Correspondence with Dr J. Carl Panetta - carl.panetta@stjude.org

N.B. the listed email address panetta@wagner.bd.psu.edu appears to be dysfunctional. After 20 minutes of searching, I finally found this address: carl.panetta@stjude.org

Dear Dr Panetta, 02/08/08

My name is James Lawson, I work at the University of Auckland Bioengineering Institute in Auckland, New Zealand. Our group, lead by Dr Poul Nielsen, is developing an XML based language called CellML which is designed to facilitate creation and sharing of mathematical models of, but not limited to, cell biology and physiology. If you're interested in finding out more about CellML, please visit our website, www.cellml.org

I am the curator of the repository of models we currently have, which includes about 280 models. The reason for my correspondence with you is that the model you and your colleague Denise Kirschner described in the paper "Modeling immunotherapy of the tumor - immune interaction" are coded into CellML in our model repository. I hope you approve of our efforts in translating your model into CellML.

Unfortunately the CellML version of your model that we have encoded is not in a working state and is unable to be simulated as yet.

I realise that the paper was published almost ten years ago, so my request might reach a little too far, but I was wondering if you might be able to provide the original XPPAUT code for the model. I've used XPPAUT .ode files from many models to fix our CellML representations of these models, so I believe this would be very useful.

Thank you very much. Any assistance you can give would be greatly appreciated.

Kind regards, James Lawson

James, 03/08/08

Thanks for your e-mail and your interest in the model. Your project sounds very interesting. The work I did for that project was at a different institution, and after looking through my old electronic files, I have not been able to find that (or any other work) from then! What I do remember about that project is that the ODEs were very stiff and needed an appropriate solver to handle them.

Sorry I can't be of more help.

Sincerely, J. Carl Panetta

Dear Dr Panetta, 03/08/08

Thanks for your help. Perhaps, if you remember, you might be able to give me some indication of which equations (as numbered in the paper) are required for the model? CellML can't yet handle matrices yet, unfortunately.

Thanks, James Lawson

James, 04/08/08

The scaled (non-dimensionalized) form is probably the best. It is equations 6-9. If you would like it in the unscaled form then use equation 1-5.

Dear Dr Panetta, 06/08/08

Thanks for your help. I just coded up the non-dimensionalized system and it is now giving me trains of spikes. I can't seem to generate some of the other behaviour. Getting the model to this state should be enough for me to move on and perhaps come back to it later. Since we have hundreds of models to curate, the approach I take is to get as many models to the point that they integrate and produce some output similar to figures in the paper they were based off. Once this process is more complete I can come back and put the finishing touches on the models.

I know it has been quite a while since the model was published, but if you're so inclined to help to get this model running better than it is now, you are very much welcome, and I would be most obliged to work with you on this. I could perhaps start by sending a screenshot of the output I get in our CellML simulator.

If not, I understand, since you are now working at a totally different institution.

In any case, I really appreciate your help - I have at least got the model producing some appropriate output now!

Thank you.

Kind regards, James Lawson

Dear Dr Panetta, 06/08/08

Sorry to bother you again. I'm probably missing something really obvious - I'm a biologist not so much a mathematician, but what should the values for E(0), T(0), IL(0), and for that matter the non-dimensionalized X(0), Y(0) and Z(0)? In the paper it says that, for example the value for X(0) = Xsubscript0, but I can't seem to find any values for Xsubscript0 or any equations that work it out.

In my model I just don't define initial values for X, Y, or Z and it seems to work, although I can only produce the simple spiking output shown in diagram 2D.

Just one more query:

In the legend for figure 2, it says that curve A was generated by equating c to "c = 5e - 5" - I can't seem to find what 'e' is supposed to be anywhere.

Hopefully soon I'll have your model up and running on cellML.org for the world to use!

Thanks very much.

Kind regards, James Lawson