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I'm really sorry wasting your time...I was expecting the values to be
on the rows :)
sorry again and thank you, Paolo

On Thu, Apr 19, 2012 at 5:14 PM,
<cellml-tools-developers-request at cellml.org> wrote:
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> Today's Topics:
>
> ? 1. Re: cellml-tools-developers Digest, Vol 48, Issue 3
> ? ? ?(Paolo Pannarale)
> ? 2. Re: cellml-tools-developers Digest, Vol 48, Issue 3 (Alan Garny)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 19 Apr 2012 16:27:47 +0200
> From: Paolo Pannarale <p.pannarale at gmail.com>
> Subject: Re: [cellml-dev] cellml-tools-developers Digest, Vol 48,
> ? ? ? ?Issue 3
> To: cellml-tools-developers at cellml.org
> Message-ID:
> ? ? ? ?<CAB5pjwYaF-7uwmPwGRjXEgCdAD3qxcW0PDXpnCW7zdohmB__+Q at
> mail.gmail.com>
> Content-Type: text/plain; charset=windows-1252
>
> The model, csv and graph are available at
> http://dl.dropbox.com/u/6304831/cellml.zip
> Anyway, following your instructions if I plot the exported values I
> obtain something a way long different from the opencell plot.
> This result doesn't surprise me, given that the time column contain
> only 3 different values (0,1000, 0.66) but the opencell plot has
> maximum time of 100000 sec...
> the variable plotted is
> product_of_Bioenvironment_RxR1P1MM_ICFormation_of_svp_hasPubchemCID95069/concentration(nM)
>
> Thank you, Paolo
>
>
> On Thu, Apr 19, 2012 at 3:28 PM,
> <cellml-tools-developers-request at cellml.org> wrote:
>> Send cellml-tools-developers mailing list submissions to
>> ? ? ? ?cellml-tools-developers at cellml.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> ? ? ? ?http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>> or, via email, send a message with subject or body 'help' to
>> ? ? ? ?cellml-tools-developers-request at cellml.org
>>
>> You can reach the person managing the list at
>> ? ? ? ?cellml-tools-developers-owner at cellml.org
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of cellml-tools-developers digest..."
>>
>>
>> Today's Topics:
>>
>> ? 1. simulation result values (Paolo Pannarale)
>> ? 2. Re: simulation result values (Alan Garny)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Thu, 19 Apr 2012 15:21:16 +0200
>> From: Paolo Pannarale <p.pannarale at gmail.com>
>> Subject: [cellml-dev] simulation result values
>> To: cellml-tools-developers at cellml.org
>> Message-ID:
>> ? ? ? ?<CAB5pjwYwvt0Yf6568z17aviOn-gi9jzWOs96VAf7Prs-SMygMw at
>> mail.gmail.com>
>> Content-Type: text/plain; charset="windows-1252"
>>
>> Dear developers, I can't figure out the meaning of the cellml
>> simulation results: in the opencell gui i can simulate and visualize a
>> pretty and meaningful graph, but when i export to csv from the tool or
>> I run simulations directly from the api I get incomprehensible values,
>> like those attached.
>>
>> time(second)
>> 0,1000,1000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.06642155452508047,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.06642155452508047,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
>>
>> concentration
>> 1075.453950162427,985.8966564968832,-3.2401152126481507e-7,0.0017073150312856896,0.0021341651307573623,0.08536660523029449,11.429613243724534,1134.012527460086,623.7692668788601,-4.9754442208586574e-8,5.246469165173447e-8,12.153744231278361,0.004233483169828203,-0.01707158946604455,3.6743312415570034e-8,-1.3658520250283731e-8,-1.707332020011408e-8,-6.829328080132369e-7,0.00012979771147818286,0.7170886834213565,0.39443821246781974,-2.860463367001941e-8,-8.412955989197195e-9,0.01434715355653333,7.113033199338675e-9,0.01707158946604455,0.0000020779036877091203,1.7073150312856898e-9,6.829260125142758e-8,1.7854320581180872e-21,0.06629175681360229,-0.01707158946604455,2.0779036877091204,0.0017073150312856898,0.06829260125142758,1.3658520250285516e-8,0.00012979771147818286,0.002116748697947301,0.0000011429613243724535,0.00170733210460589,0.0682932841842356,-1.3658520250283731e-8,0.0006076872115639181,0.0021167415849141016,1.1429613243724535,-1.707332020011408e-8,-6.829328080132369e-7,0.01434715355653333,7.113033199338675e-9,0.7485231202546321,1.360815032952103,-3.6743312415570034e-8,3.6743312415570034e-8,-4.975444220858658e-9,-5.970533065030388e-11,-3.1035291940416664e-9,0.7170886834213565,5.246469165173447e-9,-2.860463367001941e-8,0.39443821246781974,6.295762998208136e-11,-8.412955989197195e-9
>>
>> How can I reproduce the plot from these values?
>> BR, Paolo
>>
>> --
>> ?[M]y work, which I?ve done for a long time, was not pursued? in order
>> ?to gain? the praise? I now enjoy, but chiefly? from a craving after
>> knowledge, which? I notice? resides? in me more? than? in most other
>> men. And wherewithal, whenever I found out anything remarkable, I have
