Neurofitter is software for parameter tuning of electrophysiological neuron models.

It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuronsimulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm OptimizationEvolutionary Strategies, etc.

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What is a Neuron Transistor ?


The term “neuron” comes from the name used to describe the conducting nerve cell of the brain, spinal cord, and nerves. Human neurons consist of a cell body containing a nucleus, several nerve processes, and an axon or nerve fiber. The association between the Neuron Chip and the human nerve cell is the similarity of the three parts of a human nerve cell and the Neuron transistor

ip’s three, 8-bit CPUs. One C P U handles protocol for communication to and from the chip, another handles the application progr

am, and a third handles input/output information.

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Changing CakePHP pagination URLs

CakePHP framework provides a great pagination helper but its default URLs aren’t that great. By default it generates URLs that look like: http://domain/news/page:2. I spent a long time looking for a way to skip “page:” part in URLs and in links generated by the helper, or even just change the string “page” to something else. It showed up that there’s no easy way to configure the paginator that way. So I came up with a workaround that will change your CakePHP pagination URLs to: http://domain/news/2

Assuming that you already created pagination on your site according to CakePHP instructions we will start making a few changes. We begin with the view where we want to modify automatically generated links into the new ones:

$prev_link = str_replace(‘page:’, ”, $paginator->prev(‘« Prev’));

$prev_link = preg_replace(‘/\/1″/’, ‘”‘, $prev_link);

$next_link = str_replace(‘page:’, ”, $paginator->next(‘Next »’));

echo $prev_link;

echo $next_link;

This will take out “page:” part from the prev/next links and make them only contain the page number instead. Also, we replace http://domain/news/1 with only http://domain/news in order to avoid alias URLs and penalties for duplicate content by search engines. Be sure to apply the same method to the rest of your links such as those generated by numbers() method etc., if you are using them.

Now we need to make sure that the Cake makes correct interpretation of the passed argument. In our router file we add something like:

Router::connect(‘/news/*’, array(‘controller’ => ‘news’, ‘action’ => ‘display’));

This will forward our pagination links to news controller and its display() method. Our page number parameter will be passed as argument to this method. Let’s take a look at the code in news_controller.php:

public function display($option=”) {

if (is_numeric($option)) {

$this->passedArgs['page'] = $option;

$items = $this->paginate(‘News’);


As we can see we take the passed argument and assign it to the passedArgs array under the ‘page’ key where all named URL parameters are held. This way the paginator will understand that we are on the page passed by our URL.

That’s it. If you’ve done it correctly you now have nice pagination URLs like:




instead of:


http://domain/news/page:1 (duplicate)



CakePHP Session Troubleshooting

I use CakePHP on a day to day basis for project ranging from a single controller with a couple of views through to projects with large amounts of Controllers, Models, Views and Relationships.

This morning I was trying to build a simple Google Analytics component (which I will release as soon as it is done) and I needed to use the Session component…easy enough I hear you say…WRONG! I sat there for over an hour trying to figure out why my session was clearing every time I refreshed.

I searched high and low to find a solution, I tested the PHP session configuration by turning off “Session.start” in core.php and using the php “session_start()” function instead, everything worked fine.

After pulling out all my hair (what was left of it), I started thinking that it could be something to do with something being output before the header. I wasn’t getting any “Header Already Sent” warnings but I was still skeptical.

BINGO! I removed a single space after the closing php tag in one of my controllers and everything started working again.

It was so simple yet I have seem multiple threads on forums with the same problem but with no posted solution, hence why I am posting this for future reference (and when I inevitably forget).

So when troubleshooting CakePHP sessions make sure the first thing you do is remove any excess whitespace from your controllers, models and components.

A simple space after the ?> tag can cause all sorts of weird Session behaviour.

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