Checked Nov.

2024

Free Neuroscience Textbooks and Online Tutorials

(Compiled by Carlos Aizenman, Brown University, Dept. of Neuroscience)

Maintaining a current list of digital educational resources is tricky. Software gets out of
date and is not updated, someone leaves a university and stops maintaining the
resource, grant funds to develop a resource run out and university refuses to continue
supporting the resource, etc. If you notice any of the resources here no longer work,
please let me know. Also, if you know of any ones not included please let me know as
well, especially free ones.

Simulators:

Electrophysiology of the Neuron: eotnprogram.org

A re-write of a program and book put out by John Huguenard and David McCormick.
Very flexible and can simulate real neurons as you can add a ton of different channels,
can be used for passive properties too. Has some built in lessons (book can be
downloaded for free) or you can design your own. Students have to download onto their
computers, doesn’t work well on Windows 10 tablets.

MetaNeuron: http://www.metaneuron.org
I use this for my class to simulate AP properties, recovery from inactivation and to teach
how to build IV curves. Downloadable and works well, but not a huge amount of
features. Great for a large class as it always works.

Neuromembrane: neuromembrane.ualberta.ca
More feature rich than MetaNeuron, shows activation and inactivation gates. Access
online, but can crash if too many people are accessing at once (like a large class). Lots
of adjustable parameters and neat animation (but play it at 4x speed - it gets repetitive
after a while). Currently not responding, I hope this is temporary.

NGS: The Nernst/Goldman Equation Simulator 12+ - App

StoreApplehttps://apps.apple.com › app › the-...
Excellent online Nernst Goldman Simulator. Change conductances, ion concentrations
and temperature. Runs as a Flash app on a browser, or as a downloadable Flash app,
so Flash needs to be enabled. Now only officially available as an iOS app, as Flash
is no longer supported.
This is an alternative Vm calculator, but not as polished:
https://www.physiologyweb.com/calculators/ghk_equation_calculator.html

Neuronify: http://ovilab.net/neuronify/
Checked Nov. 2024

This is a great neural circuits simulator, just drag and drop neurons, add synapses and
spiking properties and create all sorts of circuits. Also can add sensors, like a light
sensor using computer’s camera so you can look at RF, ON/OFF surround, etc. Works
on a computer or using an app on an iPad. Really nicely done.

NeuroWiki: https://github.com/CWRUChielLab/JSNeuroSim/tree/master/simulations
Amazing Javascript simulations of various cells, and circuits, and other properties by
Hillel Chiel as part of a neurophysiology course at Case Western:
https://canvas.case.edu/courses/18412/modules

Crescent Loom: https://crescentloom.com

Awesome drag-and-drop neural network simulator that allows you to custom build a
virtual aquatic creature and it’s nervous system. Can be played as a game or used as a
neuroethology sandbox. Extremely well done, and very fun to use.

Neurosim 5: https://www.st-andrews.ac.uk/~wjh/neurosim/modules.html
Fully fleshed simulation for teaching, runs in windows but can be run via a server and
accessed via the web, so could be integrated into Canvas or other class environments.
Not free, but not expensive.

Physiogy Experiments: Monash University -

https://ilearn.med.monash.edu.au/physiology/experiments.html
Great neuron simulators, particularly for systems neuro: nice visual recording simulation
- change contrast, orientation and create downloadable data. Auditory tuning and
somatosensory.

Neurons In Action: http://neuronsinaction.com/home/main

Not free. Commercially available as a set of tutorials built on NEURON environment but
with accessible user interface. Some are pretty good, but they are not free, and
interface is a bit clunky and non-intuitive. Good for a graduate or undergrad course.
They’ll send you a free copy if you tell them you might use it for a class. Probably
won’t run for long, not maintained by publisher.

Emergent: https://www.emersim.org/
Neural network simulator with a GUI. Fairly advanced but can be made accessible to
students with a little up-front teaching, at least one undergrad course here uses it
effectively.

Xolotl: https://xolotl.readthedocs.io/en/master/
Checked Nov. 2024

xolotl is a fast single-compartment and multi-compartment simulator written in C++ with

a MATLAB interface. Downside is that it needs Matlab, which is not free.

