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

[Genesis-sim-users] NeuroMorpho.Org v7.1 released March 30th, 2017

[NeuroMorpho A. <nm...@gm...>]

Dear colleagues,

We’re pleased to announce the March 30, 2017 release of Version 7.1 of NeuroMorpho.Org<http://neuromorpho.org/>, including 11,948 additional reconstructions from 72 new datasets. The repository now provides access to 62,304 cells (a 65% yearly increase since the March 2016 release) from 40 species and 278 labs. Notably, glia arbors are now included in the database in addition to neuron. Please visit the What’s new page<http://neuromorpho.org/WIN.jsp> for details on the added data and other updates. The literature coverage database was also updated to include publications through March 2017. We are continuously grateful to all the data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely,

The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO>



----------------

Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD

University Professor

Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/>

Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/>

Director, Center for Neural Informatics, Structures, & Plasticity<http://krasnow1.gmu.edu/cn3>

MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444

Ph. +1(703)993-4383/+1(703)673-8894

Author of “Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>” (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>)

Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021>

Re: [Genesis-sim-users] help with compiling Genesis 2.4 on RHEL-6 system

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

Hi Susan,

That is certainly a strange error. I see that you are using gcc 5.3 on a 
RHEL system.

I've recently compiled GENESIS under Fedora 20 with gcc 4.8, and Fedora 
25 with gcc 6.3.

The older compiler worked fine, but for the newer compiler, I found that 
very recent glibc versions removed a deprecated definition in 
<sys/wait.h>, and I had to make a change in src/sys/system.c.

If anyone needs this fix, I can put this change on the github repo**at 
https://github.com/genesis-sim/genesis-2.4. 
<https://github.com/genesis-sim/genesis-2.4> This is where I put the 
latest fixes and changes.

This wasn't your problem, but it could be something to do with a change 
in a file included by sys/code_lib.c, which dates from 2005 and earlier.

Perhaps this caused the undefined reference to 'yylex' or the multiple 
definitions of 'main', which is only defined once in code_lib.c.

Can you send me (but not the whole mailing list) your full make.out 
file, and the Makefile that was generated by ./configure? I will do what 
I can to solve this.

Dave Beeman

On 03/27/2017 02:48 PM, Susan Chacko wrote:

> Hi,
>
> I'm attempting to compile Genesis 2.4 from source in response to one of
> our users, and am hitting a wall here.
>
> To summarize, I did a
> ./configure --prefix=/some/path/here
>
> The configure went fine (config output appended at the end of this
> message).
> The subsequent make failed. The first error was in the 'sys' subdirectory:
>
> $ /usr/local/GCC/5.3.0/bin/gcc -O2 -D__NO_MATH_INLINES -DBSD -DLinux
> -lfl -DBSD -o code_lib code_lib.c
> /tmp/ccLCiLkb.o: In function `main':
> code_lib.c:(.text.startup+0x0): multiple definition of `main'
> /usr/lib/../lib64/libfl.a(libmain.o):(.text+0x0): first defined here
> /usr/lib/../lib64/libfl.a(libmain.o): In function `main':
> (.text+0xb): undefined reference to `yylex'
> collect2: error: ld returned 1 exit status
>
> Any ideas what is going on? It seems to be related to the flex library.
> We have the following flex libraries installed:
>
> flex-2.5.35-9.el6.x86_64
> flex-devel-2.5.35-9.el6.x86_64
>
> Any suggestions for how to proceed? Much appreciated.
> Susan
>
> -----------configure output----------------
> checking for gcc... /usr/local/GCC/5.3.0/bin/gcc
> checking whether the C compiler works... yes
> checking for C compiler default output file name... a.out
> checking for suffix of executables...
> checking whether we are cross compiling... no
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether /usr/local/GCC/5.3.0/bin/gcc accepts -g... yes
> checking for /usr/local/GCC/5.3.0/bin/gcc option to accept ISO C89...
> none needed
> checking how to run the C preprocessor... /usr/local/GCC/5.3.0/bin/gcc -E
> checking for X... libraries , headers
> checking for gethostbyname... yes
> checking for connect... yes
> checking for remove... yes
> checking for shmat... yes
> checking for IceConnectionNumber in -lICE... yes
> checking for ranlib... ranlib
> checking for bison... bison -y
> checking for flex... flex
> checking lex output file root... lex.yy
> checking lex library... -lfl
> checking whether yytext is a pointer... yes
> checking for main in -lncurses... yes
> checking for grep that handles long lines and -e... /bin/grep
> checking for egrep... /bin/grep -E
> checking for ANSI C header files... yes
> checking for sys/types.h... yes
> checking for sys/stat.h... yes
> checking for stdlib.h... yes
> checking for string.h... yes
> checking for memory.h... yes
> checking for strings.h... yes
> checking for inttypes.h... yes
> checking for stdint.h... yes
> checking for unistd.h... yes
> checking size of long int... 8
> configure: creating ./config.status
> config.status: creating Makefile
>
>
>
>

[Genesis-sim-users] help with compiling Genesis 2.4 on RHEL-6 system

[Susan C. <su...@he...>]

Hi,

I'm attempting to compile Genesis 2.4 from source in response to one of 
our users, and am hitting a wall here.

