From p.gleeson at ucl.ac.uk  Tue Nov  1 18:31:09 2011
From: p.gleeson at ucl.ac.uk (P Gleeson)
Date: Tue, 1 Nov 2011 18:31:09 +0000
Subject: [neuroConstruct] Problem generating cells?
In-Reply-To: <CAHxRZu6mncGTvESFFt1Fe=u7-RFnLbT1L6LFngWZxe8Vo1E+fw@mail.gmail.com>
References: <CAHxRZu6mncGTvESFFt1Fe=u7-RFnLbT1L6LFngWZxe8Vo1E+fw@mail.gmail.com>
Message-ID: <4EB03AED.3050009@ucl.ac.uk>

Hi,

The issue with that file is that there are just cells in there, i.e. 
<neuroml><cells><cell ...><cell ...></cells></neuroml>. These are 
imported fine into neuroConstruct, but what you have then is a project 
with cells & no cell groups so the default network can't be generated.

You could add cell groups manually but ideally what you want is info on 
populations (& potentially projections) in the neuroml file, which 
reference these cells. These will be used for the cell groups & the 
instances of positions are used, so you're basically at the point of 
having generated the network at that stage, so you can visualise the 
full network.

One point about visualisations though, as your cells are small, you 
might want ot use smaller than the default region size (1um cubed) to be 
able to view them in 3d...

Padraig



On 31/10/11 18:40, Stephen Larson wrote:
> Hello,
>
>     We're importing this NeuroML into Neuroconstruct and asking it to 
> "generate cell positions" and it seems that NeuroConstruct is just 
> hanging.  There doesn't seem to be any meaningful console output. 
>  This is using version 1.5.1.  Any suggestions?  The NeuroML is valid 
> per the NeuroML validator online.
>
> Thanks,
>  Stephen
>
>
> _______________________________________________
> neuroConstruct mailing list
> neuroConstruct at ucl.ac.uk
> http://www.mailinglists.ucl.ac.uk/mailman/listinfo/neuroconstruct
> Please note that the neuroConstruct mailing list is publicly archived


-- 
-----------------------------------------------------
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.gleeson at ucl.ac.uk
-----------------------------------------------------

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From aditya_gilra at yahoo.com  Mon Nov  7 12:13:17 2011
From: aditya_gilra at yahoo.com (Aditya Gilra)
Date: Mon, 7 Nov 2011 17:43:17 +0530 (IST)
Subject: [neuroConstruct] channel units bug in exporting a single neuroml
	file
Message-ID: <1320667997.83986.YahooMailNeo@web95906.mail.in.yahoo.com>

Hi,
Do we have a web interface for bug reports or should I mail to this list?

Am using neuroconstruct 1.5.1.
I exported a single/unified neuroml file for say the granulecell in the example models,
i.e. export->neuroml-> select 'level 3' and tick 'generate single neuroml level 3 file' and then click 'generate all neuroml scripts'.
Now this creates an nml file with <channels units="SI Units"> tag amongst other tags. However, some of the channels continue to have physiological units. There is no overriding units attribute in their <channel_type> tags either. An example is the Gran_KA_98 channel. Of course this problem does not occur if multiple xml files for each channel, cell, network are created, since each channel has its own units.
Let me know when you fix this (after you've verified this is a bug.) (I suppose Padraig will be following up?)

Thanks,
Aditya Gilra.
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From p.gleeson at ucl.ac.uk  Wed Nov  9 10:48:55 2011
From: p.gleeson at ucl.ac.uk (P Gleeson)
Date: Wed, 9 Nov 2011 10:48:55 +0000
Subject: [neuroConstruct] channel units bug in exporting a single neuroml
	file
In-Reply-To: <1320667997.83986.YahooMailNeo@web95906.mail.in.yahoo.com>
References: <1320667997.83986.YahooMailNeo@web95906.mail.in.yahoo.com>
Message-ID: <4EBA5A97.2@ucl.ac.uk>

