Proposal (10%, due 10 October)
Click here for the proposal rubric.
The project proposal should be a concise statement of the biological question and why it is interesting and important. This should require no more than 3-4 sentences. You do not need to write down any equations and present any type of results whatsoever. The primary purpose of the proposal is to get groups thinking and reading early in the semester. The proposal must contain at least two scientific references: one from the primary literature (that is, a research article published in a peer-reviewed scientific journal) and one from the secondary literature (a review article or book).
Here is an example of a reasonable project proposal, taken from some of my own research:
Click here for the proposal rubric.
The project proposal should be a concise statement of the biological question and why it is interesting and important. This should require no more than 3-4 sentences. You do not need to write down any equations and present any type of results whatsoever. The primary purpose of the proposal is to get groups thinking and reading early in the semester. The proposal must contain at least two scientific references: one from the primary literature (that is, a research article published in a peer-reviewed scientific journal) and one from the secondary literature (a review article or book).
Here is an example of a reasonable project proposal, taken from some of my own research:
The interaction between the immune system and parasites is often modelled as a predator-prey interaction (Antia et al. 1994, Fenton & Perkins 2010). However, both parasites and the immune system require host resources to replicate. This suggests that parasites and hosts might compete for the same resource. In this project, we use mathematical models to ask how competition for resources between the immune system and parasites changes the dynamics of the within-host interaction.
Primary literature reference:
Antia, R., B.R. Levin, and R. M. May, 1994. Within-host population dynamics and the evolution and maintenance of microparasite virulence. Am. Nat., 144, 457-472.
Secondary literature reference:
Fenton, A. and S. E. Perkins, 2010. Applying predator-prey theory to modelling immune-mediated, within-host interspecific parasite interactions. Parasitology, 137, 1027-1038.
Rough draft (20%, due 7 November)
Click here for the rough draft rubric.
The rough draft should contain all of the elements that will be present in the final draft: Introduction, Model Description, Results, Conclusions, Acknowledgements, and References. However, emphasis should be placed on the Introduction and Model Description.
The Introduction should lay out the motivation for the question the project asks: why is this an interesting and important question. It should also explain (briefly) the work that has already been done in this area, and give a sense for how this project will expand that knowledge base.
The Model Description is exactly what it sounds like: present the equations. Make sure to explain the biological processes that are included in the model, clearly state the biological assumptions you are making, identify parameters and variables and state what units they are going to be measured in, justify the choice of parameter values (if necessary), and explain both how you are going to analyze the model and how that analysis will help you answer the question of interest.
The Results section is self-explanatory: present the results. Take care to present the results in a way that makes them easy to understand. Use visuals whenever possible - a picture really can be worth a thousand words.
The Conclusions should begin by reiterating why the question you are trying to answer is interesting and important, and then by summarizing the main take-away points from the results. Put these results in the context of what was known before. Lay out future directions: one way to do this is to think about how the results might depend on the assumptions that you made, and which assumptions would be the most important to relax in future work. For example, perhaps you assumed mass action transmission and you found that changing the value of the transmission rate parameter really strongly affected the results. Modifying how transmission is modeled would then be an important future direction, and you could suggest a more biologically reasonable assumption, for example based on the biology of a particular disease.
The Acknowledgements section is exactly what it sounds like: a section where you thank the people who helped you by providing feedback, talking through ideas, checking your work, etc.
The References should list (in proper form) all of the articles and books referenced throughout the paper. Each paper is required to identify at least 8 appropriate references. (A reference is appropriate if it is from the primary or secondary literature. Websites are not appropriate references, so no Wikipedia! If you use Wikipedia as a resource, you must find a primary or secondary literature reference that confirms Wikipedia, and cite that instead.
Remember your audience! What you write should be understandable to your classmates - you are not writing for me! Keep this in mind when you are deciding how much detail is necessary to explain the problem, the analysis, and the results.
Rough drafts will be traded between groups, so by 12:00pm (noon) on November 7, each group should email or hand in one copy to me and copies to each of the members of the group you are trading drafts with of the rough draft.
Marks on the proposals will be based primarily on completeness and effort: are all of the required sections present, are the Introduction and Model Description clear and complete, and is it clear that the group has put considerable time into the project. In particular, you will not be graded on your writing (e.g., grammar, sentence construction, word choice) in the rough draft.
Steve Ellner, one of the most important mathematical biologists of the past 25 years, has written a short piece that gives some good tips for writing about mathematical biology:
How to write a theoretical paper that people will cite
Peer reviews (10%, due 14 November)
The purpose of the peer review is two-fold. Each group will have at least five sets of eyes reading through their rough draft and providing feedback, which will really help each group to improve their report. More importantly, however, by reading someone else's project, you will return to your own project with new eyes - reading someone else's writing is one of the best ways to improve your own writing! When performing peer review, keep several questions in mind:
The peer review will be graded! On November 14, everyone must either hand in or email one copy of their peer review to me, and one copy for the group whose draft they reviewed. Reviews will be graded based on effort and identification of strengths and weaknesses: did your comments indicate that you actually read and thought about the project carefully, did you clearly identify the things you thought the writers did well, and did you provide constructive suggestions for improvement? Oftentimes, one of the most important functions of a reviewer is to improve the writing: if you have thoughts about the order of ideas, grammar, sentence construction, word choice, etc. that you feel would improve the clarity and readability of the paper, share them!
