Data analysis tools for computational neuroscience

Mostly from the comp-neuro mailing list

• Neural Ensemble: Python
  
• FIND: MATLAB based, reads from diverse format
• INCF software center: portal for a collection of tools
• PANDORA: MATLAB based, raw voltage trace analysis tool
  
• Spike Train Analysis Toolkit
  
• SimToolDB

Database

• Neurodatabase
  

A step towards Kernel Kalman filter

For an arbitrary continous nonlinearity in both state space and observation models, we came up with a analytical approximation for the extended recursive least squares filter using kernel method and some linear algebra. Now I need to fill the details and implement this. I wonder if this is the Kalman filter...cause the model and solution looks the same.

This posting is a test from my blackberry.

Excellent student project for philosophy of science

Recently in computational neuroscience mailing list (comp-neuro), renowned scholars started discussion of why neuroscience is not advancing as much as we put money, time and effort to the field. Many interesting discussions regarding the nature of biological science compared to physical science, and Kolmogorov complexity complete systems, realistic vs simple models for understanding, reproducibility of experiments and so on are all over the place.
It would be a nice class project or even a preliminary topic for a thesis to analyze these hot discussions! Any volunteers?

Input induced synchrony, and desynchrony due to internal dynamics

This is perhaps the most uninteresting network of neurons: uncoupled (independent) oscillating neurons. The only interesting thing is that they share a common input. The oscillation can be reset by the input, thus, inducing synchrony of the population.
The plot on the right is how they desynchronize over time. It is due to the variability of each neuron's period. The more variability, the faster the desynchronization.

Robustness of Cognitive processes

10:30 am
I was browsing through the TOC alert emails and found the following paper
The nature of the memory trace and its neurocomputational implications
by: P de Vries, K van Slochteren
Journal of Computational Neuroscience, Vol. 25, No. 1. (2008), pp. 188-202.

The abstract was stating exactly what I have thought about 10 years ago. I am sure the idea is generally known to many people, but this was stated as I liked:

The brain processes underlying cognitive tasks must be very robust. Disruptions such as the destruction of large numbers of neurons, or the impact of alcohol and lack of sleep do not have negative effects except when they occur in an extreme form. This robustness implies that the parameters determining the functioning of networks of individual neurons must have large ranges or there must exist stabilizing mechanisms that keep the functioning of a network within narrow bounds...

The paper builds a high level model of neural assemblies.

Donation to TortoiseSVN

I share all my research documents and code via Subversion (SVN). And for the windows machines I use TortoiseSVN, a wonderful piece of software. Today, being in a good mood, I donated US dollars to the developers.
Keep up the good work TortoiseSVN!

Living neurons as liquid in LSM, why it makes sense

8am

LCN: living cortical network
LSM: liquid state machine

Advantage of using LCN for LSM

In the original LSM framework, any dynamical system that satisfies the separation property can be used as the liquid. However, how to choose a proper liquid for a specific problem is not yet well established. Although the details are unknown, the LCN has the capability to adapt to the signals that it is exposed, and self-organize itself. Therefore, the information processing through LCN could be interesting. In fact, well known phenomenological synaptic plasticity rules including spike-timing dependent plasticity turned out to have the power of self-organization and mutual information maximization. Being a biological system that is far from being fully understood, the LCN system has the power equivalent to the brain—neurons grow axon and dendrites, self-regulate ion channels, synapses grow, split and disappear, and more. The totality of LCN cannot be simulated in a computer as a traditional LSM would work with. Even if it is possible to simulate the system, it is always computationally cheaper to use the actual physical system rather than the complicated simulation.