genesis-sim-users — A list for users to discuss scripting and using the Genesis Neural Simulator

[Genesis-sim-users] Modified tabchannel objects in Vanier piriform cortex model

[Christoph M. <me...@ro...>]

Hi all,

I am trying to use the cell models from the Vanier&Bower piriform cortex
model. However, the model uses a modified version of Genesis 2.3 with
several modified objects. One example is a modified version of the
'tabchannel' object, which I think allows for a modulation of the ion
channels caused by neuromodulators. Since I am not interested in
neuromodulation I wanted to
translate the channels to the standard tabchannel objects. However, the
last line of the channel definition calls the action INITREFCOUNT (see code
below) which is not an action of a standard tabchannel. Before I start
diving into the Code behind the mod_tabchannel object, I was wondering  if
anyone of you has an idea what this call does and how to translate it to
standard tabchannel actions.

Thanks

Christoph

int pyr_std_xdivs = 4000

// ========================================================================
//                Tabchannel Na Hippocampal cell channel
// ========================================================================

function make_pyr_Na
    if ({exists pyr_Na})
        return
    end

    create mod_tabchannel pyr_Na
    setfield pyr_Na          \
        Ek        {PYR_ENA}  \
        Gbar      0          \
        Ik        0          \
        Gk        0          \
        Xpower    2          \
        Ypower    1          \
        Zpower    0          \
        mod_index 0

    float THRESHOLD_OFFSET = 0.025

    mod_setupalpha pyr_Na X  \
            {320.0e3 * (0.0131 + PYR_EREST_ACT + THRESHOLD_OFFSET)}    \
            -320.0e3                                                   \
            -1.0                                                       \
            {-1.0 * (0.0131 + PYR_EREST_ACT + THRESHOLD_OFFSET)}       \
            -0.004                                                     \
            {-280.0e3 * (0.0401 + PYR_EREST_ACT + THRESHOLD_OFFSET)}   \
            280.0e3                                                    \
            -1.0                                                       \
            {-1.0 * (0.0401 + PYR_EREST_ACT + THRESHOLD_OFFSET)}       \
            5.0e-3                                                     \
            -size {pyr_std_xdivs} -range -0.1 0.1

    THRESHOLD_OFFSET = 0.025

    mod_setupalpha pyr_Na Y  \
            128.0                                                      \
            0.0                                                        \
            0.0                                                        \
            {-1.0 * (0.017 + PYR_EREST_ACT + THRESHOLD_OFFSET)}        \
            0.018                                                      \
            4.0e3                                                      \
            0.0                                                        \
            1.0                                                        \
            {-1.0 * (0.040 + PYR_EREST_ACT + THRESHOLD_OFFSET)}        \
            -5.0e-3                                                    \
            -size {pyr_std_xdivs} -range -0.1 0.1

    call pyr_Na INITREFCOUNT
end

-- 

*Dr. Christoph Metzner, Dipl.-Math., B.Sc.*

Wissenschaftlicher Mitarbeiter des Institutes für Robotik und Kognitive
Systeme





[image: logo-uni-email]



*Universität zu Lübeck*

*Institut für Robotik und Kognitive Systeme*



Tel +49 451 500 5694  <%2B49%20451%20500%201234>

Fax +49 451 500 5202 <%2B49%20451%20500%201235>

E-Mail me...@ro... <n.m...@in...>

www.rob.uni-luebeck.de <http://www.institut.uni-luebeck.de/>



Ratzeburger Allee 160

23562 Lübeck

[Genesis-sim-users] v6.1 of NeuroMorpho.Org released 13 May, 2015

[NeuroMorpho.Org Admin. <neu...@gm...>]

Version 6.1 of NeuroMorpho.Org was released on 13 May, 2015.

This release included two new data sets of 4597 reconstructions.
NeuroMorpho.Org now contains 31,982 reconstructions from 147 contributing
labs. More than 3 million reconstructions were downloaded in over 150,000
unique visits from 150 countries.

Please visit the What’s new <http://neuromorpho.org/neuroMorpho/WIN.jsp>
page for details on the added data and other updates including updated
Metadata Form, inclusion of publication DOIs in the Literature Coverage,
and an unabridged collection of tools and resources. The literature
coverage database was also updated to include publications through March
2015

We are continuously grateful to all the data owners who freely share their
data with the community. We appreciate any and all feedback and comments.

Sincerely,

The NeuroMorpho.Org team

[Genesis-sim-users] Call for Participation: BigNeuron Hackathons

[NeuroMorpho.Org Admin. <neu...@gm...>]

Dear Colleagues,

As many of you have been aware of, yesterday the BigNeuron project (
 https://alleninstitute.org/bigneuron <https://alleninstitute.org/bigneuron>
 and http://bigneuron.org ) was formally announced by Allen Institute for
Brain Science and 12 other partner organizations worldwide.

We will welcome and encourage your participation, especially contribution
of your neuron reconstruction and analysis algorithms.

Please consider attending one of the upcoming hackathons at Cambridge Univ,
UK, and Janelia of HHMI, USA. The detail can be seen at the end. Please
note that the application deadlines are very close, so respond quickly
please.

If you have a question, please reply to big...@gm... or
big...@al... (for better tracking).

Look forward to working with you in BigNeuron!

Best,

-
Hanchuan Peng, Ph.D.

Giorgio Ascoli, Ph.D.
Erik Meijering , Ph.D.



On behalf of the

BigNeuron Consortium

https://alleninstitute.org/bigneuron

----

BigNeuron Hackathons: Call For Participation

The mission of the BigNeuron project (http://bigneuron.org) is to define
and advance the state-of-the-art of single neuron reconstruction, an
essential unsolved challenge in brain science. BigNeuron is a community
effort to both standardize the methods to generate high quality and
consistent neuron reconstructions, and mobilize the reconstruction
community to generate interest in solving these complex and interesting
algorithmic problems.

With the big success of our first BigNeuron hackathon kicked off in Beijing
<http://www.npr.org/blogs/health/2015/03/31/396586398/hackers-needed-to-teach-computers-to-spot-sick-brain-cells>
during
March 16-20, 2015, we are now looking forward to meeting more researchers
in the neuron reconstruction community at the upcoming two hackathons at
Cambridge University, UK, and Janelia Research Campus of HHMI, USA
<https://alleninstitute.org/bigneuron/hackathons-workshops/>.

Each BigNeuron hackathon will be a one-week (5 days) long event made up of
very intensive and productive programming work together with some of the
world experts in the neuron reconstruction and analysis fields. There will
also be intensive discussion of some of the cutting edge neuronal image
data and related techniques. The events will result in some major science
publications and new tools in the neuroinformatics field, and will also
contribute to making new and fruitful connections among various groups.


Cambridge Hackathon

The cambridge hackathon will be held at the Cambridge University in UK,
during May 4-8, 2015. It is sponsored by University of Cambridge (both the
department of neuroscience and advanced imaging center there), Europe's
Human Brain Project, Wellcome Trust (UK), and Allen Institute for Brain
Science, USA. The application deadline is *April 10th, 2015*.


Janelia Hackathon

The Janelia hackathon will be sponsored and held at Janelia Research Campus
of HHMI in USA, during June 1-5, 2015. The application deadline is *April
25th, 2015*.

