Hi,
Hm yeah, that's unfortunate about the lab. It happens sometimes though... sometimes they just get too many emails, try re-sending it once, but I suspect that it might be a little late before she responds.
Anyways, about the model.
First, you have to very specifically pick what you want to model/simulate, and this will have to relate to your research question (eg, what you are trying to learn or test). I'm not too familiar with zebrafish regeneration, so I'm just going to make up a scenario. For example, you might want to model the rate at which regeneration occurs on a macroscopic level as a function of biochemical interactions at the microscopic level. Or, you could try to model the survival rate as a function of rate of regeneration. Again, I'm not too familiar with the topic, so you'll have to figure out most of this part on your own. That being said, try and keep it relatively simple, keeping in mind that you will have to implement a method to actually simulate this, so don't go overboard crazy.
Next, you have to decide what type of model to make. You can leave it as a simple mathematical model (see the one here for an example:
http://www.uni-tuebingen.de/modeling/Prog/SIR.html), or you can go for a full-on visual simulation. Both have merits, and I find that some combination works best in terms of being able to present the model/simulation. This will in part depend on what you want to model -- if you have too many actors running in the simulation at once, it gets very messy (you'll see what I mean in a minute).
As for the actual modeling. To be honest, I'm very bad with computers, and going into the project, I was just learning how to program (I was taking AP Comp Sci at the same time). But, the complexity of the model will mostly come from the actual bio knowledge that you put in, not the programming (you could have very pretty looking code, but the judges won't really care, they'll all be looking at the bio part). So my code was pretty crappy, but the program worked, and I got data out, which was really all that was important. If you can't already program (I used Java, but C++ or another language would be just as good), talk to your comp sci teacher to see if he can give you a crash course in programming. I did the vast majority of the programming myself but used GridWorld (
http://www.horstmann.com/gridworld/) to create a slightly nicer looking display (I used grids, so this was also rather convenient). But like I said, depending on what you want to do, the display and implementation will change. But from the display and basic grid functions, you can just kind of insert the formulas and equations where it seems to make sense that they are executed. As a result of the way the program runs, you will sometimes need to modify equations or create them in a logical way so that the model/simulation proceeds like an actual experiment would.
So this is what I did. I was interested in modeling superinfection (multiple infection of a single cell) dynamics on a multicellular scale. In short, my model had roughly 300 susceptible cells in the initial condition, as well as a few infected ones, and had the viruses replicate. In the experimental trials, superinfection was allowed to occur within some of the cells, but in the control trials, superinfection was not allowed. With each successive time step, cells and viruses would move around and interact as if they were in a petri dish. At the end of each trial, I examined how many strains of the virus there were and how virulent each one was to determine what the overall trend was as a result of superinfection dynamics. In terms of the modeling, I had to modify some of the equations that dealt with replication rate, etc since time steps aren't a particularly quantitative sort of measure. There were some equations in the literature for competitive superinfection dynamics within a single cell, so I utilized those at the single cell level (but those didn't exist at the multicellular level, which was why I was modeling the multicellular scale). The part where I had to invent some equations was later on in the cell-to-cell transmission of virus since I couldn't find any literature there, so I ended up using a modified version of the regular transmission equation (it made sense at the time since the biochemical routes of transmission are similar, but it is easier via cell-to-cell transmission). It's a little big vague from the description, but I can send the model to you as a Java file if you would like.
Going back to something earlier, I have a feeling that the biochemical pathway modeling up to macroscale might be most useful (but a bit more difficult) in your case. It would be somewhat similar to what I was doing in that you could have the chemical intermediates and enzymes function as agents moving throughout space, and they can interact in a probabilistic fashion based on particle collision equations and whatnot. Ultimately, all of those intermediates would form the final product that causes cellular and tissue regeneration, or something like that. Again, though, it is your choice and your project of what you choose to model.
Oh, and about the clinical data. So I validated my model by testing it with clinical data. So for my project, I pulled data from case studies of patients with superinfection by different strains of viruses (this actually is not that uncommon) and input some of the 'initial' data for the patients into the model, pretending that a blood sample or something had been drawn. I then ran that initial data though the model and compiled averages of the results to see if it matched up with the final condition of the patients. This part was actually the trickiest since sometimes, patients just have strange things happen to them, and sometimes, the model is just way wrong, so you have to keep tinkering. You could probably find regeneration data regarding zebrafish in various papers that are floating around, though again, it is tricky to find.
Feel free to ask more questions though, but I think you're on the right track.
Hope this helps!
Aaron Lin