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

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

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