Dear KiSAO/SED-ML/SBML 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:
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,
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