[cellml-discussion] MIASE: towards the description of simulation runs

[Dagmar Koehn]

Dear all,

having seen your proposal for a CellML Simulation Metadata Specification 
just recently, I thought you might be interested to know that there is a 
quite similar effort going on at the moment, called MIASE (Minimum 
Information About a Simulation Experiment). 

The aim of MIASE is to find a minimal way of describing the simulation 
run on a quantitative model. Thus, we are trying to encode information 
such as the algorithm/method used for the simulation, model changes done 
on the model in order to run the simulation properly, defining several 
tasks to be applied to the model and finally defining the output of the 
simulation.

All of this should be described independent of the format the model is 
encoded in.

MIASE is aimed at being a community effort, reaching as many research 
groups as possible. So far, it has been discussed on the Super Hackathon 
"standards and ontologies for Systems Biology" in Okinawa in January 
this year and the following email discussion has been joined by people 
from different simulation tools, such as COPASI, SBW, Virtual Cell and 
SBToolbox.

I have had a look at the CellML Simulation Metadata Specification by 
Andrew at http://www.cellml.org/specifications/metadata/simulations/ . 
It actually seems that we are heading for quite similar aims. That is 
why I just wanted to direct you to the following web resources, and I 
would like to ask you participate in the current MIASE discussion, as it 
might be nice to bring both efforts together:
- A temporary and constantly evolving draft of a MIASE object model in 
UML is available from the project's web site: 
https://sourceforge.net/projects/miase Check the CVS for the UML diagram.
- If you would like to participate in the MIASE development and 
discussion, you are most welcome to join the miase mailing list: 
https://lists.sourceforge.net/lists/listinfo/miase-discuss

Another thing that might be interesting for you is the KiSA ontology 
(Kinetic Simulation Algorithm Ontology) we have started to bring to 
life, a classification and characterization of different kinetic 
simulation algorithms described in OBO format - it might in any case be 
very helpful for the reference to the used simulation algorithms in the 
CellML Simulation Metadata Specification:
- We have made a version of the KiSAO available from the same web site: 
https://sourceforge.net/projects/miase Check the download section to get 
the current OBO file.
- Please note that we are currently working on a web browser interface 
to view and edit KiSAO which will be found at the project's web site 
hosted by the EBI: http://www.ebi.ac.uk/compneur-srv/miase/


I would be happy to answer further questions and discuss concerns.

Best regards,
Dagmar Koehn

-- 
Dagmar Köhn, EMBL - European Bioinformatics Institute, Computational Neurobiology Group, Hinxton, Cambridge, CB10 1DS, UK, http://www.ebi.ac.uk/compneur-srv/, dagmar at ebi.ac.uk, Tel: +441223494418