To summarize, I did a
./configure --prefix=/some/path/here

The configure went fine (config output appended at the end of this 
message).
The subsequent make failed. The first error was in the 'sys' subdirectory:

$ /usr/local/GCC/5.3.0/bin/gcc -O2 -D__NO_MATH_INLINES -DBSD -DLinux 
-lfl -DBSD -o code_lib code_lib.c
/tmp/ccLCiLkb.o: In function `main':
code_lib.c:(.text.startup+0x0): multiple definition of `main'
/usr/lib/../lib64/libfl.a(libmain.o):(.text+0x0): first defined here
/usr/lib/../lib64/libfl.a(libmain.o): In function `main':
(.text+0xb): undefined reference to `yylex'
collect2: error: ld returned 1 exit status

Any ideas what is going on? It seems to be related to the flex library. 
We have the following flex libraries installed:

flex-2.5.35-9.el6.x86_64
flex-devel-2.5.35-9.el6.x86_64

Any suggestions for how to proceed? Much appreciated.
Susan

-----------configure output----------------
checking for gcc... /usr/local/GCC/5.3.0/bin/gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /usr/local/GCC/5.3.0/bin/gcc accepts -g... yes
checking for /usr/local/GCC/5.3.0/bin/gcc option to accept ISO C89... 
none needed
checking how to run the C preprocessor... /usr/local/GCC/5.3.0/bin/gcc -E
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking for ranlib... ranlib
checking for bison... bison -y
checking for flex... flex
checking lex output file root... lex.yy
checking lex library... -lfl
checking whether yytext is a pointer... yes
checking for main in -lncurses... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of long int... 8
configure: creating ./config.status
config.status: creating Makefile




-- 
Susan Chacko, Ph.D.
HPC @ NIH Staff

[Genesis-sim-users] CNS 2017 annual meeting announcement

[Tam, N. <Nic...@un...>]

Organization for Computational Neurosciences (OCNS)
26th Annual Meeting
Antwerpen, Belgium
July 15-20, 2017

The main meeting (July 16-18) will be preceded by a day of tutorials (July 15) and followed by two days of workshops (July 19-20).

Invited Keynote Speakers:
Jack Cowan, University of Chicago, USA
Gustavo Deco, Universitat Pompeu Fabra, Spain
Adrienne Fairhall, University of Washington, USA
Wulfram Gerstner, EPFL, Switzerland

Registration will open on January 14, 2015.
Abstract submission will open on January 15, 2015 and close on February 22.
Workshop proposals are now being accepted.

Note that one of the authors has to register as sponsoring author for the main meeting before abstract submission is possible. In case the abstract is not accepted for presentation, the registration fee will be refunded.

For up-to-date conference information, please visit
http://www.cnsorg.org/cns-2017

----------------------------------------
OCNS is the international member-based society for computational neuroscientists.
Become a member to be eligible for travel awards and more. Visit our website for more information:
http://www.cnsorg.org<http://www.cnsorg.org/>

Re: [Genesis-sim-users] running Genesis to Windows 64-bit

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

I see that you are using the old GENESIS 2.3 distribution. Please go to 
the GENESIS web site at
http://genesis-sim.org/GENESIS/ and download the November 2014 GENESIS 
2.4 release.

The latest updates to GENESIS 2.4 (with new improvements for Cygwin) are 
at the github repository:

https://github.com/genesis-sim/genesis-2.4

This new version has many changes to allow it to work with Cygwin. There 
are special directions
for Cygwin in the installation instructions. You can also run the Linux 
version of GENESIS under
Windows using virtual machine software for linux.

A few people on the mailing list have  recently used GENESIS under 
Cygwin, so report any
problems to the list for help.

Regards,
Dave Beeman

On 12/07/2016 03:32 PM, 李艳秋 wrote:
> Hi,
> I am Yanqiu and have trouble to install Genesis to Windows.
> I have install Cygwin & Genesis and brought up xterm terminal window, 
> however, when I tested the Genesis, it failed. I mean when I typed 
> genesis Squid, nothing happened just like the picture.
> I don't know what's the problem?
> Thank you.
>
>
>
>
> ------------------------------------------------------------------------------
> Developer Access Program for Intel Xeon Phi Processors
> Access to Intel Xeon Phi processor-based developer platforms.
> With one year of Intel Parallel Studio XE.
> Training and support from Colfax.
> Order your platform today.http://sdm.link/xeonphi
>
>
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

[Genesis-sim-users] running Genesis to Windows 64-bit

[李艳秋 <liy...@16...>]

Hi,
I am Yanqiu and have trouble to install Genesis to Windows.
I have install Cygwin & Genesis and brought up xterm terminal window, however, when I tested the Genesis, it failed. I mean when I typed genesis Squid, nothing happened just like the picture.
I don't know what's the problem?
Thank you.