Hi Aditya,


On 07/11/11 12:13, Aditya Gilra wrote:
> Hi,
> Do we have a web interface for bug reports or should I mail to this list?
Posting to the list is probably best, no forum or bug tracker for 
neuroConstruct at the moment... I've cc'd the NeuroML list too.
> Am using neuroconstruct 1.5.1.
> I exported a single/unified neuroml file for say the granulecell in 
> the example models,
> i.e. export->neuroml-> select 'level 3' and tick 'generate single 
> neuroml level 3 file' and then click 'generate all neuroml scripts'.
> Now this creates an nml file with <channels units="SI Units"> tag 
> amongst other tags. However, some of the channels continue to have 
> physiological units. There is no overriding units attribute in their 
> <channel_type> tags either. An example is the Gran_KA_98 channel. Of 
> course this problem does not occur if multiple xml files for each 
> channel, cell, network are created, since each channel has its own units.
Yes, it was a problem in the neuroConstruct single L3 file export... I 
had code in place to check for a mixture of SI & Physiological units in 
the ChannelML files but for some reason I took it out.

The option of adding a flag to the <channel_type> element to specify the 
units might be the simplest, but I really don't want to go updating the 
v1.x specs at this stage with so much going on for v2.0. If others feel 
strongly about it though let me know... This issue won't be a problem in 
v2, since all quantities must specify their own units (dimensions will 
be restricted in the component class definition), e.g. v="-60mV"...

While it would be possible in theory to make a general conversion 
utility (in Python or XSL) to change an SI v1.8.1 file into 
Physiological & vice versa, it would need to know what each quantity 
was, there would be no way to automate the conversion. Unfortunately not 
something I can spend time on with lots to do for v2.0.

So I'll put back in the check in nC if a user tries to export to a 
single L3 file containing a mix of SI & Physiol ChannelML files (and a 
warning when you press "Validate" that there is a mixture...). For such 
projects, the options would be to export as individual NeuroML files 
with one model component in each, or manually convert the ChannelML 
files to the same units. This latter option is painful I know, but I've 
just done this conversion for all the standard nC example projects.

Updating the latest neuroConstruct code and example projects with 
nCupdate.sh/nCupdate.bat will get you the fix and should be able to 
export them all to valid single Level 3 files.

Regards,
Padraig


> Let me know when you fix this (after you've verified this is a bug.) 
> (I suppose Padraig will be following up?)
> Thanks,
> Aditya Gilra.
>
>
> _______________________________________________
> neuroConstruct mailing list
> neuroConstruct at ucl.ac.uk
> http://www.mailinglists.ucl.ac.uk/mailman/listinfo/neuroconstruct
> Please note that the neuroConstruct mailing list is publicly archived


-- 
-----------------------------------------------------
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.gleeson at ucl.ac.uk
-----------------------------------------------------

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From aditya_gilra at yahoo.com  Wed Nov  9 11:32:55 2011
From: aditya_gilra at yahoo.com (Aditya Gilra)
Date: Wed, 9 Nov 2011 17:02:55 +0530 (IST)
Subject: [neuroConstruct] channel units bug in exporting a single neuroml
	file
In-Reply-To: <4EBA5A97.2@ucl.ac.uk>
References: <1320667997.83986.YahooMailNeo@web95906.mail.in.yahoo.com>
	<4EBA5A97.2@ucl.ac.uk>
Message-ID: <1320838375.90782.YahooMailNeo@web95901.mail.in.yahoo.com>

Thanks Padraig,

I'm sticking to multiple neuroml files for now rather than the single file option.

However, there's a glitch in the multiple files option. When you export to neuroml as a single file, the temperature for the simulation is set as a meta:property (along with simulation time and dt). However, when exporting as multiple files, the Level3 file does not contain any meta:property tags for these. Could you include that?

I was quite surprised by the difference that 32 deg Celsius vs 35 deg Celsius makes to the action potential in the granulecell example model (KDR tau is temperature dependent) [Took me a while to figure out what was wrong!].


Best,
Aditya.