NEURON: https://www.neuron.yale.edu/neuron/what_is_neuron
Powerful neuronal model builder, can use own programming language, GUI, Python or
Matlab to interface with it. Here are some useful NEURON tools:

NetPyNe: http://www.netpyne.org
GUI for creating NEURON models and networks. Glitchy.
https://elifesciences.org/articles/44494

Tutorial from Oberlin: http://www2.oberlin.edu/octet/HowTo/NEURON/index.html

T2N: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737656/
Matlab interface

Neurotinker: http://www.neurotinker.com
Neurobytes are physically connectable neurons that allow you to build controllable
neural circuits, more “lab-like" than online sims. Expensive, though, and not yet for sale
(but apparently soon).

Braitenberg Vehicles Simulation: http://www.harmendeweerd.nl/braitenberg-vehicles/

Online simulation of a Breitenberg vehicle arena, customizable. Excellent for modelling
behavior in simple automata.

Boids: Flocking simulation: http://www.harmendeweerd.nl/boids/

Spikeling: Arduino based spiking neuron model, can be connected into a network, etc.
https://journals.plos.org/plosbiology/article/file?id=10.1371/
journal.pbio.2006760&type=printable

HHMI Biointeractive: Leech neurophysiology simulation. Cute, but not super in depth,
good for HS classes.
https://media.hhmi.org/biointeractive/vlabs/neurophysiology2/
Checked Nov. 2024

Swimmy: motor pattern generation lab exploring connectivity and CPG

https://mdcune.psych.ucla.edu/modules/swimmy

HH-Sim: https://www.cs.cmu.edu/~dst/HHsim/
Matlab Based HH simulator, but can be downloaded. Has nice exercises, can
manipulate channel gates.

Defunct Resources

Virtual Neurons: http://www.brainu.org/lesson/virtual-neurons

Simpler neural circuit simulator, designed for pre-college students, but I still use it in my
undergrad class as you can still get the basics of neural circuits and it is easy to use.

vLab from Amrita University in India: http://vlab.amrita.edu/?sub=3&brch=212

and http://vlab.amrita.edu/?sub=3&brch=43
This is a really well implemented online neurophysiology curriculum, complete with a
simulator and pre-made labs. They can be accessed as a guest for free, but cannot be
customized for your class. Sadly, these no longer work as they require Adobe Flash
and have not been updated.

Databases for Creating Virtual Labs

Allen Brain Atlas: A TON of neural data of all types: https://portal.brain-map.org

NeuroMorpho: Digital reconstructions of 100,000+ neurons from multiple species:

http://www.neuromorpho.org

Brain Museum: Comparative Brain Anatomy: http://www.brainmuseum.org/index.html

HemiBrain: Fly Connectome of a hemi-brain:

https://www.janelia.org/project-team/flyem/hemibrain

FlyWire Brain: If half of the fly brain isn’t enough, you can explore the whole fly brain
here! https://flywire.ai/

Whole neuron synaptic mapping: https://www.cell.com/neuron/fulltext/S0896-

6273(20)30138-0
Checked Nov. 2024

NITRC: database of structural MRI images:

https://www.nitrc.org/projects/candi_share/

Comparative Mammalian Brain collection: sections of brains

http://neurosciencelibrary.org/

ModelDB/NeuronDB: https://senselab.med.yale.edu/modeldb/
A ton of neuronal models ready for use.

Brain Architecture Project - http://brainarchitecture.org

Mouse and marmoset connectome, zebrafinch brain atlas, other atlases

Mouse Connectome - https://cic.ini.usc.edu

The Virtual Brain – https://www.thevirtualbrain.org/tvb/zwei/home

Tool for building connectome based human brain models

List of other neuroscience datasets, maintained by FUN:

https://docs.google.com/spreadsheets/d/1gDFNHRQiPfhnywTVe-
bqJTmAnYTaGEFL5yq6JEF8ptQ/edit#gid=772537126

Other Tools for Analyzing/Manipulating Data for Teaching:

FIJI (FIJI is just Image J): https://imagej.net/Fiji

Free set of advanced image analysis tools, could be used for analyzing morphology
data, Ca++ imaging data. Check out this tutorial:
https://www.ibiology.org/techniques/image-j/

Dataview (PC only): https://www.st-andrews.ac.uk/~wjh/dataview/

Free software suite for analyzing analog data, good for manipulating ephys data.

