially once you leave the lab. As I mentioned above, the traditional laboratory notebook is frequently viewed as a legal document that will spend most of its life in storage. It is essentially the end of the road. But that is not the way science is supposed to work. That notebook should be a step towards another project. By using a blog framework with a commenting engine, issue tracking, pull requests, and code review your notebook and repository instantly become collaborative.

Mechanics

Each blog post should provide a record of your daily goals, what you accomplished, what you learned, and how you went about it for each of your daily objectives. These blog posts are comment enabled to allow for collaboration between people in the lab and Pat. They should be pushed to your GitHub repository at least once a day (preferably at the end of the day). People who fail to update their blog notebook regularly will be publicly flogged.

We have started to create various templates for different types of blog posts in the _post_templates folder. To start a new post, you will usually copy one of those templates to the _posts or _knitr folders and rename it to be YYYY-MM-DD-post-title. The elements of the date should be separated by dashes and in place of spaces in the blog title put dashes as well. These posts are written in markdown, which is a pretty easy to learn formatting method.