<p>I work mostly with MATLAB, and if necessary C/C++. Those are generic tools, but widely used in computational neuroscience. I often analyze and model spike trains in high time resolution, and there isn't a tool that is used universally yet. I have my own set of tools that I have developed in MATLAB. Also, many others in computational neuroscience publishes their code in MATLAB or python, so that also steers the community, I think.</p>

CC BY-SA 3.0
2014-04-03T13:54:28.793Z
I'm experimenting with julia these days.
Memming
CC BY-SA 3.0
2013-04-18T15:54:03.190Z
2013-04-18T15:54:03.190Z
Memming
<p>I personally used BRIAN simulator. Its a Python based library specialised in cortical neurons modelling and make network connections. I did my master thesis using it, I also have a published IEEE paper done using it.</p>

CC BY-SA 3.0
2014-04-11T17:57:50.050Z
2014-04-11T17:57:50.050Z
Sadeem Kbah
<p>Here is a comprehensive list of <a href="http://home.earthlink.net/~perlewitz/sftwr.html">Computational Neuroscience Software</a></p>

<p>My opinion below comes form the perspective of nonlinear dynamics (using differential equations to model ion currents in neurons).  So more the math/physics/electrical engineering approach to Computational Neuroscience (not so much the Computer Science or Psychology approach):</p>

<p>Personally, I don't use pre-packaged tools like <strong>NEURON</strong> or <strong>GENESIS</strong>.  I take mathematical models established in literature (i.e. The Hodgkin Huxley model) and use Matlab or Python to model them.  I essentially do what Neuron or Genesis does, but I do it my way so I can extract the information that's relevant to me.  This is how I have been trained through physics and applied mathematics departments.  To not rely on other people's implementations.</p>

<p>For nonlinear analysis of dynamical systems (because there's really a lot of extravagant mathematics that you don't want to just code yourself) a lot of people use <strong>XPP/AUTO</strong>, designed, in part, by Bard Ermentrout (a well-known computational neuroscientist).  This is a good way to go if you're not into writing code, but I prefer a more hackable tool.  I've been learning <strong>Matcont</strong>, a similar toolbox for Matlab but since it is made with m-files (matlab's data type) you can hack it and make it into code to integrate with your own Matlab software, avoiding the GUI clicking and dragging.</p>

CC BY-SA 3.0
2013-04-15T14:12:12.913Z
2014-04-02T13:42:32.250Z
2014-04-02T13:42:32.250Z
Keegan Keplinger
<p>What are the most common software tools you use in your day to day work in computational neuroscience?</p>

<p>I am referring to neuroscience tools like <a href="http://genesis-sim.org/" rel="nofollow">GENESIS</a> and NOT to generic tools like Excel.</p>

CC BY-SA 3.0
2013-04-14T20:56:11.620Z
This would depend heavily on the area. Please specify details. You don't want electrophysiology software for example, do you? Also, this question sounds like a poll and SE is not the best format for polls.
Memming
CC BY-SA 3.0
2013-04-14T21:12:50.100Z
As is, this question is overly broad and open-ended. Please consider editing your question to be more focused and address a problem that you face, rather than simply a discussion.
Jeff
<neuroscience><software>
Computational Neuroscience software
Victor L
# Computational Neuroscience software

(Asked by: username_0 on 2013-04-14)

What are the most common software tools you use in your day to day work in computational neuroscience?

I am referring to neuroscience tools like [GENESIS](http://genesis-sim.org/) and NOT to generic tools like Excel.

**Tags:** neuroscience, software

> **Comments:**
> **username_1**: This would depend heavily on the area. Please specify details. You don't want electrophysiology software for example, do you? Also, this question sounds like a poll and SE is not the best format for polls.  
> **username_2**: As is, this question is overly broad and open-ended. Please consider editing your question to be more focused and address a problem that you face, rather than simply a discussion.  

---

## 3 answers

### Answer by username_4 on 2013-04-15. Score: 12 | Accepted answer

Here is a comprehensive list of [Computational Neuroscience Software](http://home.earthlink.net/~perlewitz/sftwr.html)

My opinion below comes form the perspective of nonlinear dynamics (using differential equations to model ion currents in neurons). So more the math/physics/electrical engineering approach to Computational Neuroscience (not so much the Computer Science or Psychology approach):

Personally, I don't use pre-packaged tools like **NEURON** or **GENESIS**. I take mathematical models established in literature (i.e. The Hodgkin Huxley model) and use Matlab or Python to model them. I essentially do what Neuron or Genesis does, but I do it my way so I can extract the information that's relevant to me. This is how I have been trained through physics and applied mathematics departments. To not rely on other people's implementations.

For nonlinear analysis of dynamical systems (because there's really a lot of extravagant mathematics that you don't want to just code yourself) a lot of people use **XPP/AUTO**, designed, in part, by Bard Ermentrout (a well-known computational neuroscientist). This is a good way to go if you're not into writing code, but I prefer a more hackable tool. I've been learning **Matcont**, a similar toolbox for Matlab but since it is made with m-files (matlab's data type) you can hack it and make it into code to integrate with your own Matlab software, avoiding the GUI clicking and dragging.


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### Answer by username_1 on 2013-04-18. Score: 5

I work mostly with MATLAB, and if necessary C/C++. Those are generic tools, but widely used in computational neuroscience. I often analyze and model spike trains in high time resolution, and there isn't a tool that is used universally yet. I have my own set of tools that I have developed in MATLAB. Also, many others in computational neuroscience publishes their code in MATLAB or python, so that also steers the community, I think.

> **Comments:**
> **username_1**: I'm experimenting with julia these days.  

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### Answer by username_3 on 2014-04-11. Score: 2

I personally used BRIAN simulator. Its a Python based library specialised in cortical neurons modelling and make network connections. I did my master thesis using it, I also have a published IEEE paper done using it.


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