PLPTH 613
Bioinformatics Applications
Spring 2009
Schedule
Research project
 K-State Online

Research project

What you should do

Tackle a scientifically interesting problem that's neither trivial nor unrealistically hard, making effective use of bioinformatics tools, methods, and principles. If you have your own data, you're welcome to use it. If you use enough of the methods we learned in the second half of the semester, you will not need to take the final exam (this must be arranged with the instructor!).

What you can do

  • Use new tools and methods we haven't studied (but in your report 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.
  • 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 can'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

Output
 Date due
 Specifications
Research-project proposal (or preproposal)
 4/16/09
 1 - 2 pages, three sections: 1) Summary What is the proposed outcome? 2) Introduction What is the problem background? 3) Methods What is your plan of work?
Project report 5/8/09
 Follow guidelines for standard scientific reporting and presentation

Proposal and report

Follow CN's guidelines in both 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.

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?
  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 reasonable 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?