Re: [SED-ML-discuss] SED-ML reports

[Frank B. <fbergman@u.washington.edu>]

Hello Richard, 

I never advocated storing the results in XML. All I wanted is a bit more information, so that two tools creating reports would be able to produce the same reports, so that they could be compared later on. For this the minimum additional information needed seems to be the order of the columns. 

(My tool currently writes out the report information in the order the DataGenerators appear in the XML file. However, I'm aware of one particular member of this group who will not like order at all, so making this a part of the spec seems wrong). 

I suppose for the time being I would have to create a custom annotation that would store: 

- column order,
- column precision, 
- desired output format
and perhaps even desired output location

best
Frank

On May 24, 2010, at 3:22 AM, Richard Adams wrote:

> 
> Hi Frank
>   I think that to be consistent with 'Plots' which is the tool's job  
> to interpret, it should be up to the tool how results are presented in  
> a 'report' format. I don't think results should be included in the  
> XML, after all this is markup language for methodological information.
>  Cheers
>    Richard
> 
>> Hello all,
>> 
>> I've had a question today that was: What does SED-ML mean by 'reports' ??
>> 
>> And honestly I was not quite sure how to answer it ... the current SED-ML
>> specification says:
>> 
>> "The Report class defines an output type that returns the simulation result
>> in actual numbers.
>> The particular columns of the report table are defined by creating a DataSet
>> for each column."
>> 
>> That might not be enough of a specification. What people probably expect is
>> to obtain results in form of CSV or SBRML, or is that a tool issue?
>> What do we expect tools to generate when we ask them for a report?
>> 
>> As far as I interpret it ... we don't say anything about serialization of
>> the report ... thus the most likely interpretation is that the tool in some
>> form presents the table with the results to the user, who then chooses a
>> serialization format for the data in the table?
>> 
>> Cheers
>> Frank
>> 
>> 
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> 
> 
> 
> -- 
> Dr Richard Adams
> Software Development Team Leader,
> Centre For Systems Biology Edinburgh
> University of Edinburgh
> Tel: 0131 650 8285
> email : ric...@ed...
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