http://www.cellml.org/repository-info/info essentially lays out the requirements for each level of curation. I think this gives a clear indication of what is required for level 0, 1, and 2 curation and my document you mention below starts to look at what is required for level 3. Just to point out that that document is the combination of discussions with many people, primarily based on a proposal from Jim Bassingthwaighte.
I think until there is some progress on defining what level 3 curation is that we don't worry about it for now, especially since it is generally regarded that no existing published models would meet all the requirements for level 3 curation. I think level 3 is something we can aspire to as people start using tools like CellML and decent testing frameworks in the actual development of new models rather than an add-on after the model is already developed (like what Randy was talking about at the CellML workshop). In terms of level 1 and 2 curation, I'm not really sure what more detail you need in the way of a specification? Currently the only way to make sure the math described by a CellML model is equivalent to a published paper is to sit down and look at them both side by side. Whether you do that looking at the content MathML directly or use some utility to render the MathML in a "more readable" format is a personal preference. Ideally this is best done by the model author, but any model curator can undertake this level of curation. Similarly, how level 2 curation is achieved is really up to the person doing the curation. I've put forward a suggestion on how this could be done, but different people can choose to use whatever tools they prefer as long as there is confidence that the required conditions have been met. Personally, I'd say the more different simulation and validation tools used the better, although the formulation and mathematics used in a given model might restrict which tools can be used and force more manual checking upon the curator. Ideally I think level 2 curation should be undertaken independently of the model author, but can't really see a reason to enforce this as the curation annotation should contain the curator data. In fact, there is no reason curation can't be done by more than one curator, whereby model users might have more confidence in a model that has been stamped level 2 by more than one person... A key point to note is that a model curated to level 2 is not necessarily also curated to level 1 - so we need to be careful about the graphical representation used on in the model repository. i.e., the first two stars being yellow should imply that the model satisfies bother level 1 and 2 curation. In general, at least for the electrophysiology models, none of the models in the repository will satisfy both curation levels 1 and 2. Also, the requirements for each of the curation levels are currently the result of many discussions on what we'd ideally like to see for each level. As people spend more time curating models and using these annotations I'd expect there could be some changes in these definitions required. So if you have any suggestions please put them forward. One that has come up a bit would be breaking level 2 into more pieces, for example pushing the units consistency requirement to a higher level. David. PS - no immediate plans to come back to Auckland, I think the 8th-18th comment was in regard to the April workshop. James Lawson wrote: > Dear all, > > Another thing Peter has asked me to seek input on is the need for a > detailed, realistic curation specification that I can follow. > Andre's 'thoughts on model curation and model repositories' goes some > way towards this but it isn't formalised and this kind of document > probably needs the input of more than one person. The proposed document > also needs to take into account the current and future state of the > repository, and provide guidelines to follow that will result in > significant, consistent progress being made in curating the models in > the repository. We need to define what is the job of the CellML team, > and what is the job of the model authors. > > In the 'current development' document on the CellML site, Matt has said > that he would draft such a document, but that it was postponed until > Andre arrived "Model curation document - matt will write an initial > draft. (postponed till Andre gets here - somewhere between the 8th and > 18th)" - what month was this? Is Andre coming again or was this > referring to the CellML workshop? > > > Regarding how I am approaching my work at the moment, different people > are saying different things about how the models should be curated. So I > am basically trying to figure out what I think the consensus is, and > trying to be consistent with what I am doing. If I could work off a > specification that tells me what I need to do and how to do it in a > specific way, I think I could be quite a lot more productive. It would > also allow me to identify what I have the skills to achieve and what I > don't, and therefore what skills I need to develop. I'm primarily using > skills that I've learned in the last 14 weeks or so, so perhaps we could > identify how I could use the skills that I have learned in my studies > more. > > Please comment. > > Kind regards, > James Lawson > > _______________________________________________ > cellml-discussion mailing list > cellml-discussion@cellml.org > http://www.cellml.org/mailman/listinfo/cellml-discussion -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] _______________________________________________ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