[Genesis-sim-users] NeuroMorpho.Org v7.0 [10th anniversary edition] released September 1st, 2016

[NeuroMorpho A. <nm...@gm...>]

Dear colleagues,

We're excited to announce that almost exactly 10 years after the original launch, NeuroMorpho.Org passed the milestone of 50,000 reconstructions in the September 1, 2016 release of Version 7.0. This major update includes 12,693 additional reconstructions from 35 new datasets. The new data added in these last 6 months equal the total amount accumulated in the first seven years. This release also introduce several new functionalities, including (1) bibliography documenting data re-use from nearly 500 citations; (2) ontology-smart searches by species, brain regions, neuron types, and experimental conditions; (3) DOI minting capability for each article-associated dataset; and (4) API enabling object-oriented access to data and metadata. The literature coverage database was also updated to include publications through August 2016. Please visit the What's new page<http://neuromorpho.org/WIN.jsp> for details on the added data and other updates. We appreciate any and all feedback and comments. We are continuously grateful to all the data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. Our apologies if you receive multiple versions of this message through cross-listing. Sincerely,

The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO>



----------------

Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD

University Professor

Director, Center for Neural Informatics, Structure, & Plasticity<http://krasnow1.gmu.edu/cn3>

Neuroscience Program<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/>

Bioengineering Department<http://bioengineering.gmu.edu/>, Volgenau School of Engineering<http://volgenau.gmu.edu/>

MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444

Ph. +1(703)993-4383/+1(703)673-8894

Author of "Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>" (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>)

Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021>

[Genesis-sim-users] NeuroMorpho.Org v6.3 released March 4th, 2016

[NeuroMorpho A. <nm...@gm...>]

Dear colleagues,

We're pleased to announce the March 4, 2016 release of Version 6.3 of NeuroMorpho.Org<http://neuromorpho.org/>, including 3638 additional reconstructions from 54 new datasets. The number of contributing laboratories now exceeds 200! The repository provides access to 37,712 neurons from 35 species and over 40 brain regions. More than 5 million reconstructions were downloaded to date, summing up to approximately 30 km of neurite cable.



Please visit the What's new page<http://neuromorpho.org/WIN.jsp> for details on the added data and other updates. The literature coverage database was also updated to include publications through February 2016. We are continuously grateful to all the data contributors<http://neuromorpho.org/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through x-listing.



Sincerely,

The NeuroMorpho.Org team<http://neuromorpho.org/acknowl.jsp#NMO>



Posted by:

----------------

Giorgio Ascoli<http://krasnow1.gmu.edu/cn3/ascoli>, PhD

University Professor

Director, Center for Neural Informatics, Structure, & Plasticity<http://krasnow1.gmu.edu/cn3>

Molecular Neuroscience Dept.<http://neuroscience.gmu.edu/>, Krasnow Institute for Advanced Study<http://krasnow1.gmu.edu/>

MS2A1 - George Mason University<http://gmu.edu/>, Fairfax, VA 22030-4444

Ph. +1(703)993-4383/+1(703)673-8894

Author of "Trees of the Brain, Roots of the Mind<http://www.amazon.com/Trees-Brain-Roots-Giorgio-Ascoli/dp/0262028980/>" (MIT Press, 2015<http://mitpress.mit.edu/books/trees-brain-roots-mind>)

Founding Editor-in-Chief, Neuroinformatics<http://link.springer.com/journal/12021>

Re: [Genesis-sim-users] Frontiers Research New Issue

[Frontiers J. <hf...@hf...>]

<html>
<head>
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<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Swis721 BlkOul BT'; font-size:28.0pt; color:red; ">Call for Papers</span></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><a href="http://www.hfsp-journal.org/index.html"><span style="font-family:'Bernard MT Condensed','serif'; font-size:52.0pt; color:red; ">HFSP</span></a><a href="http://www.hfsp-journal.org/index.html"><span style="font-family:'Bernard MT Condensed','serif'; font-size:42.0pt; "> JOURNAL</span></a></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Arial','sans-serif'; font-size:18.0pt; "> </span><span style="font-family:'Times New Roman','serif'; font-size:18.0pt; ">ISSN:  1955-2068</span><span style="font-family:'Times New Roman','serif'; font-size:48.0pt; "> </span></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><strong><span style="font-family:'Times New Roman','serif'; font-size:22.0pt; color:#A6A6A6; ">Human Frontier Science Program</span></strong></p>
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<p class="MsoNormal" style="margin-bottom:.0001pt;text-align:left;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Times New Roman','serif'; font-size:12.0pt; ">&nbsp;</span></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Times New Roman','serif'; font-size:12.0pt; ">Launched  in October 2006, the HFSP Journal aims to foster communication between  scientists publishing high quality, innovative research at the frontiers of the  life sciences. Peer review is designed to allow for the unique requirements of  such papers and is overseen by an Editorial Board with members from different  disciplines.</span></p>
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<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Bernard MT Condensed','serif'; font-size:18.0pt; ">Paper Submission Page</span></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><a href="http://www.hfsp-journal.org/submit.html"><span style="font-family:'Times New Roman','serif'; font-size:16.0pt; color:red; ">http://www.hfsp-journal.org/submit.html</span></a><span style="font-family:'Bernard MT Condensed','serif'; font-size:18.0pt; "> </span></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Times New Roman','serif'; font-size:18.0pt; ">&nbsp;</span></p>
<p class="MsoNormal" align="center" style="margin-bottom:.0001pt;text-align:center;line-height:normal;direction:ltr;unicode-bidi:embed;"><span style="font-family:'Bernard MT Condensed','serif'; font-size:18.0pt; ">JCR 2013</span></p>
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<p class="MsoNormal" style="margin-bottom:.0001pt;text-align:center;direction:ltr;unicode-bidi:embed;"><span style="line-height:115%; font-family:'Times New Roman','serif'; font-size:16.0pt; ">------------------------------------------------------------------------------------</span></p>
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Re: [Genesis-sim-users] Issues compiling Genesis-2.4

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

The first error in make.out indicates a problem with LEXLIB, so that is 
most likely the problem.
Also, it looks like you didn't uncomment the CPP line.

