NEURON
NEURON is a computer simulation environment for simulating activity in neurons and neural networks. It translates the neuron's morphology and physiological mechanisms into equivalent circuit elements and solves its equations. A good start for learning NEURON is The NEURON book.
Using NEURON in your Masters of Science thesis?
In our group we are doing computational neuroscience with extra interest on the extracellular potential surrounding the neurons. The origin of the extracellular potential is transmembrane currents. These currents are computed using NEURON.
By reading The NEURON book you will get a good fundament for doing and understanding such computations. However, some parts of the book are more important than others, and I suggest you focus on the following chapters:
- chap. 1: A tour of the NEURON simulation environment. Download NEURON and follow the example of this chapter.
- chap. 3.2: Electric circuits and chap. 3.3: Cables. If you don't know this from before, read briefly through.
- chap. 5: Representing neurons with a digital computer. Pay special attention to chapter 5.5.2 3-D specification. When dealing with extracellular potential one has to know the 3-D positions of the transmembrane currents!
- chap. 6: How to build and use models of individual cells. Go through the example of chapter 1, now by only using hoc-code.
- chap. 12: hoc, NEURON's interpreter, chap. 13 Object-oriented programming and chap. 14: How to modify NEURON itself. Look through these chapters.
After reading through the above chapters in the NEURON book, this NEURON web-tutorial will give you more training in building NEURON models.
Useful links
- Download NEURON: Here you will find NEURON distributions for Windows, Linux and Mac. Download the current standard distribution.
- NEURON web-tutorial: This very nice NEURON tutorial helps you get the feeling of building NEURON models.
- ModelDB: A database of existing NEURON models.
- NEURON help: I use this alphabetical NEURON help all the time!
- NEURON at Duke: Here you will find some well-structured information about NEURON
- NEURON at Yale: Here you will find much information (maybe not that well-structured...?) from Hines and Carnevale (the NEURON developers)
- Neurons in action: Educational pages for students using Moore's and Stuart's: Neurons in Action: Computer Simulations with NeuroLab.
- NEURON discussion forum: Here you can post questions and find old questions with answers