Here are some more details about the registration and logistics, if you
haven’t registered.  Please feel free to spread the word and we are looking
forward to your participation!


Application, Registration and Logistics

There is no registration fee for BigNeuron hackathons. BigNeuron will cover
hotel rooms for one week and meals. The attendee needs to arrange his/her
own flights/travel to the hackathon sites. Due to the limited resources to
enable the intensive and productive programming and discussion during these
hackathons, BigNeuron will be able to accept only a selected number of
applications to participate in the events. The selection criterion for
applications to attend a hackathon will be based on whether or not the
applicants would directly contribute to the project by porting their neuron
tracing/reconstruction methods for bench-testing, and other related neuron
analysis algorithms during the hackathon events. If your application for
participation is accepted, we can also provide a formal invitation letter
if needed for visa application.

Please email big...@gm... to apply before the aforementioned
deadlines, with a brief introduction about your research background and why
you want to participate.


Questions?

For more information of the BigNeuron project, visit http://bigneuron.org.
The FAQ page may answer most of the common questions. More questions should
be directly sent to either big...@gm... or
big...@al... .

[Genesis-sim-users] Open Source Brain 2015: Building and sharing standardised neuronal models

[Padraig G. <p.g...@uc...>]

The third annual Open Source Brain Workshop takes place on May 12-14th 
2015 in Alghero, Sardinia. 
http://opensourcebrain.org/docs/Help/Meetings#OSB_2015

The Open Source Brain initiative aims to encourage collaborative, open 
source model development in computational neuroscience and is primarily 
supported by the Wellcome Trust. As with past OSB meetings this workshop 
will bring together experimentalists, theoreticians and tool developers 
who are interested in creating open, community developed models of 
neuronal systems.

Researchers interested in building and sharing models of any brain 
region and from any species are welcome to attend the meeting. There 
will be presentations on the latest developments and functionality of 
the OSB resource and associated technologies including NeuroML and LEMS. 
There will also be a special focus session on Wed 13th May on creating 
and sharing experimentally constrained models of the hippocampus.

Confirmed speakers

*Giorgio Ascoli *    Krasnow Institute, George Mason University, USA
*Tiago Branco *     MRC Laboratory of Molecular Biology, Cambridge, UK
*Claudia Clopath*     Imperial College London, UK
*Michael Hines *      Yale University, USA
*Peter Jonas *      Institute of Science and Technology, Austria
*Artur Luczak *      University of Lethbridge, Canada
*Troy Margrie*        MRC National Institute for Medical Research, 
London, UK
*Michele Migliore *National Research Council, Italy & Yale University 
School of Medicine, USA
*Yiota Poirazi *      Foundation for Research & Technology Hellas, Greece
*Martin Pyka *        University of Bochum, Germany
*Stefan Remy *      German Center for Neurodegenerative Diseases, Bonn, 
Germany
*Nelson Spruston * Howard Hughes Medical Institute, Janelia Farm 
Research Campus, Virginia, USA

Full details of the workshop can be found here: 
http://opensourcebrain.org/docs/Help/Meetings#OSB_2015. The meeting is 
free to attend, but registration is required (deadline April 15th).

The OSB 2015 organising committee

-- 
-----------------------------------------------------
Padraig Gleeson
Room 321, Anatomy Building
Department of Neuroscience, Physiology&  Pharmacology
University College London
Gower Street
London WC1E 6BT
United Kingdom

+44 207 679 3214
p.g...@uc...
-----------------------------------------------------

Re: [Genesis-sim-users] Kinetikit broken by linux updates

[U.S.Bhalla <bh...@nc...>]

Dear Sabih,
     This is a problem I too have faced, and I've not been able to find 
a fix within Ubuntu. It may have to do with their 'updated' window 
managers. Only ways out I've been able to use have been a) old versions 
and b) use MOOSE for model building. MOOSE gui is still not as evolved 
as kkit though.

Sorry not to have a better solution.

Best,
     Upi

On Sunday 08 March 2015 01:42 AM, Sabih Rehman wrote:
> Hello,
> 	Upon performing updates to Ubuntu 13.10, the drag and drop functionality necessary to create new objects in the edit/draw window in Kinetikit is broken. I was able to narrow down the update that breaks the functionality to the packages xserver-common and server-xorg-core. The latest version that doesn’t have this problem the I could find is 2:1.14.3-3ununtu2 for both packages, and breaks by 2:1.14.6-0ubuntu1. The most recent updates in Ubuntu 14.10 also do not solve this problem. I have tried editing the code of Kinetikit to move the tools from the control window to the edit window but this does not restore functionality. Is there a known fix for this problem? Thank you.
>
> Best,
> Sabih Rehman
> ------------------------------------------------------------------------------
> Dive into the World of Parallel Programming The Go Parallel Website, sponsored
> by Intel and developed in partnership with Slashdot Media, is your hub for all
> things parallel software development, from weekly thought leadership blogs to
> news, videos, case studies, tutorials and more. Take a look and join the
> conversation now. http://goparallel.sourceforge.net/
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

[Genesis-sim-users] Kinetikit broken by linux updates

[Sabih R. <sa...@gm...>]

Hello,
	Upon performing updates to Ubuntu 13.10, the drag and drop functionality necessary to create new objects in the edit/draw window in Kinetikit is broken. I was able to narrow down the update that breaks the functionality to the packages xserver-common and server-xorg-core. The latest version that doesn’t have this problem the I could find is 2:1.14.3-3ununtu2 for both packages, and breaks by 2:1.14.6-0ubuntu1. The most recent updates in Ubuntu 14.10 also do not solve this problem. I have tried editing the code of Kinetikit to move the tools from the control window to the edit window but this does not restore functionality. Is there a known fix for this problem? Thank you.

Best,
Sabih Rehman

Re: [Genesis-sim-users] V-clamp on dendrites?

[Jaeger, D. <dj...@em...>]

I believe the gain you need is pretty linearly related to your local input resistance.  It determines how much current is injected per mV deviation from command potential, and in turn this current will deflect the local Vm proportional to input resistance (Ohms law).  If you try to move Vm too fast you get numerical instability.  Glad to hear the problem is solved.  -Dieter

From: Kai Du [mailto:kai...@gm...]
Sent: Wednesday, March 04, 2015 1:45 PM
To: Jaeger, Dieter
Cc: gen...@li...
Subject: Re: [Genesis-sim-users] V-clamp on dendrites?

Hi Dieter Jarger,

Thank you for your suggestions. It works!
I have to use a very small "gain" to avoid clamp to be crushed:
========================================================
 setfield ^ gain 1e-9 tau_i 1e-7 tau_d 1.0e-8 saturation 1e-8
========================================================

These are the parameters used in my current clamp model and works well for my detailed model ( compartment length is ~ 5um ).

2015-03-03 14:31 GMT-08:00 Jaeger, Dieter <dj...@em...<mailto:dj...@em...>>:
Hello –

how small are you dendritic compartments?  Any one compartment in the dendrite that is abnormally small can cause such problems.  We use the attached for a voltage clamp that worsk well in the soma of simulated neurons (we haven’t clamped dendrites, but it *SHOULD* be similar).  You may have to decrease the gain if you are in high-input resistance area.  Your taus and gain are too aggressive.  This wouldn’t work in a real preparation, either!