Fix these, do a "make clean" and try again. Also did you try using 
"./configure" to generate a
Makefile, instead of hand editing it?

Dave Beeman

On 11/13/2015 09:38 AM, Szabolcs Káli wrote:
> Hi,
>
> I have taken a quick look at the files that you sent, and compared 
> them to my own installation (64-bit Linux, but Mint not Centos). Apart 
> from differences in X11 settings (which are probably due to the 
> different distribution), I saw one conspicuous difference: you did not 
> uncomment the following line in the Makefile:
>
> LIBS= $(LEXLIB) -lm
>
> I do not know enough about the Genesis source code to judge whether 
> this may underlie the error, but it may be worth a try...
>
> Best regards,
>
> Szabolcs Káli
>
> Laboratory of Cerebral Cortex Research
> Institute of Experimental Medicine
> Hungarian Academy of Sciences
>
> H-1083 Budapest Szigony utca 43.
> Phone: +36-1-2109413
> Fax: +36-1-2109412
> E-mail: kal...@ko...
> www.koki.mta.hu
>
> ----- On Nov 9, 2015, at 11:05 PM, Mwajim Al <rah...@gm...> 
> wrote:
>
>
>     Hello all -
>
>     I am new to genesis and linux. I've been trying to install
>     genesis-2.4 on my 64-bit machine which is running Centos linux.
>     The configure process went fine, However, there are numerous error
>     messages associated with the make command. I have attached the
>     make.out file for illustration. I also uncommented the relevant
>     lines in the makefile.dist file. I think this might have to do
>     with the X11 files. However, these files are installed, and I am
>     unsure as to what components I need to further download relevant
>     for the complete compilation to work. Has anyone who has installed
>     genesis-2.4 on a 64-bit computer in a centos linux environment
>     gone please offer some advice?
>
>     Thanks,
>     genesis newbie.
>
>
>     ------------------------------------------------------------------------------
>
>     _______________________________________________
>     Genesis-sim-users mailing list
>     Gen...@li...
>     https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

Re: [Genesis-sim-users] Issues compiling Genesis-2.4

[Szabolcs K. <ka...@ko...>]

Hi, 

I have taken a quick look at the files that you sent, and compared them to my own installation (64-bit Linux, but Mint not Centos). Apart from differences in X11 settings (which are probably due to the different distribution), I saw one conspicuous difference: you did not uncomment the following line in the Makefile: 

LIBS= $(LEXLIB) -lm 

I do not know enough about the Genesis source code to judge whether this may underlie the error, but it may be worth a try... 

Best regards, 

Szabolcs Káli 

Laboratory of Cerebral Cortex Research 
Institute of Experimental Medicine 
Hungarian Academy of Sciences 

H-1083 Budapest Szigony utca 43. 
Phone: +36-1-2109413 
Fax: +36-1-2109412 
E-mail: kal...@ko... 
www.koki.mta.hu 

----- On Nov 9, 2015, at 11:05 PM, Mwajim Al <rah...@gm...> wrote: 

> Hello all -

> I am new to genesis and linux. I've been trying to install genesis-2.4 on my
> 64-bit machine which is running Centos linux. The configure process went fine,
> However, there are numerous error messages associated with the make command. I
> have attached the make.out file for illustration. I also uncommented the
> relevant lines in the makefile.dist file. I think this might have to do with
> the X11 files. However, these files are installed, and I am unsure as to what
> components I need to further download relevant for the complete compilation to
> work. Has anyone who has installed genesis-2.4 on a 64-bit computer in a centos
> linux environment gone please offer some advice?

> Thanks,
> genesis newbie.

> ------------------------------------------------------------------------------

> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

Re: [Genesis-sim-users] Issues compiling Genesis-2.4

[Cengiz G. <cg...@em...>]

Hi,

It seems several things went wrong in there. I'd search for the word
"error" in make.out and try to fix them one by one. First thing is your
YACC installation. Maybe use different options in the Makefile? I'm not
familiar with the configure script if there is one shipped with 2.4.

-Cengiz

On Mon, Nov 9, 2015 at 5:05 PM, Mwajim Al <rah...@gm...> wrote:

>
> Hello all -
>
> I am new to genesis and linux. I've been trying to install genesis-2.4 on
> my 64-bit machine which is running Centos linux. The configure process went
> fine, However, there are numerous error messages associated with the make
> command. I have attached the make.out file for illustration. I also
> uncommented the relevant lines in the makefile.dist file. I think this
> might have to do with the X11 files. However, these files are installed,
> and I am unsure as to what components I need to further download relevant
> for the complete compilation to work. Has anyone who has installed
> genesis-2.4 on a 64-bit computer in a centos linux environment gone please
> offer some advice?
>
> Thanks,
> genesis newbie.
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
>
>

[Genesis-sim-users] Issues compiling Genesis-2.4

[Mwajim Al <rah...@gm...>]

Hello all -

I am new to genesis and linux. I've been trying to install genesis-2.4 on
my 64-bit machine which is running Centos linux. The configure process went
fine, However, there are numerous error messages associated with the make
command. I have attached the make.out file for illustration. I also
uncommented the relevant lines in the makefile.dist file. I think this
might have to do with the X11 files. However, these files are installed,
and I am unsure as to what components I need to further download relevant
for the complete compilation to work. Has anyone who has installed
genesis-2.4 on a 64-bit computer in a centos linux environment gone please
offer some advice?

