Selecting a published model to reproduce

The first half of the course provides you with the programming and conceptual tools that you need to construct your own models of biological systems.

In the second half of the course, you will focus on re-creating a published model of a biological system.

More advanced students may wish to construct a model on their own; they may do so with the approval of the course instructors.

Otherwise, you will need to select an appropriate paper from the published peer-reviewed technical literature.

Papers may be found by using Google Scholar, Science Citation Index, PubMed, and other bibliographic data bases available through the library.

To submit a paper for approval, you must fill out a rubric that will help you determine whether the paper is suitable for the course, and you must email a PDF of the paper to all of the course instructors.

If the rubric is not filled out, the instructors will not look at the paper for approval.

Here are the criteria that must be addressed in the rubric:

• Are all equations necessary to reconstruct the model present? You may need to look at supplementary information for a paper to answer this question.

• Are values given for all parameters of the model? You may need to look at the supplementary information for a paper to answer this question.

• Are all initial conditions for the model specified, or can they be deduced from the information given in the paper?

• Does the model have more than about 15 state variables? If the model is too complex, it may be very difficult to reproduce.

• Does the model involve complex mathematics that you do not understand? (For example, does the model involve partial differential equations?) If the paper presents a mathematical analysis of the model, this may be acceptable, if the authors also make comparisons to biological data.

• Is the model just a set of equations that fit a specific data set? If so, this is not appropriate for this course. The model equations should need to be simulated to predict how the outcomes will change.

• Is there a clear comparison between the model predictions and actual data? If a purely theoretical model is proposed that is not related to actual biological measurements, this is also unlikely to be suitable for this course.

Receiving approval for the term paper by the deadline is worth 1 point towards the 50 points for the term paper.

Here are links to papers that have previously been used by students in the course as the basis for model reconstruction. These papers should not be used for your own term papers.

• A model of $\beta$-cell mass, insulin and glucose kinetics: Pathways to diabetes

• A dynamical model of human immune response to influenza A virus infection

• Modeling the interactions between osteoblast and osteoclast activities in bone remodeling

• A mathematical model of spontaneous calcium (II) oscillations in astrocytes

• A mathematical modelling for the cheliped regeneration with handedness in fiddler crab

• Mathematical modeling of lipase and protease production by Penicillium restrictum in a batch fermenter

• Blood-stage dynamics and clinical implications of mixed Plasmodium vivax - Plasmodium falciparum infections

• A simple mathematical model of signaling resulting from the binding of lipopolysaccharide with Toll-like receptor 4 demonstrates inherent preconditioning behavior

• Global dynamics of a dengue epidemic mathematical model

• An in silico approach to the analysis of acute wound healing

• Bubonic plague: a metapopulation model of a zoonosis

• A quantitative model of human DNA base excision repair. I. mechanistic insights

• A mathematical model of cell-to-cell spread of HIV-1 that includes a time delay

• Bifurcation, stabilization, and ethanol productivity enhancement for a membrane fermentor

Here is an amusing essay on the difficulties of reading scientific papers, which is not only funny, but potentially very useful: How to read a scientific paper.