[Comp-neuro] Re: Attractors, variability, noise, and other subversive ideas

Ross Gayler r.gayler at gmail.com
Tue Aug 19 03:58:20 CEST 2008


> By making his model source code freely available for years, Jim Bower
> has actually been shoring up reproducibility in computational modeling.
> It is hardly necessary to mention that reproducibility has elsewhere
> been called a cornerstone of scientific method.
> ...
> To everyone who has published results obtained by studying computational
> models of neurons or neural systems--at any level of abstraction--
> free your source code!

I couldn't agree more with the call for reproducible computational research.
However, availability of source code is a necessary but but not sufficient 
condition.  There has been a steady thread of writing on reproducible
research 
And associated tools over the last decade but it tends to be scattered
across 
disciplines.

http://www.reproducibleresearch.org/ provides pointers into some of this
literature.

Fully reproducible research is something to aspire to.

--Ross
 

-----Original Message-----
From: comp-neuro-bounces at neuroinf.org
[mailto:comp-neuro-bounces at neuroinf.org] On Behalf Of Ted Carnevale
Sent: Thursday, 14 August 2008 6:06 AM
To: CompNeuro List
Subject: Re: [Comp-neuro] Re: Attractors, variability, noise,and other
subversive ideas

james bower wrote:
> This is one of the first times in history that a complex realistic model 
> has spread across labs and opinions -- and speaks very well for the 
> future - this is what the GENESIS project was about to begin with -- and 
> now, more than 20 years later, it is starting to happen, not only with 
> GENESIS but through Neuro-DB built by Michael Hines and the Neuron group 
> at Yale as well.

Thanks for the plug, Jim.  And also for your advocacy of fresh ideas
(whether I agree with all of them or not) in computational/theoretical
neuroscience, or whatever it should be called.

Allow me this minor typographical correction:  it's ModelDB.
For those who may not yet know about it, here's the URL:
http://senselab.med.yale.edu/modeldb/
As of today, it contains source code for 394 published models,
most of which is ready to run.  We invite authors of published
models to submit them to ModelDB for attributed re-use and extension.

Now for my own bit of advocacy--

By making his model source code freely available for years, Jim Bower
has actually been shoring up reproducibility in computational modeling.
It is hardly necessary to mention that reproducibility has elsewhere
been called a cornerstone of scientific method.  How subversive of
his own polemic is that?!

As much as we might disagree on other issues, I am sure that Jim,
and also Bard (who has likewise shared code freely) will join me in
this call to arms:
To everyone who has published results obtained by studying computational
models of neurons or neural systems--at any level of abstraction--
free your source code!

--Ted
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