-Dieter



From: Kai Du [mailto:kai...@gm...<mailto:kai...@gm...>]
Sent: Monday, March 02, 2015 12:50 PM
To: gen...@li...<mailto:gen...@li...>
Subject: [Genesis-sim-users] V-clamp on dendrites?

Hi All Genesis Users,

Do you ever have any experience in applying V-clamp on dendrites?

I just tried to apply the V-clamp to dendrites and I found it had to use a time step of 1e-20 second!!! or  simulations were simply crushed!

Do you how can we change the parameters in the  "V-clamp" settings so we can use a bigger time-step to clamp dendrites.

This is what I use now:
===================================================
create RC /clamp/lowpass
  setfield ^ R 1 C 1e-5

 create diffamp /clamp/vClamp
   setfield ^ saturation 999.0 gain 1

  create PID /clamp/PID     // Values taken from squid example
 setfield ^ gain 1e-5 tau_i 1e-5 tau_d 1e-7 saturation 999.0
============================================================


btw, I also tried V-clamp on passive dendrites, it also need a very "small" time-step, say, 1e-14 second. By contrast, the V-clamp works well to the soma -- a time step of 7e-6 second was needed.

--
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden



--
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden

Re: [Genesis-sim-users] V-clamp on dendrites?

[Kai Du <kai...@gm...>]

Dear Dave,

Thank you so much for the link! It helps me a lot to understand the "clamp"
in GENESIS.

2015-03-03 17:08 GMT-08:00 Dave Beeman <db...@co...>:

> As Dieter pointed out, it could be that the smaller size of the dendrite
> compartment might require different voltage clamp parameters.
>
> Also look at the "Mini-Tutorial on Voltage Clamp Circuitry Tuning" on the
> GENESIS web site.  Here is a direct link:
>
> http://genesis-sim.org/GENESIS/UGTD2-CNS/Tutorials/
> advanced-tutorials/Mini-tuts/vclamp/index.html
>
> I hope that this is helpful.
>
> Dave Beeman
>
>
> On Mon, 2 Mar 2015, Kai Du wrote:
>
>  Hi All Genesis Users,
>> Do you ever have any experience in applying V-clamp on dendrites?
>>
>> I just tried to apply the V-clamp to dendrites and I found it had to use a
>> time step of 1e-20 second!!! or  simulations were simply crushed!
>>
>> Do you how can we change the parameters in the  "V-clamp" settings so we
>> can
>> use a bigger time-step to clamp dendrites.
>>
>> This is what I use now:
>> ===================================================
>> create RC /clamp/lowpass
>>   setfield ^ R 1 C 1e-5
>>
>>  create diffamp /clamp/vClamp
>>    setfield ^ saturation 999.0 gain 1
>>
>>   create PID /clamp/PID     // Values taken from squid example
>>  setfield ^ gain 1e-5 tau_i 1e-5 tau_d 1e-7 saturation 999.0
>> ============================================================
>>
>>
>> btw, I also tried V-clamp on passive dendrites, it also need a very
>> "small"
>> time-step, say, 1e-14 second. By contrast, the V-clamp works well to the
>> soma -- a time step of 7e-6 second was needed.
>>
>> --
>> Best Regards,
>>
>> Kai Du,
>> PhD student
>> Department of Neuroscience
>> Karolinska Institutet
>> Retzius väg 8
>> S-17177 Stockholm, Sweden
>>
>>


-- 
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden

Re: [Genesis-sim-users] V-clamp on dendrites?

[Kai Du <kai...@gm...>]

Hi Dieter Jarger,

Thank you for your suggestions. It works!
I have to use a very small "gain" to avoid clamp to be crushed:
========================================================
 setfield ^ gain 1e-9 tau_i 1e-7 tau_d 1.0e-8 saturation 1e-8
========================================================

These are the parameters used in my current clamp model and works well for
my detailed model ( compartment length is ~ 5um ).

2015-03-03 14:31 GMT-08:00 Jaeger, Dieter <dj...@em...>:

>  Hello –
>
>
>
> how small are you dendritic compartments?  Any one compartment in the
> dendrite that is abnormally small can cause such problems.  We use the
> attached for a voltage clamp that worsk well in the soma of simulated
> neurons (we haven’t clamped dendrites, but it **SHOULD** be similar).
> You may have to decrease the gain if you are in high-input resistance
> area.  Your taus and gain are too aggressive.  This wouldn’t work in a real
> preparation, either!
>
>
>
> -Dieter
>
>
>
>
>
>
>
> *From:* Kai Du [mailto:kai...@gm...]
> *Sent:* Monday, March 02, 2015 12:50 PM
> *To:* gen...@li...
> *Subject:* [Genesis-sim-users] V-clamp on dendrites?
>
>
>
> Hi All Genesis Users,
>
>
>
> Do you ever have any experience in applying V-clamp on dendrites?
>
>
>
> I just tried to apply the V-clamp to dendrites and I found it had to use a
> time step of 1e-20 second!!! or  simulations were simply crushed!
>
>
>
> Do you how can we change the parameters in the  "V-clamp" settings so we
> can use a bigger time-step to clamp dendrites.
>
>
>
> This is what I use now:
>
> ===================================================
>
> create RC /clamp/lowpass
>
>   setfield ^ R 1 C 1e-5
>
>
>
>  create diffamp /clamp/vClamp
>
>    setfield ^ saturation 999.0 gain 1
>
>
>
>   create PID /clamp/PID     // Values taken from squid example
>
>  setfield ^ gain 1e-5 tau_i 1e-5 tau_d 1e-7 saturation 999.0
>
> ============================================================
>
>
>
>
>
> btw, I also tried V-clamp on passive dendrites, it also need a very
> "small" time-step, say, 1e-14 second. By contrast, the V-clamp works well
> to the soma -- a time step of 7e-6 second was needed.
>
>
>
> --
>
> Best Regards,
>
> Kai Du,
> PhD student
> Department of Neuroscience
> Karolinska Institutet
> Retzius väg 8
> S-17177 Stockholm, Sweden
>



-- 
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden

Re: [Genesis-sim-users] V-clamp on dendrites?

[Dave B. <db...@Co...>]

As Dieter pointed out, it could be that the smaller size of the dendrite
compartment might require different voltage clamp parameters.

Also look at the "Mini-Tutorial on Voltage Clamp Circuitry Tuning" on the
GENESIS web site.  Here is a direct link:

http://genesis-sim.org/GENESIS/UGTD2-CNS/Tutorials/advanced-tutorials/Mini-tuts/vclamp/index.html

I hope that this is helpful.

