How to prepare a course protocol

The course focuses on the function of synaptically coupled neuronal networks in the brain. Step by step, simulation experiments of increasing complexity will be performed. The students’ task is to document what they did, why they did it, and what was the outcome, using precise language and appropriate terminology. In addition, students will need to design meaningful illustrations and parameter tables describing the simulation.

How to achieve this?

Simulations with NEST Desktop can be exported to PDF, PNG or SVG files. For PDF export, students can increase the zoom factor of the browser before printing the page. Image files can be imported to a document processor, e.g. LibreOffice or LaTeX for annotated illustrations of the simulation. It is important, however, that the writing is focused, and images to import into the protocol are carefully selected. As a final step, the protocol will be exported to a single PDF file and submitted by email to the course instructors.

Protocols must be concise, complete and correct. For each assignment, students must separately address the following four aspects:

  1. What is the scientific question or problem that is approached by the simulation? Use correct terminology in descriptions. Keep neurobiological aspects and mathematical modeling concepts apart.

  1. Which exact simulation setup was used to answer this question? List and describe all its components (e.g. neurons, devices), specify how they are connected together (e.g. electrodes, synapses), and provide tables of all relevant parameters. Default settings need to be stated at the beginning of each section. The goal is to make simulations fully reproducible.

  1. What was the outcome of the simulations performed? A meaningful set of figures should be selected to underpin the outcome of the simulations. In most cases, figures are helpful to illustrate the text-based description of the role of a specific parameter for the behavior of the system in question (e.g. a neuron, a network).

  1. What are the conclusions in view of the simulation results? Based on the simulation results obtained, formulate appropriate answers to the original questions. Distinguish aspects of biology/biophysics and possible issues (e.g. shortcomings) of the numerical model.