Re: [SED-ML-discuss] log axes on plots or lines

[Nicolas Le n. <le...@eb...>]

On 04/08/10 18:57, Frank Bergmann wrote:

> unless someone shows me a plot that contains (in the same coordinate
> system) both logarithmic curves / segments and non-logarithmic ones I
> say it should be on the Plot2d/3d!.

This discussion already happened, and you already asked for examples, and 
we decided to put those attributes on curves and surfaces (they were 
initially, in Okinawa, on plots). Examples would be for instance energies 
put on the same figure than equilibrium constants. It happens very 
frequently. Admittedly, all the examples I saw used the hybrid log/linear 
only on the y axis of a 2D plot. But if we do it, let's do it in a general 
manner.

> Again this is not a transformation, it is a mode of representing the
> data. If a user would like the data to be transformed this should happen
> on the DataGenerators.

Exactly, and you may want to output a data in a linear way in a report and 
a log way in a curve for instance. A very practical example is BioModels DB 
models 1/2. The "useful" output, the physiologically relevant one, is the 
EPSC, that is the current in function of linear time, but the author 
presented log plots because the states transitions had very different 
time-scales.

> Cheers Frank
>
> On Aug 4, 2010, at 1:05 PM, Richard Adams wrote:
>
>>
>> Hello SEDMLers
>>
>> There seems to be some discrepancies as to where the logX/logY/logZ
>> attributes should go, from looking in the spec - E.g., section 4.6.2
>> text says these attributes go in the Plot2d/3d elements, but the UML
>> diagrams show these attributes in the Curve/Surface elements. The
>> example files also differ, SEDML3.xml has them in 'Plot' but SEDML12
>> and 21 have them in 'Curve'. Which is correct? Cheers Richard
>>
>>
>>
>> -- Dr Richard Adams Software Development Team Leader, Centre For
>> Systems Biology Edinburgh University of Edinburgh Tel: 0131 650 8285
>> email : ric...@ed...
>>
>> -- The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>>
>>
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-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
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