<< Chapter < Page Chapter >> Page >

Running simulations

In this section we will step through 2 different simulations using the matlab code. In the First simulation we will stimulate several cells in an assembly and several "noise" cells. Then the assembly will activate, shut down the noise and eventually die out. In the second we will have to different assemblies "compete".

Simulation 1

I have created a code called pattern _ maker.m which is an easy way to get a matrix will a designated number of cells, number of patterns, and number of cells per pattern. We will start with a network with 50 excitatory cells and train it with 8 patterns, containing 8 cells in each pattern. Type help pattern _ maker into a matlab prompt to get the details:

>> help pattern_maker pattern_maker.m - creates a pattern matrix. Each row represents a pattern with 1's for active cells, 0's for inactive cells. pattern = pattern_maker(n_cells,n_patterns,n_active) where: n_cells = number of cells n_pattern = number of patterns n_active = number active units per pattern output: pattern = n_patterns x n_cells matrix with each row a randomized pattern with n_active units

Now lets create a variable pp which will store the pattern matrix.

>> pp = pattern_maker(50,8,8);

Now that we have a pattern we can run the main piece of code that will do the simulation: LF _ network.m. Note that many of the parameters are only accessible in the code and would have to be directly edited if the user wishes to change them.

>> help LF_network LF_network.m - This function runs the Lansner-Fransen type simulations as detailed in their paper - "Modelling Hebbian cell assemblies comprised of cortical neurons". There are an equal number of excitory and inhibitory cells. Each excitory cell has a companion inhibitory cell which synapses onto it. The network is trained with different patterns loaded in. Then its calls a code which produces connection strengths. Positive strengths form Excitory to Excitory connections. Negative strengths form connections from Excitory to Inhibitory cells. [v_ex,v_in] = LF_network(dt,Tcutoff,Tfin,I0,stim_cells,Patterns) where: dt = time step Tcutoff = time cutoff for stimulated cells Tfin = time end simulation I0 = stimulation size for cells stim_cells = vector of cells recieving stimulus Patterns = matrix where each row is a pattern the network is trained with returns: v_ex = Voltages for excitory cells, indexed as ve(cell,timestep,compartment)v_in = Voltages for inhibitory cells, indexed as vi(cell,timestep,compartment)ex. pp = pattern_maker(50,8,8) [v_ex, v_in] = LF_network(.01,50,350,1,[1 6 8 10 25],pp);

As explained in the help file above one must choose the cell numbers to stimulate. In order to pick several cells in one assembly we will enter the following command to get the indices of one of the patterns:

>> find(p(1,:)==1) ans = 19 23 28 29 32 35 36 42

Thus we will choose to stimulate cells 19, 23, 28, 29 and add the noise stimuli of cells 45, 46, and 47. The simulation will last for 350 ms and the stimulation will last for 50 ms. A 1.5 nA stimulus is injected into each respective cell soma. After the output is saved we load the results in a code which displays the results: viewer.m.

Questions & Answers

Is the "growth and maintenance phase" in a cell's life cycle when cell division is about to occur
Somto Reply
what is the common name of Basidiomycetes
Ogechukwu Reply
الاجزاء النباتية لابد من تعقيمها قبل زراعتها في القوارير
yes
tariq
whats this?
tariq
do you speak arabic?!
what are bio elements
Shahzad Reply
which are present In Body And such elements Have Great role in our Body there are 16 bio elements that maintains human Body but on The basis of amount There are 6 bio elements present in Concen. of 99% and More Valuable And Highly Concen. element is Oxygent with 65 %
Haider
how je pollution brought about
Lamina Reply
how je pollution brouhgt about
Lamina
non is pollution brouhgt about
Lamina
describe the anatomy of cell division
Ivanovic Reply
Complex traits such as height result from 
Ruben Reply
what is the difference between chloroplasts and mitochondria
Nkalubo Reply
chloroplast in plants and bacterial cell ; mitochondria in animal cells
aung
Diagram of a living cell
Eliza Reply
what is cell
Sule
A cell is the smallest basic unit of life.
John
what's biology
Ogochukwu Reply
this is da study of living and non-living thing in an eco-system
Nutty
it is the study of living and non living organism in the ecology
Akufia
I agree with you dat biology is d study of living nd nonliving features
Winner
why do plants store carbohydrates in form of starch and not glucose?
Nutty Reply
Describe the structure of starch?
Nutty
wat is diffusion
Winner
water is life!.. Discuss?
Nutty Reply
why do plants store carbohydrates in form if starch not glucose!
Nutty
study of living thing
Dennis Reply
what is beyond a liveing cell
Raymond
what is biology
Gabriel Reply
d study of living nd non living thing
Winner
what is vasectomy
Evelyn Reply
The surgical removal of d spermduct
Eniola
Got questions? Join the online conversation and get instant answers!
Jobilize.com Reply

Get the best Algebra and trigonometry course in your pocket!





Source:  OpenStax, The art of the pfug. OpenStax CNX. Jun 05, 2013 Download for free at http://cnx.org/content/col10523/1.34
Google Play and the Google Play logo are trademarks of Google Inc.

Notification Switch

Would you like to follow the 'The art of the pfug' conversation and receive update notifications?

Ask