Dave Beeman

On Mon, 2 Mar 2015, Kai Du wrote:

> Hi All Genesis Users, 
> Do you ever have any experience in applying V-clamp on dendrites? 
> 
> I just tried to apply the V-clamp to dendrites and I found it had to use a
> time step of 1e-20 second!!! or  simulations were simply crushed! 
> 
> Do you how can we change the parameters in the  "V-clamp" settings so we can
> use a bigger time-step to clamp dendrites. 
> 
> This is what I use now:
> ===================================================
> create RC /clamp/lowpass
>   setfield ^ R 1 C 1e-5
> 
>  create diffamp /clamp/vClamp
>    setfield ^ saturation 999.0 gain 1
> 
>   create PID /clamp/PID     // Values taken from squid example
>  setfield ^ gain 1e-5 tau_i 1e-5 tau_d 1e-7 saturation 999.0
> ============================================================
> 
> 
> btw, I also tried V-clamp on passive dendrites, it also need a very "small"
> time-step, say, 1e-14 second. By contrast, the V-clamp works well to the
> soma -- a time step of 7e-6 second was needed.  
> 
> --
> Best Regards,
>  
> Kai Du,
> PhD student
> Department of Neuroscience
> Karolinska Institutet
> Retzius väg 8
> S-17177 Stockholm, Sweden
> 
>

Re: [Genesis-sim-users] V-clamp on dendrites?

[Jaeger, D. <dj...@em...>]

Hello –

how small are you dendritic compartments?  Any one compartment in the dendrite that is abnormally small can cause such problems.  We use the attached for a voltage clamp that worsk well in the soma of simulated neurons (we haven’t clamped dendrites, but it *SHOULD* be similar).  You may have to decrease the gain if you are in high-input resistance area.  Your taus and gain are too aggressive.  This wouldn’t work in a real preparation, either!

-Dieter



From: Kai Du [mailto:kai...@gm...]
Sent: Monday, March 02, 2015 12:50 PM
To: gen...@li...
Subject: [Genesis-sim-users] V-clamp on dendrites?

Hi All Genesis Users,

Do you ever have any experience in applying V-clamp on dendrites?

I just tried to apply the V-clamp to dendrites and I found it had to use a time step of 1e-20 second!!! or  simulations were simply crushed!

Do you how can we change the parameters in the  "V-clamp" settings so we can use a bigger time-step to clamp dendrites.

This is what I use now:
===================================================
create RC /clamp/lowpass
  setfield ^ R 1 C 1e-5

 create diffamp /clamp/vClamp
   setfield ^ saturation 999.0 gain 1

  create PID /clamp/PID     // Values taken from squid example
 setfield ^ gain 1e-5 tau_i 1e-5 tau_d 1e-7 saturation 999.0
============================================================


btw, I also tried V-clamp on passive dendrites, it also need a very "small" time-step, say, 1e-14 second. By contrast, the V-clamp works well to the soma -- a time step of 7e-6 second was needed.

--
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden

[Genesis-sim-users] V-clamp on dendrites?

[Kai Du <kai...@gm...>]

Hi All Genesis Users,

Do you ever have any experience in applying V-clamp on dendrites?

I just tried to apply the V-clamp to dendrites and I found it had to use a
time step of 1e-20 second!!! or  simulations were simply crushed!

Do you how can we change the parameters in the  "V-clamp" settings so we
can use a bigger time-step to clamp dendrites.

This is what I use now:
===================================================
create RC /clamp/lowpass
  setfield ^ R 1 C 1e-5

 create diffamp /clamp/vClamp
   setfield ^ saturation 999.0 gain 1

  create PID /clamp/PID     // Values taken from squid example
 setfield ^ gain 1e-5 tau_i 1e-5 tau_d 1e-7 saturation 999.0
============================================================


btw, I also tried V-clamp on passive dendrites, it also need a very "small"
time-step, say, 1e-14 second. By contrast, the V-clamp works well to the
soma -- a time step of 7e-6 second was needed.

-- 
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden

[Genesis-sim-users] Corrected: v6.0 of NeuroMorpho.Org released 11 Dec, 2014

[NeuroMorpho.Org Admin. <neu...@gm...>]

Version 6.0 of NeuroMorpho.Org was released on 11 December, 2014.

This major release included a single new data set (16,050 reconstructions)
from Drosophila melanogaster (Chiang archive, see also flycircuit.tw).
NeuroMorpho.Org now contains 27,385 reconstructions from 145 contributing
labs. More than 3.4 million reconstructions were downloaded in over 140,000
unique visits from 148 countries.

Please visit the What’s new <http://neuromorpho.org/neuroMorpho/WIN.jsp>
page for details on the added data and on a novel metadata annotation
system introduced in this release that allows users to search for
reconstructions based on various aspects of their completeness (structural
domains, physical integrity, and morphological attributes). The degree of
reconstruction completeness was estimated for all publications whose data
are deposited in NeuroMorpho.Org; individual neuron-level annotation will
continue in future releases. Moreover, data in NeuroMorpho.Org are now
directly accessible via BrainInfo <http://braininfo.rprc.washington.edu/>
and NeuronDB <http://senselab.med.yale.edu/neurondb/>. Last but not least,
OntoSearch <http://neuromorpho.org/neuroMorpho/OntoSearch.jsp> was expanded
with new strains and Literature Coverage
<http://neuromorpho.org/neuroMorpho/LS.jsp> was extended through November
2014.

We are continuously grateful to all the data owners who freely share their
data with the community. We appreciate any and all feedback and comments.

Sincerely,

The NeuroMorpho.Org team

[Genesis-sim-users] v6.0 of NeuroMorpho.Org released 11 Dec, 2014

[NeuroMorpho.Org Admin. <neu...@gm...>]

Version 6.0 of NeuroMorpho.Org was released on 11 December, 2014.

This major release included a single new data set (16,050 reconstructions)
from Drosophila melanogaster (Chiang archive, see also flycircuit.tw).
NeuroMorpho.Org now contains 27,385 reconstructions from 145 contributing
labs. More than 3.4 million reconstructions were downloaded in over 140,000
unique visits from 148 countries.

Please visit the What’s new <http://neuromorpho.org/neuroMorpho/WIN.jsp>
page for details on the added data and on a novel metadata annotation
system introduced in this release that allows users to search for
reconstructions based on various aspects of their completeness (structural
domains, physical integrity, and morphological attributes). The degree of
reconstruction completeness was estimated for all publications whose data
are deposited in NeuroMorpho.Org; individual neuron-level annotation will
continue in future releases. Moreover, data in NeuroMorpho.Org are now
directly accessible via BrainInfo <http://braininfo.rprc.washington.edu/>
and NeuronDB <http://senselab.med.yale.edu/neurondb/>. Last but not least,
OntoSearch <http://neuromorpho.org/neuroMorpho/OntoSearch.jsp> was expanded
with new strains and Literature Coverage
<http://neuromorpho.org/neuroMorpho/LS.jsp> was extended through November
2014.

We are continuously grateful to all the data owners who freely share their
data with the community. We appreciate any and all feedback and comments.

Sincerely,

The NeuroMorpho.Org team

[Genesis-sim-users] v6.0 of NeuroMorpho.Org released 11 Dec, 2014

[NeuroMorpho.Org Admin. <neu...@gm...>]

Version 6.0 of NeuroMorpho.Org was released on 11 December, 2014.

This major release included a single new data set (16,050 reconstructions)
from Drosophila melanogaster (Chiang archive, see also flycircuit.tw).
NeuroMorpho.Org now contains 27,385 reconstructions from 145 contributing
labs. More than 3.4 million reconstructions were downloaded in over 140,000
unique visits from 148 countries.