Thanks,
genesis newbie.

[Genesis-sim-users] v6.2 of NeuroMorpho.Org released 6 October, 2015

[NeuroMorpho A. <nm...@gm...>]

Dear colleagues,

We're pleased to announce the October 6, 2015 release of Version 6.2 of NeuroMorpho.Org<http://neuromorpho.org/>, including 2160 additional reconstructions from 21 new archives and intriguing species such as Bottlenose dolphin, Chimpanzee, Clouded leopard, Giraffe, Humpback whale, Locust, Manatee, Minke whale, Pouched lamprey, and Siberian tiger. As many as 58 papers were published using data downloaded from NeuroMorpho.Org in the first six month of 2015 alone.

NeuroMorpho.Org
Neuron Morphology
Read more...<http://neuromorpho.org/>





The repository now contains 34,082 neurons from 165 labs<http://neuromorpho.org/neuroMorpho/about.jsp>. Please visit the What's new page<http://neuromorpho.org/neuroMorpho/WIN.jsp> for details on the added data and other updates. The literature coverage database was also updated to include publications through September 2015. We are continuously grateful to all the data contributors<http://neuromorpho.org/neuroMorpho/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through x-listing. Sincerely,

The NeuroMorpho.Org team<http://neuromorpho.org/neuroMorpho/acknowl.jsp#NMO>

[Genesis-sim-users] v6.2 of NeuroMorpho.Org released 6 October, 2015

[Giorgio A. <as...@gm...>]

Dear colleagues,
We’re pleased to announce the October 6, 2015 release of Version 6.2 of NeuroMorpho.Org<http://neuromorpho.org/>, including 2160 additional reconstructions from 21 new archives and intriguing species such as Bottlenose dolphin, Chimpanzee, Clouded leopard, Giraffe, Humpback whale, Locust, Manatee, Minke whale, Pouched lamprey, and Siberian tiger. As many as 58 papers were published using data downloaded from NeuroMorpho.Org in the first six month of 2015 alone.

The repository now contains 34,082 neurons from 165 labs<http://neuromorpho.org/neuroMorpho/about.jsp>. Please visit the What’s new page<http://neuromorpho.org/neuroMorpho/WIN.jsp> for details on the added data and other updates. The literature coverage database was also updated to include publications through September 2015. We are continuously grateful to all the data contributors<http://neuromorpho.org/neuroMorpho/acknowl.jsp#DC> who freely share their hard-won tracings with the community. We appreciate any and all feedback and comments. Our apologies if you receive multiple versions of this message through x-listing. Sincerely,
The NeuroMorpho.Org team<http://neuromorpho.org/neuroMorpho/acknowl.jsp#NMO>

[Genesis-sim-users] Frontiers Research New Issue

[Frontiers J. <hf...@hf...>]

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[Genesis-sim-users] CIENCIA ETV JOURNAL-New Release 2015

[Ciencia E. ISI-J. I. J. <ci...@ci...>]

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Re: [Genesis-sim-users] Weird arithmetic error in Genesis

[james b. <bo...@ut...>]

thanks everyone

hope everyone who went enjoyed Prague  would have loved to be there - but way too busy here.

Jim


> On Jul 22, 2015, at 3:56 PM, Dave Beeman <db...@Co...> wrote:
> 
> Thanks to Hugo and Dieter for the explanations. Thet other thing to
> keep in mind is that at the scripting level, all floating point variables
> are 32 bit floats, not doubles.  This can be a source of roundoff errors
> and is the reason that some XODUS dialogs will report numbers like
> "0.0000000237" or similar. At the C code level, most important
> variables that are used in numerical solution (particularly those
> involving time) have been converted to doubles.
> On Wed, 22 Jul 2015, Cengiz Günay wrote:
> 
>> Thanks, Hugo! That's quite clear. It's good to hear that you're still on the
>> list. Thankfully my code did not actually contain this overflow error, it
>> was something I was trying to verify the calculations. Is it safe to say
>> that all floating point variables in Genesis are double precision? Do you
>> know if this is also true for "extended fields" in generic objects created
>> using addfield?
>> -Cengiz
>> On Wed, Jul 22, 2015 at 6:14 PM, Hugo Cornelis <hug...@gm...>
>> wrote:
>> Hi Cengiz,
>> I quickly checked the behaviour of both commands with GDB, and here is
>> what happens:
>> The first result 0.5500000385 is correct, GDB reports
>> 0.55000003851059043 as the double precisions result.
>> For the behaviour of the second command:
>> echo { 2012303744.1 / 3658733824 }
>> What happens goes as follows:
>> The second argument in the input, the integer 3658733824, is larger
>> than the highest signed 32bit integer (which is 2147483647).
>> GENESIS uses the sscanf() function to read the integer from the
>> command line.  This function does not generate an error when an
>> overflow occurs and simply returns 2147483647, so GENESIS continues
>> its operation with this result assuming everything is fine.
>> So internally the command is treated as this command:
>> echo { 2012303744.1 / 2147483647 }
>> for which GDB returns:
>> 0.93705195236813832
>> Obviously, this behaviour is totally undesired and GENESIS should emit
>> an error message for the integer overflow, but does not.
>> The work around is as you say, to suffix a .0 after the integer to
>> force GENESIS to use floating point calculations.
>> Hugo
>> On Wed, Jul 22, 2015 at 10:48 PM, Cengiz Günay <cg...@em...>
>> wrote:
>>      Hi,
>> I have been pulling my hair trying to debug arithmetic
>> inconsistencies in Genesis that are caused by large truncation
>> errors from simplest calculations and inconsistent PI
>> definitions, which I realize have been known and we need to be
>> cautious about. However, I wanted to report something really
>> disturbing:
>> > echo { 2012303744.1 / 3658733824.0 }
>> 0.5500000385
>> > echo { 2012303744.1 / 3658733824 }
>> 0.9370519524
>> Does anyone have an explanation for this behavior? This can
>> cause seriously wrong calculations and hidden bugs.
>> I think the take home message is to always put a .0 behind
>> integer numbers that are going to be in floating point
>> calculations. :)
>> Best,
>> -Cengiz
>> --
>> Cengiz Gunay
>> Postdoctoral Fellow, Dept. of Biology
>> Visiting Faculty, Dept. of Math & CS
>> Emory University
>> http://www.biology.emory.edu/research/Prinz/Cengiz/
>> ---------------------------------------------------------------------------
>> ---
>> _______________________________________________
>> Genesis-sim-users mailing list
>> Gen...@li...
>> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
>> --
>> Hugo
>> --
>>                   Hugo Cornelis, Ph.D.
>>                     Agora Classica -- CTO
>>               http://www.agoraclassica.com/
>>             GENESIS-3 -- lead architect
>>               http://www.genesis-sim.org/
> ------------------------------------------------------------------------------
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users

