Project Proposals are due Friday, March 6, 2020 by 11:59 PM. A representative from each group should submit a single pdf by email using the following filename structure (CSMProposal_Lastname1_Lastname2_....pdf).
- Find a partner or two. You must work in groups of two or three. Please let the instructors know if you are having trouble finding a partner and we will assist.
- Find a paper that describes a model you find interesting – biology, approach, etc. Some guidance on picking a research topic can be found here in this article by Uri Alon.
- Read it carefully and identify the key questions addressed by the model.
- What are the open questions? These can be explicit or ones that occur to you.
- Read some related papers to get a broader perspective and gather more ideas.
- How can the model be altered, extended, differently analyzed to address one or more of these questions?
- What tools will you need to carry out this extended investigation?
- What simulations, analyses, i.e., experiments, will you perform?
- What pitfalls might you encounter and what strategies will you use to overcome these?
Proposals should be no more than 1 page (not including references) and should contain the following:
- Background. Introduction that describes the biological context and previous models from which you will build.
- Aims. A succinct statement of the questions that you will address and how you will use modeling to address them.
- Approach. Description of what work you will perform and what tools you will use. Be as specific as possible here. Think in terms of the figures that you might obtain as results.
- Possible pitfalls. Describe problems that you anticipate and possible strategies for overcoming them, e.g., how will you estimate parameters for new interactions in the model if you are unable to find estimates in the literature? What if the simulation tool you are using doesn’t provide facility for an analysis you need to perform?
- References. Provide references to all papers that are providing, background, models, or data that you are using for your project. These should all be cited in the preceding sections of your proposal. If your proposal is building on a model that was previously developed, it should clearly indicate which reference that model is coming from.
In keeping with the themes of the course projects should focus on mechanistic as opposed to statistical models, i.e., models that have predictive capabilities independent of the data to which they are fit. If you have any doubts about the suitability of your topic for the course, please consult one of the instructors. If you submit an off-topic proposal, you will be asked to rewrite it.
You may not 'recycle' papers or reports that you wrote for some other class or as part of a research project.