Please visit the What’s new <http://neuromorpho.org/neuroMorpho/WIN.jsp>
page for details on the added data and on a novel metadata annotation
system introduced in this release that allows users to search for
reconstructions based on various aspects of their completeness (structural
domains, physical integrity, and morphological attributes). The degree of
reconstruction completeness was estimated for all publications whose data
are deposited in NeuroMorpho.Org; individual neuron-level annotation will
continue in future releases. Moreover, data in NeuroMorpho.Org are now
directly accessible via BrainInfo <http://braininfo.rprc.washington.edu/>
and NeuronDB <http://senselab.med.yale.edu/neurondb/>. Last but not least,
OntoSearch <http://neuromorpho.org/neuroMorpho/OntoSearch.jsp> was expanded
with new strains and Literature Coverage
<http://neuromorpho.org/neuroMorpho/LS.jsp> was extended through November
2014.

Re: [Genesis-sim-users] GENESIS 2.4 final release now available

[Hugo C. <hug...@gm...>]

Congratulations Dave, impressive amount of work.

If you need information of any kind for your auditory cortex modeling, with
interfacing to the STDP object or hsolve, I am always happy to help you out.


Hugo


On Wed, Nov 12, 2014 at 4:39 AM, Dave Beeman <db...@co...> wrote:

> The November 2014 GENESIS 2.4 release is the first major revision of
> the GENESIS 2 neural simulator since the "final" release of GENESIS
> 2.3 in March 2006. Afterwards, development efforts shifted towards
> GENESIS 3 (G-3), a 21st century neural simulator without the
> limitations of GENESIS 2 and other simulators that were developed in
> the late 1980's and 90's. At this point, G-3 is still in the
> development stage.
>
> Although GENESIS 2.3 was intended to be the last release of the GENESIS 2
> series, it has continued to used and to evolve, with modifications needed
> to efficiently implement synaptic plasticity in large networks and many
> contributions from users. This has made it necessary for a new November
> 2014 GENESIS 2.4 release.
>
> This new release is now avalable for download from the GENESIS 2 website
> http://genesis-sim.org/GENESIS/.
>
> If any of you will be attending SfN, you can find out more about it at
> my poster 99.09 (TT88) on Sat, Nov. 15, 2014, 1:00 PM - 5:00 PM
>
> The GENESIS 2.4 release includes:
>
> *   The 'stdp_rules' object, documentation, and Scripts for
>      implementing spike timing dependent plasticity in networks of
>      hsolved cells
>
> *   New network connection commands allow distance-dependent
>      connection probabilities and/or weights, or the use of periodic
>      boundary conditions for network connectivity.
>
> *   The chemesis library for modeling second messengers and calcium
> dynamics
>
> *   Various user-contributed bug-fixes, utilities, and improvements.
>
> *   A new autoconf-based build system, so that a simple "./configure"
>      command will create the appropriate Makefile. This has been tested
>      under recent Linux and Mac OSX versions. The older method is also
>      available for platforms not supported by autoconf.
>
> *   HTML indexing in the 'genesis' directory and subdirectories, for
>      easy browsing of the GENESIS directory system and documentation.
>
> *   New tutorial Scripts for chemesis, gpython-tools, purkinje,
>      stdp_rules, VAnet2
>
> Dave Beeman
>
>
> ----------------------------------------------------------------------------
> Prof. David Beeman, GENESIS Users Group
> email: ge...@ge... - dbeeman@.colorado.edu
> GENESIS WWW site: http://www.genesis-sim.org/GENESIS/
>
> ----------------------------------------------------------------------------
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
>



-- 
Hugo



--

                  Hugo Cornelis Ph.D.

                    Agora Classica -- CTO
              http://www.agoraclassica.com/ <http://www.genesis-sim.org/>

            GENESIS-3 -- lead architect
              http://www.genesis-sim.org/

            Neurospaces Project Architect
              http://www.neurospaces.org/

[Genesis-sim-users] GENESIS 2.4 final release now available

[Dave B. <db...@Co...>]

The November 2014 GENESIS 2.4 release is the first major revision of
the GENESIS 2 neural simulator since the "final" release of GENESIS
2.3 in March 2006. Afterwards, development efforts shifted towards
GENESIS 3 (G-3), a 21st century neural simulator without the
limitations of GENESIS 2 and other simulators that were developed in
the late 1980's and 90's. At this point, G-3 is still in the
development stage.

Although GENESIS 2.3 was intended to be the last release of the GENESIS 2 
series, it has continued to used and to evolve, with modifications needed 
to efficiently implement synaptic plasticity in large networks and many 
contributions from users. This has made it necessary for a new November 
2014 GENESIS 2.4 release.

This new release is now avalable for download from the GENESIS 2 website
http://genesis-sim.org/GENESIS/.

If any of you will be attending SfN, you can find out more about it at
my poster 99.09 (TT88) on Sat, Nov. 15, 2014, 1:00 PM - 5:00 PM

The GENESIS 2.4 release includes:

*   The 'stdp_rules' object, documentation, and Scripts for
     implementing spike timing dependent plasticity in networks of
     hsolved cells

*   New network connection commands allow distance-dependent
     connection probabilities and/or weights, or the use of periodic
     boundary conditions for network connectivity.

*   The chemesis library for modeling second messengers and calcium  dynamics

*   Various user-contributed bug-fixes, utilities, and improvements.

*   A new autoconf-based build system, so that a simple "./configure"
     command will create the appropriate Makefile. This has been tested
     under recent Linux and Mac OSX versions. The older method is also
     available for platforms not supported by autoconf.

*   HTML indexing in the 'genesis' directory and subdirectories, for
     easy browsing of the GENESIS directory system and documentation.

*   New tutorial Scripts for chemesis, gpython-tools, purkinje,
     stdp_rules, VAnet2

Dave Beeman

----------------------------------------------------------------------------
Prof. David Beeman, GENESIS Users Group
email: ge...@ge... - dbeeman@.colorado.edu
GENESIS WWW site: http://www.genesis-sim.org/GENESIS/
----------------------------------------------------------------------------

[Genesis-sim-users] Testers needed for 'nearly final' GENESIS 2.4 release on non-Linux systems

[Dave B. <db...@Co...>]

I have put together what will become the final release of GENESIS 2.4
during the first week of November.  It has been pretty well tested
under Fedora and Ubuntu Linux, and I don't expect any problems with
other recent Linux distributions. It also has been successfully tested
with 32 bit Cygwin under Windows. GENESIS 2.4 has a lot of new features,
but none of them are likely to present any compilation problems that don't
already exist with the 2006 GENESIS 2.3 version.

However, it has been a long time since the testing of GENESIS 2.3
on systems such as Solaris/opensolaris, MacOS, and some of the older
platforms that are listed in genesis/src/README, or Makefile.dist.
Before I make this the final release, I would like to make any
Makefile, documentation, or source code changes needed to insure that
it will compile on these other systems.

If any of you have access to an opensolaris or Solaris system, or
use GENESIS on a Mac, it would be a big help to me if you would take
a half hour to try a compile of the new release.