Tutorial for using python for ephys data:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4969392/

List of low or no cost ephys software: https://www.winltp.com/LowCostNoCost.html

Napari imaging: https://napari.org

Multi-dimensional image viewer for python (still in “alpha” stage)
Checked Nov. 2024

Case Studies

Journal of Undergraduate Neuroscience Education - https://www.funjournal.org

Monthly case studies in neuroscience, with objectives, exercises, etc.

National Center for Case Study Teaching Science (University at Buffalo) -

https://sciencecases.lib.buffalo.edu
Search by keyword, cases are free to access, other resources require paid subscription.

NeuroCaseNet - https://qubeshub.org/community/groups/neurocasenet
Group that actively maintains databases of neuro case studies, and creates some new
ones. Free to access once you sign up. Also has a FB page.

Free Textbooks:

WebVision:http://webvision.med.utah.edu

Neuroscience Online (free college-level interactive textbook): (I think this is the best
one, in terms of level and comprehensiveness).
https://nba.uth.tmc.edu/neuroscience/

Neuroanatomy:
https://nba.uth.tmc.edu/neuroanatomy/

Computational Cognitive Neuroscience:

https://grey.colorado.edu/CompCogNeuro/index.php/CCNBook/Main

The Nervous System In Action (Michael Mann, PhD): Free, bare-bones, but
comprehensive intro to neurophysiology.
https://michaeldmann.net/The%20Nervous%20System%20In%20Action.html

Open Neuroscience Initiative (Austin Lim, ed.): Another great free Neuroscience
textbook. Basic college level.
https://www.austinlim.com/open-neuroscience-initiative

Introduction to Behavioral Neuroscience: great textbook going from channels to

behavior.
https://openstax.org/details/books/introduction-behavioral-neuroscience

Neuroscience: Canadian 2d Edition

Checked Nov. 2024

Ju et al. 2020
Open introductory neuroscience textbook, a little too basic, but nicely put together.
https://ecampusontario.pressbooks.pub/neurosciencecdn2/

An Introduction to Neuroscience: ed. Kirby, Glenn, Sandstrom and Williams

A faculty created open source neuroscience textbook. It is still a work in progress, but
the one chapter that is posted on Neurophysiology is very good, so I included it in this
list.
https://rcalinjageman.github.io/an_introduction_to_neuroscience/index.html

The Brain From Top to Bottom (McGill)

More like a series of infographics than a textbook, but good for HS students
https://thebrain.mcgill.ca

Links to Tutorials and Online Course Material:

Excellent Intro to Python by Trent Wirth: https://trentwirth.github.io/3010/site/index.html

Lab Manual for a Neurophysiology Lab Course at Smith:

https://www.science.smith.edu/~rolivo/bio330/index.html

CRAWDAD: An Online Manual for Neurophysiology

https://nbb.emory.edu/wyttenbach/crawdad/

MDCUNE - digital neuro course with lots of labs.

https://mdcune.psych.ucla.edu
https://mdcune.psych.ucla.edu/modules/ineuro
https://mdcune.psych.ucla.edu/modules/bioinformatics

INCF training space:

https://www.incf.org/resources/training

iBiology: https://www.ibiology.org - A TON of talks on several biology topics and

techniques. Lots of neuroscience.

Brain Facts from SfN: https://www.brainfacts.org/the-brain-facts-book - Free eBook,

neuroscience primer for middle through high-school
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Axon Guide: https://www.moleculardevices.com/sites/default/files/en/assets/ebook/dd/

axon-guide-to-electrophysiology-and-biophysics-laboratory-techniques.pdf

Manual for ephys experiments. Centred on Axon equipment but great in general. To
request a clean copy go here: http://go.moleculardevices.com/l/83942/2016-06-
28/545czf?cmp=70170000001DREf

Scientifica: Ephys company that has some useful how-to’s in their blogs:
https://www.scientifica.uk.com/learning-zone
https://www.scientifica.uk.com/neurowire-blog

Neuromatch Academy: a plattform for live courses on computational neuroscience, but

includes access to free resources as well and suitable for self-study.
https://neuromatch.io/neuroscience/

Neuro4ML: Neuroscience for machine learners

Self guided course material, mainly a series of video tutorials, with python-based
exercises and links to relevant reference material. Could be used in part or in whole to
integrate various topics to a computational neuroscience course.
https://neuro4ml.github.io/