>________________________________
>From: P Gleeson <p.gleeson at ucl.ac.uk>
>To: Aditya Gilra <aditya_gilra at yahoo.com>
>Cc: "neuroconstruct at ucl.ac.uk" <neuroconstruct at ucl.ac.uk>; neuroml-technology at lists.sourceforge.net
>Sent: Wednesday, 9 November 2011 4:18 PM
>Subject: Re: [neuroConstruct] channel units bug in exporting a single neuroml file
>
>
>Hi Aditya,
>
>
>On 07/11/11 12:13, Aditya Gilra wrote: 
>Hi,
>>Do we have a web interface for bug reports or should I mail to this list?
>>
Posting to the list is probably best, no forum or bug tracker for neuroConstruct at the moment... I've cc'd the NeuroML list too.
>
>Am using neuroconstruct 1.5.1.
>>I exported a single/unified neuroml file for say the granulecell in the example models,
>>i.e. export->neuroml-> select 'level 3' and tick 'generate single neuroml level 3 file' and then click 'generate all neuroml scripts'.
>>Now this creates an nml file with <channels units="SI Units"> tag amongst other tags. However, some of the channels continue to have physiological units. There is no overriding units attribute in their <channel_type> tags either. An example is the Gran_KA_98 channel. Of course this problem does not occur if multiple xml files for each channel, cell, network are created, since each channel has its own units.
Yes, it was a problem in the neuroConstruct single L3 file export... I had code in place to check for a mixture of SI & Physiological units in the ChannelML files but for some reason I took it out. 
>
>The option of adding a flag to the <channel_type> element to
    specify the units might be the simplest, but I really don't want to
    go updating the v1.x specs at this stage with so much going on for
    v2.0. If others feel strongly about it though let me know... This
    issue won't be a problem in v2, since all quantities must specify
    their own units (dimensions will be restricted in the component
    class definition), e.g. v="-60mV"...
>
>While it would be possible in theory to make a general conversion
    utility (in Python or XSL) to change an SI v1.8.1 file into
    Physiological & vice versa, it would need to know what each
    quantity was, there would be no way to automate the conversion.
    Unfortunately not something I can spend time on with lots to do for
    v2.0.
>
>So I'll put back in the check in nC if a user tries to export to a
    single L3 file containing a mix of SI & Physiol ChannelML files
    (and a warning when you press "Validate" that there is a
    mixture...). For such projects, the options would be to export as
    individual NeuroML files with one model component in each, or
    manually convert the ChannelML files to the same units. This latter
    option is painful I know, but I've just done this conversion for all
    the standard nC example projects. 
>
>Updating the latest neuroConstruct code and example projects with
    nCupdate.sh/nCupdate.bat will get you the fix and should be able to
    export them all to valid single Level 3 files.
>
>Regards,
>Padraig
>
>
>
>Let me know when you fix this (after you've verified this is a bug.) (I suppose Padraig will be following up?)
>>
>Thanks,
>>Aditya Gilra.
>>
>>
>>
_______________________________________________
neuroConstruct mailing list neuroConstruct at ucl.ac.uk http://www.mailinglists.ucl.ac.uk/mailman/listinfo/neuroconstruct Please note that the neuroConstruct mailing list is publicly archived
>
>
>-- 
-----------------------------------------------------
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.gleeson at ucl.ac.uk -----------------------------------------------------
>
>
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From p.gleeson at ucl.ac.uk  Thu Nov 10 18:01:38 2011
From: p.gleeson at ucl.ac.uk (P Gleeson)
Date: Thu, 10 Nov 2011 18:01:38 +0000
Subject: [neuroConstruct] channel units bug in exporting a single neuroml
	file
In-Reply-To: <1320838375.90782.YahooMailNeo@web95901.mail.in.yahoo.com>
References: <1320667997.83986.YahooMailNeo@web95906.mail.in.yahoo.com>
	<4EBA5A97.2@ucl.ac.uk>
	<1320838375.90782.YahooMailNeo@web95901.mail.in.yahoo.com>
Message-ID: <4EBC1182.20100@ucl.ac.uk>

Hi Aditya,

That's fixed in the neuroConstruct SVN now. The meta:property tags are 
of course highly non standard. The dt and sim duration belong rightly in 
a SED-ML file, along with details of what to save, plot etc. I'm working 
on an option exporting valid SED-ML beside the NeuroML.

With regards to the temperature, this could be set in the SED-ML too, 
though there will probably have to be some concept of a (global) 
temperature in a NeuroML 2 file (e.g. as a property of a <network>, or 
maybe <population>, as different cells in different parts of the brain 
could in theory have different temps...).