You can get it either from the link to the
"October 2014 final beta release of GENESIS 2.4" at
genesis-sim.org/GENESIS, or directly from
genesis-sim.org/GENESIS/genesis-ftp/genesis-2.4beta-src.tar.gz

It will unpack to genesis-2.4beta/genesis, with a 'index.html' file in the 
'genesis' directory that you can use to browse the documentation and the 
various 'README' files to learn about new features and installation. The 
genesis/src/README (or README.html) file describes the installation 
procedure and editing of 'Makefile.dist'.  I would like to know about any 
changes that are required in these Makefile settings, or in the 
description of installation for newer Solaris or MacOS versions. If it 
compiles and runs one of the simulations in Scripts, I will consider it as 
having passed the test, so this should not take long.

Of course, other GENESIS users are welcome to get and try this preview
of the final release.

Thanks for your help,
Dave Beeman

----------------------------------------------------------------------------
Prof. David Beeman, GENESIS Users Group
Dept. of Electrical, Computer, and Energy Engineering
University of Colorado, Boulder, CO 80309
email: ge...@ge... - db...@co...
GENESIS 2 WWW site: http://www.genesis-sim.org/GENESIS/
----------------------------------------------------------------------------

Re: [Genesis-sim-users] How to draw color bar in GENESIS?

[Kai <kai...@gm...>]

Thank you so much! 

发自我的 iPhone

> 在 2014年10月2日，下午9:39，U.S.Bhalla <bh...@nc...> 写道：
> 
> Dear Kai,
>     There is a snippet of code for the color bar from kkit/xinterface.g. Here it is:
> 
> function make_colorbar(parent, above)
>     str parent
>     pushe {parent}
>     create xdialog Color [0,0:{above},30%,30] \
>         -script "set_item_color <w> <v>"
>     create xcoredraw cdraw [0:last,0:{above},70%,30] \
>         -xmin 0 -xmax 63 -ymin -0.5 -ymax 0.5 
>     create neutral scale
>     createmap scale cdraw 64 1 -delta 1 1 -origin 0 0 
>     create xview cdraw/view -path {parent}/cdraw/scale[] -field x \ 
>         -viewmode colorview -autoscale 1 -sizescale 1.2 \
>         -script "set_colorbar_color "{parent}"/cdraw <x>"
>     call cdraw/view RESET
>     call cdraw/view PROCESS
>     pope
> end
> 
> parent is the element to be the parent of the colorbar. 
> above is the graphical widget sitting above the colorbar.
> 
> Best,
>     Upi
> 
>> On Friday 03 October 2014 03:42 AM, Kai Du wrote:
>> Hi All, 
>> 
>> I have used the "xdraw" object to make a graphic presentation of "Vm". I also used the command  "xcolorscale hot"  to make it look more beautiful. 
>> 
>> The problem is how to draw a "color bar" in the figure? Does anyone have a clue?   
>> 
>> -- 
>> Best Regards,
>>  
>> Kai Du, 
>> PhD student
>> Department of Neuroscience
>> Karolinska Institutet
>> Retzius väg 8
>> S-17177 Stockholm, Sweden
>> 
>> 
>> ------------------------------------------------------------------------------
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>> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
>> 
>> 
>> _______________________________________________
>> Genesis-sim-users mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
> 

Re: [Genesis-sim-users] How to draw color bar in GENESIS?

[U.S.Bhalla <bh...@nc...>]

Dear Kai,
     There is a snippet of code for the color bar from 
kkit/xinterface.g. Here it is:

function make_colorbar(parent, above)
     str parent
     pushe {parent}
     create xdialog Color [0,0:{above},30%,30] \
         -script "set_item_color <w> <v>"
     create xcoredraw cdraw [0:last,0:{above},70%,30] \
         -xmin 0 -xmax 63 -ymin -0.5 -ymax 0.5
     create neutral scale
     createmap scale cdraw 64 1 -delta 1 1 -origin 0 0
     create xview cdraw/view -path {parent}/cdraw/scale[] -field x \
         -viewmode colorview -autoscale 1 -sizescale 1.2 \
         -script "set_colorbar_color "{parent}"/cdraw <x>"
     call cdraw/view RESET
     call cdraw/view PROCESS
     pope
end

parent is the element to be the parent of the colorbar.
above is the graphical widget sitting above the colorbar.

Best,
     Upi

On Friday 03 October 2014 03:42 AM, Kai Du wrote:
> Hi All,
>
> I have used the "xdraw" object to make a graphic presentation of "Vm". 
> I also used the command  "xcolorscale hot"  to make it look more 
> beautiful.
>
> The problem is how to draw a "color bar" in the figure? Does anyone 
> have a clue?
>
> -- 
> Best Regards,
>
> Kai Du,
> PhD student
> Department of Neuroscience
> Karolinska Institutet
> Retzius väg 8
> S-17177 Stockholm, Sweden
>
>
> ------------------------------------------------------------------------------
> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
>
>
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

[Genesis-sim-users] How to draw color bar in GENESIS?

[Kai Du <kai...@gm...>]

Hi All,

I have used the "xdraw" object to make a graphic presentation of "Vm". I
also used the command  "xcolorscale hot"  to make it look more beautiful.

The problem is how to draw a "color bar" in the figure? Does anyone have a
clue?

-- 
Best Regards,

Kai Du,
PhD student
Department of Neuroscience
Karolinska Institutet
Retzius väg 8
S-17177 Stockholm, Sweden

Re: [Genesis-sim-users] Testers needed for GENESIS 2.4 beta

[Gilles D. <gr...@sc...>]

Well, that stty bug was tricky to track down, but I found and fixed it.
It turns out this was a bug even in 2.3, but for some reason it didn't
show up when I was testing it back then.  (I'm not sure why any more,
and I don't have my Makefile from when I built 2.3 back in 2006 to see
what compiler flags I used.)

The problem is that when you use the "termio" structure rather than the
"termios" one, at least on Linux systems, the c_cc array in the structure
is smaller - it only has 8 members rather than the 19 that termios has.
So when the code tries to set new_tty_stdin.c_cc[VEOL], that ends up
clobbering the o_flag field of the following structure, old_tty_stdout,
which has the saved state.

My fix is two-fold: first, check before setting the c_cc members to make
sure the array is big enough, and second, for Linux systems use termios
as for Mac & FreeBSD systems.  That seems to fix the problem.  My patch
below has this two fixes plus a correction for a typo in the non-TERMIO
section of the code.