Final draft (50%, due 3 December)
Click here for the final draft rubric.
The final draft should incorporate the feedback provided by the peer review, at the authors' discretion - just because it is suggested doesn't mean you have to do it!
Because being able to communicate ideas in written form is an absolutely essential skill, in science and in life, ~30% of the marks will be based solely on writing, and ~70% on how effectively you have achieved the goals of this project.
Self-assessment and assessment of group members (10%, due 3 December)
Click here for the assessment survey.
Click here for the rough draft rubric.
The rough draft should contain all of the elements that will be present in the final draft: Introduction, Model Description, Results, Conclusions, Acknowledgements, and References. However, emphasis should be placed on the Introduction and Model Description.
The Introduction should lay out the motivation for the question the project asks: why is this an interesting and important question. It should also explain (briefly) the work that has already been done in this area, and give a sense for how this project will expand that knowledge base.
The Model Description is exactly what it sounds like: present the equations. Make sure to explain the biological processes that are included in the model, clearly state the biological assumptions you are making, identify parameters and variables and state what units they are going to be measured in, justify the choice of parameter values (if necessary), and explain both how you are going to analyze the model and how that analysis will help you answer the question of interest.
The Results section is self-explanatory: present the results. Take care to present the results in a way that makes them easy to understand. Use visuals whenever possible - a picture really can be worth a thousand words.
The Conclusions should begin by reiterating why the question you are trying to answer is interesting and important, and then by summarizing the main take-away points from the results. Put these results in the context of what was known before. Lay out future directions: one way to do this is to think about how the results might depend on the assumptions that you made, and which assumptions would be the most important to relax in future work. For example, perhaps you assumed mass action transmission and you found that changing the value of the transmission rate parameter really strongly affected the results. Modifying how transmission is modeled would then be an important future direction, and you could suggest a more biologically reasonable assumption, for example based on the biology of a particular disease.
The Acknowledgements section is exactly what it sounds like: a section where you thank the people who helped you by providing feedback, talking through ideas, checking your work, etc.
The References should list (in proper form) all of the articles and books referenced throughout the paper. Each paper is required to identify at least 8 appropriate references. (A reference is appropriate if it is from the primary or secondary literature. Websites are not appropriate references, so no Wikipedia! If you use Wikipedia as a resource, you must find a primary or secondary literature reference that confirms Wikipedia, and cite that instead.
Remember your audience! What you write should be understandable to your classmates - you are not writing for me! Keep this in mind when you are deciding how much detail is necessary to explain the problem, the analysis, and the results.
Rough drafts will be traded between groups, so by 12:00pm (noon) on November 7, each group should email or hand in one copy to me and copies to each of the members of the group you are trading drafts with of the rough draft.
Marks on the proposals will be based primarily on completeness and effort: are all of the required sections present, are the Introduction and Model Description clear and complete, and is it clear that the group has put considerable time into the project. In particular, you will not be graded on your writing (e.g., grammar, sentence construction, word choice) in the rough draft.
Steve Ellner, one of the most important mathematical biologists of the past 25 years, has written a short piece that gives some good tips for writing about mathematical biology:
How to write a theoretical paper that people will cite
Peer reviews (10%, due 14 November)
The purpose of the peer review is two-fold. Each group will have at least five sets of eyes reading through their rough draft and providing feedback, which will really help each group to improve their report. More importantly, however, by reading someone else's project, you will return to your own project with new eyes - reading someone else's writing is one of the best ways to improve your own writing! When performing peer review, keep several questions in mind:
- Do I understand the big picture of this project?
- Do I understand how the biology was translated into a mathematical model and what assumptions are being made?
- Do I understand the analysis - how it is being done and why it is being done?
- Could I reproduce these results myself, based only on what is written?
- Are the results presented in a way that is attractive and informative?
The peer review will be graded! On November 14, everyone must either hand in or email one copy of their peer review to me, and one copy for the group whose draft they reviewed. Reviews will be graded based on effort and identification of strengths and weaknesses: did your comments indicate that you actually read and thought about the project carefully, did you clearly identify the things you thought the writers did well, and did you provide constructive suggestions for improvement? Oftentimes, one of the most important functions of a reviewer is to improve the writing: if you have thoughts about the order of ideas, grammar, sentence construction, word choice, etc. that you feel would improve the clarity and readability of the paper, share them!
Final draft (50%, due 3 December)
Click here for the final draft rubric.
The final draft should incorporate the feedback provided by the peer review, at the authors' discretion - just because it is suggested doesn't mean you have to do it!
Because being able to communicate ideas in written form is an absolutely essential skill, in science and in life, ~30% of the marks will be based solely on writing, and ~70% on how effectively you have achieved the goals of this project.
Self-assessment and assessment of group members (10%, due 3 December)
Click here for the assessment survey.