Genomics Research: Timeline and Benchmarks

The goal of this project is to have you do independent research exploring a question that reflects your own interests. Moving a scientific research project from conception to completion can be challenging or overwhelming. In particular, it requires moving forward with the refinement of the research question, an analysis of past work, and data collection, synthesis and interpretation all at the same time. I've provided the timeline and questions below to help guide you through this complex task. The reflective questions will help you think through challenges and revise your plans. They will also let me understand better how to help you.

Phase 1: Developing a feasible research question and plan

Due end of lab Thursday Nov 5:

While your research question will evolve in response to your research results, it is important to get a clear articulation of your starting question. You will want to refer back to this when you get overwhelmed by data analysis options. You will want to update your question if it changes markedly or becomes more narrowly focused as you begin to understand the data.

Record in lab notebook:

In a short paragraph, describe your ideas for a research question

Describe any challenges you are facing in trying to develop a research question. What seem to be the places where you are getting stuck or overwhelmed?

A critical part of research is tying to the work that has gone before. The scientific literature is the primary tool for doing this. Not only do you need to know what other people have concluded that is fundamental to your work, you will also findexamples of research methods and analysis strategies that will be useful as you move forward.

Provide citations for 3-5 papers that you have found that will help you further explore this question

Were you able to find papers that were clearly helpful? If not, can you summarize what you felt were the primary challenges?

Describe your approach(es) to finding these research papers

Doing scientific research is not unlike navigating through a city or mountain range. On the one hand you need to know where you are going. On the other, you have to modify your route as obstacles arise or you learn new things about the landscape you are traversing. Sometimes as a scientist you will decide you are not going where you had originally planned, that it is easier to go around an obstacle than over it, or that there are important new areas to explore. However, just as an initial plan is very valuable for a traveler, an initial plan for your research is essential to guiding your research and increases the odds that you will get to a useful and interesting conclusion. You will want to update your plan as you gain experience with the data analysis and learn new things.

In a short paragraph, describe a rough outline of which bioinformatic analyses you might attempt, including details of what databases and tools might be useful

What have been the primary challenges you have faced in identifying useful databases and using the bioinformatic tools

The details of your experiment/wet-lab study will probably be best decided after you have made some headway on the bioinformatics research. However, it is very valuable to start thinking toward that experiment at this time.

At this point in your project, do you have any rough ideas for an experiment or wet-lab study?

Phase Two: Moving Forward

One of the major challenges of research is getting caught up in the details and forgetting to synthesize results, think about how they related to one another, and reflect on whether your path is still the best one. I've provided two assignments that will help you make sure you are not leaving these important steps to the end.

Due in class Monday Nov 9:

• Your draft Introduction section, including background from literature, your research question, methods that you plan to use (bioinformatic study, experimental methods, wet lab methods) Please submit this by email.

Did you learn things in your literature review that made you rethink or refine your question?

Are their big gaps in your understanding of prior work that you still need to fill ?

Due Wed Nov 11

• Your plan for the wetlab/experimental aspect of your project. Please submit by email, using the following questionnaire Experimental Design Plan (Microsoft Word 35kB Nov9 09)
  

How does the wetlab/experimental aspect of your project complement the bioimformatics study?

Now that you have defined the wetlab/experiment, do you need to revise your bioinformatics study plan?

Due Thur Nov 12

• Your draft Materials and Methods section WITH a timeline of work. Please submit by email.
  

Does your research plan appear to be a path that will allow you to address your question?

Are there some pieces that should get priority over others? How will you know if you need to change your priorities

Phase III Wrapping up

Due before Thanksgiving

Now that you have all of your initial data have your research question changed?

What are your primary results and first order conclusions?

Due Monday Dec 7

Manuscript

Due Tuesday Dec 8

Presentation