--- shell/shell_tty.c.onlcrbug	2005-10-24 01:31:22.000000000 -0500
+++ shell/shell_tty.c	2014-07-25 15:59:25.000000000 -0500
@@ -154,7 +154,7 @@ static char rcsid[] =
 #include <termio.h>
 #endif
 
-#if defined(__FreeBSD__) || defined(__APPLE__)
+#if defined(__FreeBSD__) || defined(__APPLE__) || defined(Linux)
 struct termios old_tty_stdin, old_tty_stdout, new_tty_stdin, new_tty_stdout;
 #else
 struct termio old_tty_stdin, old_tty_stdout, new_tty_stdin, new_tty_stdout;
@@ -473,7 +473,7 @@ void normal_tty()
      * reset the terminal parameters to their original state
      */
 #ifdef TERMIO
-#if defined(__FreeBSD__) || defined(__APPLE__)
+#if defined(__FreeBSD__) || defined(__APPLE__) || defined(Linux)
     tcsetattr(fileno(stdin), TCSANOW, &old_tty_stdin);
     tcsetattr(fileno(stdout), TCSANOW, &old_tty_stdout);
 #else
@@ -517,7 +517,7 @@ void terminal_setup()
      * save the old terminal parameters
      */
 #ifdef TERMIO
-#if defined(__FreeBSD__) || defined(__APPLE__)
+#if defined(__FreeBSD__) || defined(__APPLE__) || defined(Linux)
     tcgetattr(fileno(stdin), &old_tty_stdin);
     tcgetattr(fileno(stdout), &old_tty_stdout);
 #else
@@ -525,7 +525,7 @@ void terminal_setup()
     ioctl(fileno(stdout), TCGETA, &old_tty_stdout);
 #endif
 #else
-    ioctl(fileno(stdin), TIOCGETP, &old_tty_stdint);
+    ioctl(fileno(stdin), TIOCGETP, &old_tty_stdin);
     ioctl(fileno(stdout), TIOCGETP, &old_tty_stdout);
 #endif
     /*
@@ -673,12 +673,17 @@ tset()
      */
     new_tty_stdin.c_lflag &= ~(ECHO | ICANON);
     new_tty_stdin.c_oflag |= ONLCR;
-    new_tty_stdin.c_cc[VEOF] = 1;
-    new_tty_stdin.c_cc[VEOL] = 1;
+    /* on some systems the c_cc array is too small so test before setting: */
+    if (sizeof(new_tty_stdin) >
+           ((void *)&new_tty_stdin.c_cc[VEOF] - (void *)&new_tty_stdin))
+        new_tty_stdin.c_cc[VEOF] = 1;
+    if (sizeof(new_tty_stdin) >
+           ((void *)&new_tty_stdin.c_cc[VEOL] - (void *)&new_tty_stdin))
+        new_tty_stdin.c_cc[VEOL] = 1;
     /*
      * set the new parameters
      */
-#if defined(__FreeBSD__) || defined(__APPLE__)
+#if defined(__FreeBSD__) || defined(__APPLE__) || defined(Linux)
     tcsetattr(fileno(stdin), TCSANOW, &new_tty_stdin);
 #else
     ioctl(fileno(stdin), TCSETA, &new_tty_stdin);



On Mon, 21 Jul 2014 7:21 PM, Dave Beeman wrote:
> 
> Thanks for the report. I will get it into the public genesis-2.4beta-src
> release that I am putting out tonight.
> 
> The fix for the terminal window will have to wait for the final
> November release.
> 
> The latest version at https://github.com/dbeeman/genesis-2.4beta-files
> has some fixes for Mac OS X, but I am still looking for Mac testers.
> 
> Dave Beeman
> 
> 
> On Mon, 21 Jul 2014, Gilles Detillieux wrote:
> 
> > I've tested it briefly on Scientific Linux 5.10, an RHEL 5 clone
> > system.  There's a slight bug in the Linux section of src/Makefile.dist:
> > the XINCLUDE= line is missing the -I option argument, and instead just
> > lists the include directory name.  This results in a bunch of spurious
> > linker warnings like the following:
> >
> > cc: /usr/include/X11: linker input file unused because linking not done
> >
> > The fix is simple enough:
> >
> > --- Makefile.dist.orig  2014-07-20 18:05:25.000000000 -0500
> > +++ Makefile.dist       2014-07-21 16:11:00.000000000 -0500
> > @@ -836,7 +836,7 @@
> >  # MACHINE=Linux
> >  # OS=BSD
> >
> > -# XINCLUDE=/usr/include/X11
> > +# XINCLUDE=-I/usr/include/X11
> >
> >  ## Choose ONE XLIB line to uncomment:
> >  ## For 32-bit architectures
> >
> > (Note that this is a capital "i" option, not a lower-case "L".  It's
> > hard to tell with some fonts.)
> >
> > Another problem is that after running genesis, the ioctl/stty settings
> > for the terminal window aren't properly restored.  It seems the "onlcr"
> > mode is turned off and not turned back on after quitting.  I haven't
> > looked at the code enough to find a fix for that problem.
> >
> > I ran the Squid script as a test, and it seems to behave as it did under
> > 2.3.  I haven't tested any further yet.
> >
> > Gilles
> >
> > On 07/15/2014 02:56 PM, Dave Beeman wrote:
> >> I am preparing a beta release of GENESIS 2.4, in preparation
> >> for the tutorial that Hugo Corenelis will give at CNS 2014.
> >> There will be further additions in the final November release,
> >> but the present version is looking pretty good.
> >>
> >> However, compilation has only been tested on recent Fedora and Ubuntu
> >> Linux distribution.  It would be a big help to me if I could get a
> >> few volunteers to try an installation on other Linux versions,
> >> and MacOS in particular.
> >>
> >> If anyone is using GENESIS under Cygwin, it would be wonderful if
> >> someone would build a Cygwin binary.
> >>
> >> The files and installation instructions can be viewed and downloaded
> >> at https://github.com/dbeeman/genesis-2.4beta-files.
> >>
> >> I'm not asking for any extensive testing, but only for reports of any
> >> issues that may come up during installation. However, there are some
> >> worthwhile new features that you may want to look at.  By helping us
> >> testing, you will not only help make a better final release, but have
> >> a chance to preview these additions:
> >>
> >> * The new 'stdp_rules' object for efficiently implementing spike
> >>      timing dependent plasticity in large networks of hsolved
> >>      multicompartmental cells.
> >>
> >> * A new version of the chemesis library for modeling second messengers
> >>     and calcium dynamics is now installed by default.
> >>
> >> * New tutorial Scripts and Doc entries were added for:
> >>       o chemesis
> >>       o the gpython-tools Python utility collection
> >>       o An updated Purkinje tutorial
> >>       o stdp_rules, including 'NewPlasticityObjects' documentation for
> >>         implementing similar objects.
> >>
> >>       o An improved hsolved implementation of the dual exponential
> >>         conductance version of the Vogels-Abbott network model. It serves
> >>         as a tutorial on how to achieve a speed improvement of 10 to 20
> >>         times when using hsolve with network models.
> >>
> >> * Bug fixes and Makefile improvements to ease installation.
> >>
> >> Thanks for your help,
> >> Dave Beeman


-- 
Gilles R. Detillieux              E-mail: <gr...@sc...>
Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
Dept. of Physiology and Pathophysiology, Faculty of Health Sciences,
Univ. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)

[Genesis-sim-users] Announcement: GENESIS 2.4 beta tutorial at CNS

[Hugo C. <hug...@gm...>]

This is a public announcement of the GENESIS-2.4 tutorial at the
Computational Neuroscience meeting (CNS) in Quebec City and the
official public beta release of GENESIS 2.4.  This new release
includes support for spike-timing dependent plasticity in large
networks of multicompartmental cells, bug fixes, comes with new python
utilities and tutorial materials.

The "Ultimate GENESIS Tutorial Distribution", included in this
release, contains updated course materials for the tutorial
Constructing biologically realistic neuron and network models with
GENESIS.

The tutorial brings together material that is available as separate
downloads from the GENESIS web site and through the GENESIS Users
Group. It includes several simulator-independent tutorials on
biologically realistic neural modeling, as well as both tutorial and
research simulations that have been implemented with GENESIS.