Re: [Genesis-sim-users] Weird arithmetic error in Genesis

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

I think you overflowed your integer welcome.   If you shorten your numbers by a few digits you will do much better.  Of course forcing to float is even better.  Not sure where the digits that an int can’t hold actually go.  It could be bad, i.e. random memory overwrite.  -Dieter

From: Cengiz Günay [mailto:cg...@em...]
Sent: Wednesday, July 22, 2015 4:49 PM
To: gen...@li...
Subject: [Genesis-sim-users] Weird arithmetic error in Genesis

Hi,
I have been pulling my hair trying to debug arithmetic inconsistencies in Genesis that are caused by large truncation errors from simplest calculations and inconsistent PI definitions, which I realize have been known and we need to be cautious about. However, I wanted to report something really disturbing:

> echo { 2012303744.1 / 3658733824.0 }
0.5500000385
> echo { 2012303744.1 / 3658733824 }
0.9370519524
Does anyone have an explanation for this behavior? This can cause seriously wrong calculations and hidden bugs.

I think the take home message is to always put a .0 behind integer numbers that are going to be in floating point calculations. :)
Best,
-Cengiz

--
Cengiz Gunay
Postdoctoral Fellow, Dept. of Biology
Visiting Faculty, Dept. of Math & CS
Emory University
http://www.biology.emory.edu/research/Prinz/Cengiz/

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Re: [Genesis-sim-users] Weird arithmetic error in Genesis

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

Thanks to Hugo and Dieter for the explanations. Thet other thing to
keep in mind is that at the scripting level, all floating point variables
are 32 bit floats, not doubles.  This can be a source of roundoff errors
and is the reason that some XODUS dialogs will report numbers like
"0.0000000237" or similar. At the C code level, most important
variables that are used in numerical solution (particularly those
involving time) have been converted to doubles.
On Wed, 22 Jul 2015, Cengiz Günay wrote:

