Introduction to Genome Bioinformatics, PLPTH 890

Research project

What you should do

What you can do

• Use new tools and methods we haven't studied (but in your report and presentation you must explain them well).
• Collaborate with classmates. If you do, you'll need to 1) specify this in your proposal, and 2)  be familiar with your partners' contributions to the project.
  
• Acquire noncommercial software packages and public datasets and install them on the course host machine or other suitable computer. Check with instructor for help.
• Consult instructors before and during the work, in order to identify resources or solve problems.
• Instead of attacking a problem,
• do a survey of some hot bioinformatics topic and demonstrate tools and approaches for addressing it, or
• develop a research proposal for a larger bioinformatics project, based on some preliminary results you collect. CN will supply guidelines if you choose this option. In this case the first proposal will be a preproposal -- literally, a proposal to develop a proposal.
  

What you shouldn't do

• Wet-lab work. You may use your own laboratory data, however.
  
• Get someone else to do part of the work, without having made this an explicit part of your proposal. You'll get credit only for the work you do yourself, alone or with the support of an approved collaborator.

Due dates

Proposal, report, and presentation

Follow CN's guidelines in all three of these productions. Start the proposal with a summary of what you propose to do, then proceed to any necessary scientific background. Treat this proposal as though you were requesting funding; that is, give the recipient enough information to enable a decision about the merit of your project. Would you give money to someone whose proposal amounted to the following?

"I will get some mosquito DNA sequence and try to find (or maybe write) some software to find ribosomal binding sites and then try to find some software to design primers."

This person hasn't taken the project seriously enough to devote an hour's effort to preparatory research, and hasn't told what and why, only presented the weakest of "hows".

Assessment

The grade on this project will take into account the quality of

1. the proposal:
   • is it well organized and written?
   • is it specific about the aims and methods of the project, including the software and database resources to be used?
   • if a collaborative effort, does it detail the roles of the participants and justify a joint approach?
   • is there hard evidence -- in the form of preliminary results -- that you have done enough preparatory research to give a reasonable idea of the size, and merit, of the project?
   • is the project likely to be bioinformatically interesting and to advance your bioinformatical knowledge and skill and that of classmates?
2. the report:
   • is it well organized and written?
   • have you followed the line of work proposed?
   • have you justified any change of direction? (It will help if you checked with the instructor before making major changes)
   • have you sought and applied appropriate tools and methods?
   • are the results nontrivial, giving evidence of a reasonably substantial amount of work that has advanced your bioinformatical knowledge and skill and that of your classmates?
   • if a collaborative effort, does it integrate the work of all participants in a way that justifies the collaboration?
3. the class presentation:
   • is it well organized?
   • does it show evidence of preparation both in delivery and in response to questions?
   • has the time requirement been met smoothly?
   • has the audience learned something useful?
   • if a collaborative effort, has each participant shown understanding of the work of the others?