>> thought it my duty to put down my discovery on paper, so that all
>> ingenious people might be informed thereof.?
>> (van Leeuwenhoek, Letter to the Royal Society, June 12 1716)
>>
>> ?Make it as simple as possible. But not simpler?.
>> (Albert Einstein)
>>
>> "The best way to predict the future is to invent it".
>> (Alan Kay)
>>
>> ___________________________________
>>
>> Questo documento ? indirizzato esclusivamente al destinatario.
>> Tutte le informazioni ivi contenute, compresi eventuali allegati,
>> sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
>> in materia di "privacy" e ne ? proibito l'utilizzo da parte di
>> altri soggetti. Se avesse ricevuto per errore questo messaggio,
>> La preghiamo cortesemente di contattare il mittente al pi? presto
>> e di cancellare il messaggio subito dopo. Grazie.
>> ----
>> This document is exclusively intended for the stated addressee.
>> All information therein, including any attachment, are reserved
>> as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
>> by third parties. In case you received this message by mistake,
>> please inform the sender and delete the message afterward.
>> Thank you.
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 19 Apr 2012 15:28:08 +0200
>> From: "Alan Garny" <alan.garny at inria.fr>
>> Subject: Re: [cellml-dev] simulation result values
>> To: "'A list for the developers of CellML tools'"
>> ? ? ? ?<cellml-tools-developers at cellml.org>
>> Message-ID: <00a801cd1e30$428a0f20$c79e2d60$@inria.fr>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Paolo,
>>
>> Could you share with us the CSV file that you get from OpenCell? Attached
>> is
>> the kind of CSV file you should be getting. If you open that file in Excel,
>> you will see that the first row refers to the name of the model's different
>> variables. The first column refers to the variable of integration (time in
>> your case, it would seem) and the subsequent columns to a given model
>> parameter. With the attached, if I am interested in plotting the membrane
>> (potential) against time, I will use the first two columns.
>>
>> HTH, Alan.
>>
>>> -----Original Message-----
>>> From: cellml-tools-developers-bounces at cellml.org [mailto:cellml-tools-
>>> developers-bounces at cellml.org] On Behalf Of Paolo Pannarale
>>> Sent: 19 April 2012 15:21
>>> To: cellml-tools-developers at cellml.org
>>> Subject: [cellml-dev] simulation result values
>>>
>>> Dear developers, I can't figure out the meaning of the cellml simulation
>> results:
>>> in the opencell gui i can simulate and visualize a pretty and meaningful
>> graph,
>>> but when i export to csv from the tool or I run simulations directly from
>> the api I
>>> get incomprehensible values, like those attached.
>>>
>>> time(second)
>>> 0,1000,1000,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.06642155452508047,0,0,0,0,0,0,
>>>
>> 0,0,0,0,0,0,0,0,0,0,0,0.06642155452508047,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
>>> 0,0,0,0,0,0,0,0
>>>
>>> concentration
>>> 1075.453950162427,985.8966564968832,-3.2401152126481507e-
>>> 7,0.0017073150312856896,0.0021341651307573623,0.0853666052302944
>>> 9,11.429613243724534,1134.012527460086,623.7692668788601,-
>>> 4.9754442208586574e-8,5.246469165173447e-
>>> 8,12.153744231278361,0.004233483169828203,-
>>> 0.01707158946604455,3.6743312415570034e-8,-1.3658520250283731e-8,-
>>> 1.707332020011408e-8,-6.829328080132369e-
>>> 7,0.00012979771147818286,0.7170886834213565,0.39443821246781974,-
>>> 2.860463367001941e-8,-8.412955989197195e-
>>> 9,0.01434715355653333,7.113033199338675e-
>>> 9,0.01707158946604455,0.0000020779036877091203,1.707315031285689
>>> 8e-9,6.829260125142758e-8,1.7854320581180872e-
>>> 21,0.06629175681360229,-
>>> 0.01707158946604455,2.0779036877091204,0.0017073150312856898,0.0
>>> 6829260125142758,1.3658520250285516e-
>>> 8,0.00012979771147818286,0.002116748697947301,0.0000011429613243
>>> 724535,0.00170733210460589,0.0682932841842356,-
>>> 1.3658520250283731e-
>>> 8,0.0006076872115639181,0.0021167415849141016,1.1429613243724535
>>> ,-1.707332020011408e-8,-6.829328080132369e-
>>> 7,0.01434715355653333,7.113033199338675e-
>>> 9,0.7485231202546321,1.360815032952103,-3.6743312415570034e-
>>> 8,3.6743312415570034e-8,-4.975444220858658e-9,-5.970533065030388e-
>>> 11,-3.1035291940416664e-9,0.7170886834213565,5.246469165173447e-
>>> 9,-2.860463367001941e-8,0.39443821246781974,6.295762998208136e-
>>> 11,-8.412955989197195e-9
>>>
>>> How can I reproduce the plot from these values?
>>> BR, Paolo
>>>
>>> --
>>> ?[M]y work, which I?ve done for a long time, was not pursued? in order ?to
>>> gain? the praise? I now enjoy, but chiefly? from a craving after
>> knowledge,
>>> which? I notice? resides? in me more? than? in most other men. And
>> wherewithal,
