Re: [SED-ML-discuss] KiSAO: algorithm parameter survey

[Anna Z. <zhu...@eb...>]

Dear KiSAO/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/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
>