Cheers,
Padraig



On 09/11/11 11:32, Aditya Gilra wrote:
> Thanks Padraig,
>
> I'm sticking to multiple neuroml files for now rather than the single 
> file option.
> However, there's a glitch in the multiple files option. When you 
> export to neuroml as a single file, the temperature for the simulation 
> is set as a meta:property (along with simulation time and dt). 
> However, when exporting as multiple files, the Level3 file does not 
> contain any meta:property tags for these. Could you include that?
>
> I was quite surprised by the difference that 32 deg Celsius vs 35 deg 
> Celsius makes to the action potential in the granulecell example model 
> (KDR tau is temperature dependent) [Took me a while to figure out what 
> was wrong!].
>
> Best,
> Aditya.
>
>     ------------------------------------------------------------------------
>     *From:* P Gleeson <p.gleeson at ucl.ac.uk>
>     *To:* Aditya Gilra <aditya_gilra at yahoo.com>
>     *Cc:* "neuroconstruct at ucl.ac.uk" <neuroconstruct at ucl.ac.uk>;
>     neuroml-technology at lists.sourceforge.net
>     *Sent:* Wednesday, 9 November 2011 4:18 PM
>     *Subject:* Re: [neuroConstruct] channel units bug in exporting a
>     single neuroml file
>
>     Hi Aditya,
>
>
>     On 07/11/11 12:13, Aditya Gilra wrote:
>>     Hi,
>>     Do we have a web interface for bug reports or should I mail to
>>     this list?
>     Posting to the list is probably best, no forum or bug tracker for
>     neuroConstruct at the moment... I've cc'd the NeuroML list too.
>>     Am using neuroconstruct 1.5.1.
>>     I exported a single/unified neuroml file for say the granulecell
>>     in the example models,
>>     i.e. export->neuroml-> select 'level 3' and tick 'generate single
>>     neuroml level 3 file' and then click 'generate all neuroml scripts'.
>>     Now this creates an nml file with <channels units="SI Units"> tag
>>     amongst other tags. However, some of the channels continue to
>>     have physiological units. There is no overriding units attribute
>>     in their <channel_type> tags either. An example is the Gran_KA_98
>>     channel. Of course this problem does not occur if multiple xml
>>     files for each channel, cell, network are created, since each
>>     channel has its own units.
>     Yes, it was a problem in the neuroConstruct single L3 file
>     export... I had code in place to check for a mixture of SI &
>     Physiological units in the ChannelML files but for some reason I
>     took it out.
>
>     The option of adding a flag to the <channel_type> element to
>     specify the units might be the simplest, but I really don't want
>     to go updating the v1.x specs at this stage with so much going on
>     for v2.0. If others feel strongly about it though let me know...
>     This issue won't be a problem in v2, since all quantities must
>     specify their own units (dimensions will be restricted in the
>     component class definition), e.g. v="-60mV"...
>
>     While it would be possible in theory to make a general conversion
>     utility (in Python or XSL) to change an SI v1.8.1 file into
>     Physiological & vice versa, it would need to know what each
>     quantity was, there would be no way to automate the conversion.
>     Unfortunately not something I can spend time on with lots to do
>     for v2.0.
>
>     So I'll put back in the check in nC if a user tries to export to a
>     single L3 file containing a mix of SI & Physiol ChannelML files
>     (and a warning when you press "Validate" that there is a
>     mixture...). For such projects, the options would be to export as
>     individual NeuroML files with one model component in each, or
>     manually convert the ChannelML files to the same units. This
>     latter option is painful I know, but I've just done this
>     conversion for all the standard nC example projects.
>
>     Updating the latest neuroConstruct code and example projects with
>     nCupdate.sh/nCupdate.bat will get you the fix and should be able
>     to export them all to valid single Level 3 files.
>
>     Regards,
>     Padraig
>
>
>>     Let me know when you fix this (after you've verified this is a
>>     bug.) (I suppose Padraig will be following up?)
>>     Thanks,
>>     Aditya Gilra.
>>
>>
>>     _______________________________________________
>>     neuroConstruct mailing list
>>     neuroConstruct at ucl.ac.uk  <mailto:neuroConstruct at ucl.ac.uk>
>>     http://www.mailinglists.ucl.ac.uk/mailman/listinfo/neuroconstruct
>>     Please note that the neuroConstruct mailing list is publicly archived
>
>
>     -- 
>     -----------------------------------------------------
>     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.gleeson at ucl.ac.uk  <mailto:p.gleeson at ucl.ac.uk>
>     -----------------------------------------------------
>
>
>


-- 
-----------------------------------------------------
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.gleeson at ucl.ac.uk
-----------------------------------------------------

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