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[cellml-discussion] KiSAO: algorithm parameter survey


Chronological Thread 
  • From: zhutchok at ebi.ac.uk (Anna Zhukova)
  • Subject: [cellml-discussion] KiSAO: algorithm parameter survey
  • Date: Fri, 27 May 2011 12:53:00 +0100
Dear KiSAO/CellML/SED-ML users,

This is a reminder, that the KiSAO parameter survey closes next Tuesday,
31st May.

https://www.surveymonkey.com/s/kisao_parameters
<https://www.surveymonkey.com/s/kisao_parameters>

Thank you for your continued co-operation and support,

Sincerely,

BioModels.net Team

Anna Zhukova wrote:
> Dear KiSAO/CellML/SED-ML users,
>
> As many of you are aware, the current implementation of the Kinetic
> Simulation Algorithm Ontology (KiSAO http://www.biomodels.net/kisao)
> in OBO format is rather restrictive. For example, the multiple
> inheritance means that many algorithms occupy more than one position
> in the ontology, and often appear at different levels in the various
> component branches. An example of this would be the
> 'Bortz-Kalos-Liebowitz method', which possesses the characteristics
> 'discrete variables', 'progression with adaptive time steps',
> 'non-spatial description' and 'stochastic system behaviour', and hence
> appears in all four branches. This is in fact true of virtually all
> the methods in the ontology.
>
> In our efforts to improve both the hierarchical arrangements of KiSAO
> terms, as well as make it more useful to the community from a
> reasoning standpoint, we are currently in the process of
> re-implementing KiSAO in OWL. This much richer language allows us to
> create a separate branch of algorithm characteristics ('progression
> with adaptive time steps', etc.), and subsequently link the algorithms
> to the characteristics using the 'hasProperty' relationship. This work
> is well under way.
>
> In addition, we plan to incorporate, for each KiSAO method,
> information regarding the parameters that can be used in the
> simulation experiment settings. We would like to engage the community
> at this stage, and have created a survey to address the subject. It
> should take very little time to complete, as is it mostly composed of
> check boxes. It addresses the main points below:
>
> * For the list of parameters we plan to include, are there any that
> you would like to suggest?
> * Of the list of parameters on the survey page, do you think they are
> appropriately named, or are there more suitable names you have in mind?
> * Do you know of any algorithms that you would like to see
> incorporated (associated references appreciated)?
>
> The survey can be found here:
>
> https://www.surveymonkey.com/s/kisao_parameters
>
> The deadline for submitting responses to this survey is 31st May,
> 2011, after which we will notify you of the results.
>
> Thank you for your continued co-operation and support,
>
> Sincerely,
>
> BioModels.net Team
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