> Thanks, Hugo! That's quite clear. It's good to hear that you're still on the
> list. Thankfully my code did not actually contain this overflow error, it
> was something I was trying to verify the calculations. Is it safe to say
> that all floating point variables in Genesis are double precision? Do you
> know if this is also true for "extended fields" in generic objects created
> using addfield?
> 
> -Cengiz
> 
> On Wed, Jul 22, 2015 at 6:14 PM, Hugo Cornelis <hug...@gm...>
> wrote:
> 
> 
> Hi Cengiz,
> 
> 
> I quickly checked the behaviour of both commands with GDB, and here is
> what happens:
> 
> 
> The first result 0.5500000385 is correct, GDB reports
> 0.55000003851059043 as the double precisions result.
> 
> 
> For the behaviour of the second command:
> 
> echo { 2012303744.1 / 3658733824 }
> 
> What happens goes as follows:
> 
> The second argument in the input, the integer 3658733824, is larger
> than the highest signed 32bit integer (which is 2147483647).
> 
> GENESIS uses the sscanf() function to read the integer from the
> command line.  This function does not generate an error when an
> overflow occurs and simply returns 2147483647, so GENESIS continues
> its operation with this result assuming everything is fine.
> 
> So internally the command is treated as this command:
> 
> echo { 2012303744.1 / 2147483647 }
> 
> for which GDB returns:
> 
> 0.93705195236813832
> 
> Obviously, this behaviour is totally undesired and GENESIS should emit
> an error message for the integer overflow, but does not.
> 
> The work around is as you say, to suffix a .0 after the integer to
> force GENESIS to use floating point calculations.
> 
> 
> Hugo
> 
> 
> 
> On Wed, Jul 22, 2015 at 10:48 PM, Cengiz Günay <cg...@em...>
> wrote:
>       Hi,
> 
> I have been pulling my hair trying to debug arithmetic
> inconsistencies in Genesis that are caused by large truncation
> errors from simplest calculations and inconsistent PI
> definitions, which I realize have been known and we need to be
> cautious about. However, I wanted to report something really
> disturbing:
> 
> > echo { 2012303744.1 / 3658733824.0 }
> 0.5500000385
> > echo { 2012303744.1 / 3658733824 }
> 0.9370519524
> 
> Does anyone have an explanation for this behavior? This can
> cause seriously wrong calculations and hidden bugs.
> 
> I think the take home message is to always put a .0 behind
> integer numbers that are going to be in floating point
> calculations. :)
> 
> Best,
> -Cengiz
> 
> --
> Cengiz Gunay
> Postdoctoral Fellow, Dept. of Biology
> Visiting Faculty, Dept. of Math & CS
> Emory University
> http://www.biology.emory.edu/research/Prinz/Cengiz/
> 
> 
> ---------------------------------------------------------------------------
> ---
> 
> _______________________________________________
> Genesis-sim-users mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genesis-sim-users
> 
> 
> 
> 
> --
> Hugo
> 
> 
> 
> --
> 
>                   Hugo Cornelis, Ph.D.
> 
>                     Agora Classica -- CTO
>               http://www.agoraclassica.com/
> 
>             GENESIS-3 -- lead architect
>               http://www.genesis-sim.org/
> 
> 
> 
>

Re: [Genesis-sim-users] Weird arithmetic error in Genesis

[Cengiz G. <cg...@em...>]

Thanks, Hugo! That's quite clear. It's good to hear that you're still on
the list. Thankfully my code did not actually contain this overflow error,
it was something I was trying to verify the calculations. Is it safe to say
that all floating point variables in Genesis are double precision? Do you
know if this is also true for "extended fields" in generic objects created
using addfield?

-Cengiz

On Wed, Jul 22, 2015 at 6:14 PM, Hugo Cornelis <hug...@gm...>
wrote:

>
>
> Hi Cengiz,
>
>
> I quickly checked the behaviour of both commands with GDB, and here is
> what happens:
>
>
> The first result 0.5500000385 is correct, GDB reports 0.55000003851059043
> as the double precisions result.
>
>
> For the behaviour of the second command:
>
> echo { 2012303744.1 / 3658733824 <%203658733824> }
>
> What happens goes as follows:
>
> The second argument in the input, the integer 3658733824, is larger than
> the highest signed 32bit integer (which is 2147483647).
>
> GENESIS uses the sscanf() function to read the integer from the command
> line.  This function does not generate an error when an overflow occurs and
> simply returns 2147483647, so GENESIS continues its operation with this
> result assuming everything is fine.
>
> So internally the command is treated as this command:
>
> echo { 2012303744.1 / 2147483647 <%202147483647> }
>
> for which GDB returns:
>
> 0.93705195236813832
>
> Obviously, this behaviour is totally undesired and GENESIS should emit an
> error message for the integer overflow, but does not.
>
> The work around is as you say, to suffix a .0 after the integer to force
> GENESIS to use floating point calculations.
>
>
> Hugo
>
>
>
> On Wed, Jul 22, 2015 at 10:48 PM, Cengiz Günay <cg...@em...> wrote:
>
>> Hi,
>>
>> I have been pulling my hair trying to debug arithmetic inconsistencies in
>> Genesis that are caused by large truncation errors from simplest
>> calculations and inconsistent PI definitions, which I realize have been
>> known and we need to be cautious about. However, I wanted to report
>> something really disturbing:
>>
>> > echo { 2012303744.1 / 3658733824.0 }
>> 0.5500000385
>> > echo { 2012303744.1 / 3658733824 <%203658733824> }
>> 0.9370519524
>>
>> Does anyone have an explanation for this behavior? This can cause
>> seriously wrong calculations and hidden bugs.
>>
>> I think the take home message is to always put a .0 behind integer
>> numbers that are going to be in floating point calculations. :)
>>
>> Best,
>> -Cengiz
>>
>> --
>> Cengiz Gunay
>> Postdoctoral Fellow, Dept. of Biology
>> Visiting Faculty, Dept. of Math & CS
>> Emory University
>> http://www.biology.emory.edu/research/Prinz/Cengiz/
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>> _______________________________________________
>> Genesis-sim-users mailing list
>> 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/
>
>

Re: [Genesis-sim-users] Weird arithmetic error in Genesis

[Cengiz G. <cg...@em...>]

Thanks, Dieter. I realized it must be an integer overflow after I sent out
the message.

Also the discrepancy I was working on to debug was totally my fault! :) It
turns out I missed to update the values in some compartments.

