Documentation and other Academic Content#
Goals#
Learn about how to create and maintain a Lab-notebooks
Learn why documenting your day-to-day work is essential for every good scientist.
Introduction#
Academic content can take on many forms besides the classic report or thesis paper, especially now that it’s become easier than ever to create an online presence. A community of scientists is switching to creating websites documenting their research endeavors in-depth, often alongside classic journal publications.
These “living publications” often take the form of an e-book that is freely accessible online. An example of this can be found here in the publication “Neuroscout: a unified platform for generalizable and reproducible fMRI research”.
In the chapter communication and collaboration, you’ll learn how to create such an online presence. An in-depth introduction to how to create a website using open-source tools can be found in the course creating interactive content with “Jupyter Books”!; this template can be simply adapted to host a book or publication.
Creating a Lab-notebook#
The underlying content is often derived from the documentation scientists write alongside their scientific work. A useful tool to take notes and document your work is a so-called “lab notebook.”
Getting into the habit of maintaining a lab notebook is crucial for beginner scientists, regardless of their field of study, but it is also a relevant skill for every professional.
It is a tool to record all of your observations, measurements, calculations, and ideas related to a scientific experiment or project. A well-kept lab notebook serves as a permanent record of your work and can be a valuable resource for future reference, collaboration, and communication with others. Storing it online, e.g., on a project repository on GitHub, allows you to access your notes from anywhere in the world.
Your Lab Notebook may be project-specific or kept more in the form of a “research diary,” where you jot down what you have been working on throughout a day or week.
Content could be:
Date and title of the experiment,
project or sub-task that you’ve been working on
background information,
links or snippets of relevant literature
Code and related bugs you may have encountered, including how you’ve solved them
Procedure, including step-by-step instructions and any deviations from the plan
Observations, including data and measurements recorded during the experiment
Calculations, including formulas and results
Drawings, Graphs, and visual aids
Questions that came up during your work
Problems you may have encountered
Maintaining a Lab-notebook#
How often you update and how extensive your entries are is entirely up to you. A good habit is to take short notes at the end of each workday and translate them into your Lab notebook once a week. This not only helps you keep tabs on the work you’ve been doing but also helps you think about and engage with your work more deeply. It further provides a handy resource for progress meetings with other students or Professors and P.I.s.
Jupyter Notebooks:#
A popular file format for writing a lab notebook and for scientific content creation is the Jupyter Notebook, as it provides a convenient and interactive environment for text content, visualizations, and code snippets.
Whether you’re taking notes, collecting code snippets in your lab notebook, or writing a report or research paper, Jupyter Notebooks can help you organize and communicate your findings effectively.
An in-depth lesson on content creation with Jupyter Notebooks can be found in the sub-chapter Jupyter Notebooks.
Achknowledgments#
Most of what you’ll see within this lecture was prepared and adapted for this course by Peer Herholz, Michael Ernst & Felix Körber
Michael Ernst
Phd student - Fiebach Lab, Neurocognitive Psychology at Goethe-University Frankfurt