The latest version of this GENESIS tutorial distribution will be
available at http://genesis-sim.org/GENESIS/UGTD.html.

The GENESIS tutorial at the CNS meeting is introductory and aimed at
people who are new to or have only elementary knowledge about the
GENESIS-2 simulator, as well as those who have used GENESIS in the
past and would like to learn of new developments in cortical network
modeling with GENESIS.

* introduction and overview

** Why are we doing this?

** resources

** installation and configuration overview

* single neuron modeling and visualization

* debugging model and script

* fast simulations with hsolve

* network modeling

* spike-timing dependent plasticity

During the last hour of the tutorial, I will show in detail how to
technically debug models, scripts and source code, at various levels
of implementation.

The latest news can always be found at http://genesis-sim.org/GENESIS/


-- 
Hugo



--

                  Hugo Cornelis Ph.D.

            GENESIS-3 -- lead architect
              http://www.genesis-sim.org/

            Neurospaces Project Architect
              http://www.neurospaces.org/

[Genesis-sim-users] GENESIS 2.4 beta release and modeling tutorials

[Dave B. <db...@Co...>]

There is now a stable public beta release of GENESIS 2.4 available
on the web site for the GENESIS neural simulator. Although there have
been development releases of GENESIS 3, this is the first new release
of GENESIS 2 since the March 2006 release of GENESIS 2.3.

This new release was made necessary by the many improvements and user
contributions over the past few years, and the incorporation of new
objects for efficiently modeling synaptic plasticity in large networks
of realistic multicompartmental cells.  The final release will be in
November 2014.

There is also a new July 2014 version of the "Ultimate GENESIS
Tutorial Distribution", a complete self-paced GENESIS modeling course,
combined with GENESIS binary and source distributions and installation
instructions. It provides an easy way to get everything by downloading
a single package. This was prepared as course materials for the
tutorial "Constructing biologically realistic neuron and network
models with GENESIS" to be given on July 26th at CNS 2014.

These may be downloaded from the GENESIS 2 home page at
http://genesis-sim.org/GENESIS/

Those who wish to follow or contribute to the development of
the final release can get the latest versions at the github
repository: https://github.com/dbeeman/genesis-2.4beta-files

Dave Beeman

------------------------------------------------------------
Prof. David Beeman, GENESIS Users Group
Dept. of Electrical, Computer, and Energy Engineering
University of Colorado, Boulder, CO 80309
email: ge...@ge... - db...@co...
GENESIS 2 WWW site: http://genesis-sim.org/GENESIS/
------------------------------------------------------------

Re: [Genesis-sim-users] Testers needed for GENESIS 2.4 beta release

[Dave B. <db...@Co...>]

Thanks for the report. I will get it into the public genesis-2.4beta-src
release that I am putting out tonight.

The fix for the terminal window will have to wait for the final
November release.

The latest version at https://github.com/dbeeman/genesis-2.4beta-files
has some fixes for Mac OS X, but I am still looking for Mac testers.

Dave Beeman


On Mon, 21 Jul 2014, Gilles Detillieux wrote:

> I've tested it briefly on Scientific Linux 5.10, an RHEL 5 clone
> system.  There's a slight bug in the Linux section of src/Makefile.dist:
> the XINCLUDE= line is missing the -I option argument, and instead just
> lists the include directory name.  This results in a bunch of spurious
> linker warnings like the following:
>
> cc: /usr/include/X11: linker input file unused because linking not done
>
> The fix is simple enough:
>
> --- Makefile.dist.orig  2014-07-20 18:05:25.000000000 -0500
> +++ Makefile.dist       2014-07-21 16:11:00.000000000 -0500
> @@ -836,7 +836,7 @@
>  # MACHINE=Linux
>  # OS=BSD
>
> -# XINCLUDE=/usr/include/X11
> +# XINCLUDE=-I/usr/include/X11
>
>  ## Choose ONE XLIB line to uncomment:
>  ## For 32-bit architectures
>
> (Note that this is a capital "i" option, not a lower-case "L".  It's
> hard to tell with some fonts.)
>
> Another problem is that after running genesis, the ioctl/stty settings
> for the terminal window aren't properly restored.  It seems the "onlcr"
> mode is turned off and not turned back on after quitting.  I haven't
> looked at the code enough to find a fix for that problem.
>
> I ran the Squid script as a test, and it seems to behave as it did under
> 2.3.  I haven't tested any further yet.
>
> Gilles
>
> On 07/15/2014 02:56 PM, Dave Beeman wrote:
>> I am preparing a beta release of GENESIS 2.4, in preparation
>> for the tutorial that Hugo Corenelis will give at CNS 2014.
>> There will be further additions in the final November release,
>> but the present version is looking pretty good.
>>
>> However, compilation has only been tested on recent Fedora and Ubuntu
>> Linux distribution.  It would be a big help to me if I could get a
>> few volunteers to try an installation on other Linux versions,
>> and MacOS in particular.
>>
>> If anyone is using GENESIS under Cygwin, it would be wonderful if
>> someone would build a Cygwin binary.
>>
>> The files and installation instructions can be viewed and downloaded
>> at https://github.com/dbeeman/genesis-2.4beta-files.
>>
>> I'm not asking for any extensive testing, but only for reports of any
>> issues that may come up during installation. However, there are some
>> worthwhile new features that you may want to look at.  By helping us
>> testing, you will not only help make a better final release, but have
>> a chance to preview these additions:
>>
>> * The new 'stdp_rules' object for efficiently implementing spike
>>      timing dependent plasticity in large networks of hsolved
>>      multicompartmental cells.
>>
>> * A new version of the chemesis library for modeling second messengers
>>     and calcium dynamics is now installed by default.
>>
>> * New tutorial Scripts and Doc entries were added for:
>>       o chemesis
>>       o the gpython-tools Python utility collection
>>       o An updated Purkinje tutorial
>>       o stdp_rules, including 'NewPlasticityObjects' documentation for
>>         implementing similar objects.
>>
>>       o An improved hsolved implementation of the dual exponential
>>         conductance version of the Vogels-Abbott network model. It serves
>>         as a tutorial on how to achieve a speed improvement of 10 to 20
>>         times when using hsolve with network models.
>>
>> * Bug fixes and Makefile improvements to ease installation.
>>
>> Thanks for your help,
>> Dave Beeman
>>
>> ----------------------------------------------------------------------------
>> Prof. David Beeman, GENESIS Users Group
>> Dept. of Electrical, Computer, and Energy Engineering
>> University of Colorado, Boulder, CO 80309
>> email: ge...@ge... - db...@co...
>> GENESIS 2 WWW site: http://www.genesis-sim.org/GENESIS/
>> ----------------------------------------------------------------------------
>>
>>
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>
> -- 
> Gilles R. Detillieux              E-mail: <gr...@sc...>
> Spinal Cord Research Centre       WWW:    http://www.scrc.umanitoba.ca/
> Dept. of Physiology and Pathophysiology, Faculty of Health Sciences,
> Univ. of Manitoba  Winnipeg, MB  R3E 0J9  (Canada)
>
>
> ------------------------------------------------------------------------------
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