>>> whenever I found out anything remarkable, I have thought it my duty to put
>>> down my discovery on paper, so that all ingenious people might be informed
>>> thereof.?
>>> (van Leeuwenhoek, Letter to the Royal Society, June 12 1716)
>>>
>>> ?Make it as simple as possible. But not simpler?.
>>> (Albert Einstein)
>>>
>>> "The best way to predict the future is to invent it".
>>> (Alan Kay)
>>>
>>> ___________________________________
>>>
>>> Questo documento ? indirizzato esclusivamente al destinatario.
>>> Tutte le informazioni ivi contenute, compresi eventuali allegati, sono
>> soggette a
>>> riservatezza secondo i termini del D.Lgs. 196/2003 in materia di "privacy"
>> e ne ?
>>> proibito l'utilizzo da parte di altri soggetti. Se avesse ricevuto per
>> errore questo
>>> messaggio, La preghiamo cortesemente di contattare il mittente al pi?
>> presto e
>>> di cancellare il messaggio subito dopo. Grazie.
>>> ----
>>> This document is exclusively intended for the stated addressee.
>>> All information therein, including any attachment, are reserved as per
>> Italian
>>> D.Lgs. 196/2003 about privacy, and cannot be used by third parties. In
>> case you
>>> received this message by mistake, please inform the sender and delete the
>>> message afterward.
>>> Thank you.
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: dummy.csv
>> Type: application/vnd.ms-excel
>> Size: 26353 bytes
>> Desc: not available
>> URL:
>> <http://lists.cellml.org/pipermail/cellml-tools-developers/attachments/20120419/e239c99c/attachment.xlb>
>>
>> ------------------------------
>>
>> _______________________________________________
>> cellml-tools-developers mailing list
>> cellml-tools-developers at cellml.org
>> http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>>
>>
>> End of cellml-tools-developers Digest, Vol 48, Issue 3
>> ******************************************************
>
>
>
> --
> ?[M]y work, which I?ve done for a long time, was not pursued? in order
> ?to gain? the praise? I now enjoy, but chiefly? from a craving after
> knowledge, which? I notice? resides? in me more? than? in most other
> men. And wherewithal, whenever I found out anything remarkable, I have
> thought it my duty to put down my discovery on paper, so that all
> ingenious people might be informed thereof.?
> (van Leeuwenhoek, Letter to the Royal Society, June 12 1716)
>
> ?Make it as simple as possible. But not simpler?.
> (Albert Einstein)
>
> "The best way to predict the future is to invent it".
> (Alan Kay)
>
> ___________________________________
>
> Questo documento ? indirizzato esclusivamente al destinatario.
> Tutte le informazioni ivi contenute, compresi eventuali allegati,
> sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
> in materia di "privacy" e ne ? proibito l'utilizzo da parte di
> altri soggetti. Se avesse ricevuto per errore questo messaggio,
> La preghiamo cortesemente di contattare il mittente al pi? presto
> e di cancellare il messaggio subito dopo. Grazie.
> ----
> This document is exclusively intended for the stated addressee.
> All information therein, including any attachment, are reserved
> as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
> by third parties. In case you received this message by mistake,
> please inform the sender and delete the message afterward.
> Thank you.
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 19 Apr 2012 17:14:40 +0200
> From: "Alan Garny" <alan.garny at inria.fr>
> Subject: Re: [cellml-dev] cellml-tools-developers Digest, Vol 48,
> ? ? ? ?Issue 3
> To: "A list for the developers of CellML tools"
> ? ? ? ?<cellml-tools-developers at cellml.org>
> Message-ID: <00c301cd1e3f$24555f00$6d001d00$@inria.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> It all works. See attachment.
>
> Alan
>
>> -----Original Message-----
>> From: cellml-tools-developers-bounces at cellml.org [mailto:cellml-tools-
>> developers-bounces at cellml.org] On Behalf Of Paolo Pannarale
>> Sent: 19 April 2012 16:28
>> To: cellml-tools-developers at cellml.org
>> Subject: Re: [cellml-dev] cellml-tools-developers Digest, Vol 48,
>> Issue 3
>>
>> The model, csv and graph are available at
>> http://dl.dropbox.com/u/6304831/cellml.zip
>> Anyway, following your instructions if I plot the exported values I
>> obtain something a way long different from the opencell plot.
>> This result doesn't surprise me, given that the time column contain
>> only 3 different values (0,1000, 0.66) but the opencell plot has
>> maximum time of
>> 100000 sec...
>> the variable plotted is
>> product_of_Bioenvironment_RxR1P1MM_ICFormation_of_svp_hasPubchemCI
>> D95069/concentration(nM)
>>
>> Thank you, Paolo
> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>
>
> End of cellml-tools-developers Digest, Vol 48, Issue 4
> ******************************************************



