[omaha] help getting started

[Wes Turner]

This may be of use in neural simulation (and a bit OT for a Python mailing
list, but field-relevant nonetheless):

- "Brain Computation Is Organized via Power-of-Two-Based Permutation Logic"
http://journal.frontiersin.org/article/10.3389/fnsys.2016.00095/full


*The Theory of Connectivity and its Predictions: A permutation-Based Wiring
Logic To Cover Every Possibility*
To explore these questions, we have put forth the Theory of Connectivity
that proposes a rather simple mathematical rule in organizing the
microarchitecture of cell assemblies into the specific-to-general
computational primitives that would readily enable knowledge and adaptive
behaviors to emerge in the brain (Tsien, 2015a,b; Li et al., 2016). The
theory specifies that within each computational building block, termed
“functional connectivity motif” (FCM), the total number of principal
projection-cell cliques with distinct inputs should follow the
power-of-two-based permutation equation of N = 2i–1 (N is the number of
distinct neural cliques that can cover all possible permutations and
combinations of specific-to-general input patterns, whereas i is the number
of distinct information inputs; Figure 1). As such, each FCM consists of
principal projection neuron cliques receiving specific inputs, as well as
other principal projection neuron cliques receiving progressively more
convergent inputs that systematically cover every possible pattern using
the power-of-two-based permutation logic (Figure 1A).

IDK how this compares with e.g. "Brian" (which is written in Python)
http://briansimulator.org/


... There are different chips for neural simulation?

- https://en.wikipedia.org/wiki/SyNAPSE
- https://en.wikipedia.org/wiki/Memristor#Applications
-
https://en.wikipedia.org/wiki/Types_of_artificial_neural_networks#Hierarchical_temporal_memory

IIUC, identifying patterns across time is a relatively hard problem for
most existing neural networks?

On Sat, Dec 3, 2016 at 11:23 AM, Wes Turner <wes.turner at gmail.com> wrote:

>
>
> On Friday, December 2, 2016, Adam Shaver via Omaha <omaha at python.org>
> wrote:
>
>> Ted,
>>
>> I use anaconda python (link <https://www.continuum.io/downloads>). It is
>> a
>> free python sandbox for scientific programming) when coding python from
>> Windows 10. I find the sandbox is a little bit safer than trying to
>> install
>> it into the Windows Program Files (and later worrying about version
>> clash).
>> Anaconda comes with Scipy and Numpy, which I'm sure you book will cover.
>>
>> As per IDE (and IDLE indirectly), my suggestion would be to use a
>> combination of the Jupyter (IPython) notebook for in-line toy-problem
>> composition with a command-line (or IDLE) to drive bigger things. If you
>> were solving some PDEs of voltage potentials, then you might want to work
>> it out in a notebook. When it's developed into an object oriented piece of
>> code, then you could drop it into your simulation harness and drive it via
>> the command-line or IDLE.
>
>
>>
> IDLE -> IPython [-> spyder]
>
> http://ipython.readthedocs.io/en/stable/overview.html#
> enhanced-interactive-python-shell
>
> IPython Notebook (now Jupyter Notebook) is built on top of IPython. The
> Jupyter Notebook interface is cool, convenient, great for publishing; but
> it *is* a an open shell with the permissions of the user account it's
> running as; running on localhost. You can configure an SSL cert, or run it
> within a Docker container ( e.g. https://github.com/jupyter/docker-stacks/
> ).
>
> - https://jupyter-notebook.readthedocs.io/en/latest/public_server.html
> - https://jupyter-notebook.readthedocs.io/en/latest/security.html
>
> Spyder has an IPython console tab/pane.
>
> https://pythonhosted.org/spyder/ipythonconsole.html
>
>
>
>>
>> At that point, you could (should) probably write
>> unit tests.
>
>
> The scientific method is testing a hypothesis. The hypothesis is a test
> (often of significance). (Otherwise it's a null hypothesis (and that may be
> p-hacking). How is this not confirmation bias? IDK)
>
> It's possible to run tests in notebooks:
>
> - https://github.com/bollwyvl/nosebook/
> - http://github.com/taavi/ipython_nose
> - https://pypi.python.org/pypi/pytest-ipynb
>
> Exploratory analysis, just utilizing an API: Jupyter Notebook,
> https://github.com/jupyter/nbdime
>
> Writing a program/API: git diff, Spyder (vim w/ python-mode, makegreen,
> and a separate IPython CLI shell)
>
>
>> Best,
>> Adam
>>
>>
>> On Fri, Dec 2, 2016 at 9:04 AM, Ted Warren via Omaha <omaha at python.org>
>> wrote:
>>
>> > Hello,
>> >
>> > My name is Ted Warren, Ph.D. I am a post-doctoral researcher at
>> Creighton
>> > University. I am a synaptic physiologist who studies neuronal circuits
>> > involved in epilepsy. I am interested in started to write code using
>> > Python, but I need some help. I have been going through the following
>> text
>> > to learn how to use Python within the context of my field: A primer on
>> > scientific programming with python, 3rd Ed. by Hans Petter Langtangen.
>> >
>> > I have been unable to download the IDLE on my computer with Windows 10.
>> I
>> > have seen on the web that there is a bug and have been unable to find
>> > anyone on the web who has been able to circumvent the problem for my
>> > computer.
>> >
>> > I was wondering if there is anyone here that could help me. I cannot get
>> > off the ground learning until I get the IDE up and running.
>> >
>> > Just FYI, python is popular in neurophysiology for analyzing and
>> modeling
>> > neural circuits ( e.g., these two neurons signal via a capacitative
>> > coupling mechanism ). I am just trying to catch up with some of
>> colleagues.
>> >
>> > If I need to go somewhere else to get an answer for my question, any
>> > suggestions for directions would be appreciated.
>> >
>> > Thank you ahead of time,
>> >
>> > Ted
>> > _______________________________________________
>> > Omaha Python Users Group mailing list
>> > Omaha at python.org
>> > https://mail.python.org/mailman/listinfo/omaha
>> > http://www.OmahaPython.org
>> >
>> _______________________________________________
>> Omaha Python Users Group mailing list
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>>
>