Lab Notebooks

It is essential to keep track of your data and analyses in order to ensure organization, transparency, and reproducibility in your research. This involves keeping a detailed record of all the experiments and analyses that you perform - both experimental and computational - on a daily basis and developing a consistent system to ensure your analyses and results can be interpreted and shared with others. Below, I outline the lab's Standard of Practice for keeping data records and lab notebooks, which I expect everyone in the lab to adhere to (and improve upon whenever possible!).

We'll be using electronic lab notebooks as much as possible to standardize/share our analysis and results. Take a look at why ELNs are the best practice! Obviously, feel free to keep a paper notebook for scratch space, but record everything online for official record keeping.

1. Project Summaries

When starting a new project, please create a project summary to help you (and me) keep sight of the goals and tasks for this project. Feel free to update as the project evolves, even if it takes a turn for the unexpected, as research often does!

2. Project Organization

It is critical to make sure that you keep your data organized (similar to how you would organize your reagents!). In this vein, please follow the practices outlined in the Computational primer(s) linked below.

Bill Noble's A Quick guide to organizing computational biology projects

Arjun Raj's Organizing data before publication

3. Project Recording - the all-important Lab Notebooks!

In each section for Experimental or Computational Notebooks, I've outlined the details of how to best document your science and take advantage of the resources available through Benchling, R Markdown, Jupyter Notebooks, and version control through github/bitbucket. One common thread is to do the following for EACH research project you undertake - essentially, every time you create a Project Summary, create a new Benchling Project:

1. Create a benchling project - SHARE with the pailab-umms organization or at least Athma (athmaapai)

2. Create a notebook entry for each segment of the project

3. Each day, outline the "experiments" (broad term here) that you are undertaking - with goals, results, and conclusions/next steps clearly outlined.

future edits:

- making folder for saving data + project summaries + manuscript writing on Dropbox

- organization for manuscript writing - see Writing Manuscripts section