--
?[M]y work, which I?ve done for a long time, was not pursued? in order
to gain? the praise? I now enjoy, but chiefly? from a craving after
knowledge, which? I notice? resides? in me more? than? in most other
men. And wherewithal, whenever I found out anything remarkable, I have
thought it my duty to put down my discovery on paper, so that all
ingenious people might be informed thereof.?
(van Leeuwenhoek, Letter to the Royal Society, June 12 1716)

?Make it as simple as possible. But not simpler?.
(Albert Einstein)

"The best way to predict the future is to invent it".
(Alan Kay)

___________________________________

Questo documento ? indirizzato esclusivamente al destinatario.
Tutte le informazioni ivi contenute, compresi eventuali allegati,
sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
in materia di "privacy" e ne ? proibito l'utilizzo da parte di
altri soggetti. Se avesse ricevuto per errore questo messaggio,
La preghiamo cortesemente di contattare il mittente al pi? presto
e di cancellare il messaggio subito dopo. Grazie.
----
This document is exclusively intended for the stated addressee.
All information therein, including any attachment, are reserved
as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
by third parties. In case you received this message by mistake,
please inform the sender and delete the message afterward.
Thank you.

---

• [cellml-dev] cellml-tools-developers Digest, Vol 48, Issue 4, Paolo Pannarale, 04/20/2012

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