-Cengiz

On Wed, Jul 22, 2015 at 5:50 PM, Jaeger, Dieter <dj...@em...> wrote:

>  I think you overflowed your integer welcome.   If you shorten your
> numbers by a few digits you will do much better.  Of course forcing to
> float is even better.  Not sure where the digits that an int can’t hold
> actually go.  It could be bad, i.e. random memory overwrite.  -Dieter
>
>
>
> *From:* Cengiz Günay [mailto:cg...@em...]
> *Sent:* Wednesday, July 22, 2015 4:49 PM
> *To:* gen...@li...
> *Subject:* [Genesis-sim-users] Weird arithmetic error in Genesis
>
>
>
> Hi,
>
> I have been pulling my hair trying to debug arithmetic inconsistencies in
> Genesis that are caused by large truncation errors from simplest
> calculations and inconsistent PI definitions, which I realize have been
> known and we need to be cautious about. However, I wanted to report
> something really disturbing:
>
> > echo { 2012303744.1 / 3658733824.0 }
> 0.5500000385
> > echo { 2012303744.1 / 3658733824 <%203658733824> }
> 0.9370519524
>
> Does anyone have an explanation for this behavior? This can cause
> seriously wrong calculations and hidden bugs.
>
> I think the take home message is to always put a .0 behind integer numbers
> that are going to be in floating point calculations. :)
>
> Best,
>
> -Cengiz
>
> --
> Cengiz Gunay
> Postdoctoral Fellow, Dept. of Biology
> Visiting Faculty, Dept. of Math & CS
> Emory University
> http://www.biology.emory.edu/research/Prinz/Cengiz/
>

Re: [Genesis-sim-users] Weird arithmetic error in Genesis

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

Hi Cengiz,


I quickly checked the behaviour of both commands with GDB, and here is what
happens:


The first result 0.5500000385 is correct, GDB reports 0.55000003851059043
as the double precisions result.


For the behaviour of the second command:

echo { 2012303744.1 / 3658733824 }

What happens goes as follows:

The second argument in the input, the integer 3658733824, is larger than
the highest signed 32bit integer (which is 2147483647).

GENESIS uses the sscanf() function to read the integer from the command
line.  This function does not generate an error when an overflow occurs and
simply returns 2147483647, so GENESIS continues its operation with this
result assuming everything is fine.

So internally the command is treated as this command:

echo { 2012303744.1 / 2147483647 }

for which GDB returns:

0.93705195236813832

Obviously, this behaviour is totally undesired and GENESIS should emit an
error message for the integer overflow, but does not.

The work around is as you say, to suffix a .0 after the integer to force
GENESIS to use floating point calculations.


Hugo



On Wed, Jul 22, 2015 at 10:48 PM, Cengiz Günay <cg...@em...> wrote:

> Hi,
>
> I have been pulling my hair trying to debug arithmetic inconsistencies in
> Genesis that are caused by large truncation errors from simplest
> calculations and inconsistent PI definitions, which I realize have been
> known and we need to be cautious about. However, I wanted to report
> something really disturbing:
>
> > echo { 2012303744.1 / 3658733824.0 }
> 0.5500000385
> > echo { 2012303744.1 / 3658733824 }
> 0.9370519524
>
> Does anyone have an explanation for this behavior? This can cause
> seriously wrong calculations and hidden bugs.
>
> I think the take home message is to always put a .0 behind integer numbers
> that are going to be in floating point calculations. :)
>
> Best,
> -Cengiz
>
> --
> Cengiz Gunay
> Postdoctoral Fellow, Dept. of Biology
> Visiting Faculty, Dept. of Math & CS
> Emory University
> http://www.biology.emory.edu/research/Prinz/Cengiz/
>
>
>
> ------------------------------------------------------------------------------
>
> _______________________________________________
> Genesis-sim-users mailing list
> 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/

[Genesis-sim-users] Weird arithmetic error in Genesis

[Cengiz G. <cg...@em...>]

Hi,

I have been pulling my hair trying to debug arithmetic inconsistencies in
Genesis that are caused by large truncation errors from simplest
calculations and inconsistent PI definitions, which I realize have been
known and we need to be cautious about. However, I wanted to report
something really disturbing:

> echo { 2012303744.1 / 3658733824.0 }
0.5500000385
> echo { 2012303744.1 / 3658733824 }
0.9370519524

Does anyone have an explanation for this behavior? This can cause seriously
wrong calculations and hidden bugs.

I think the take home message is to always put a .0 behind integer numbers
that are going to be in floating point calculations. :)

Best,
-Cengiz

--
Cengiz Gunay
Postdoctoral Fellow, Dept. of Biology
Visiting Faculty, Dept. of Math & CS
Emory University
http://www.biology.emory.edu/research/Prinz/Cengiz/

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

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

I think that the only way to understand the functions called in the
script code below would be to see Mike Vanier's C code for the
mod_tabchannel object and the function mod_setupalpha. These are
probably straightforward extensions of the src/olf tabchannel and
setupalpha code, and should contain the definition of INITREFCOUNT.
His code is usually pretty well documented, but I don't have these
files. It does not appear in the standard src/olf or newconn files.

Perhaps Simon O'Connor got these files from Mike.

Dave

On Thu, 28 May 2015, Christoph Metzner wrote:

> 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
> 
>  
> 
>  
> 
> logo-uni-email
> 
>  
> 
> Universität zu Lübeck
> 
> Institut für Robotik und Kognitive Systeme
> 
>  
> 
> Tel +49 451 500 5694 
> 
> Fax +49 451 500 5202
> 
> E-Mail me...@ro...
> 
> www.rob.uni-luebeck.de
> 
>  
> 
> Ratzeburger Allee 160
> 
> 23562 Lübeck
> 
> 
>