Grading

Research Proposal

Each student will choose a research project in consultation with the instructor, and prepare a written research proposal (~5 pages) that outlines the project design, major methods to be used, and experimental goals. Many will have a project proposal already, and it will be ok to use a modified version of that, as long as it follows the guidelines below (i.e. don't give me a 20 page proposal, and do present molecular methodology). The main aim of this proposal is to make sure that there are clearly defined aims addressing a specific problem, apropriate molecular methods and an appreciation of the wider significance of the work - all these are prerequisites for the planning and execution of a successful project.

The basic elements of the proposal should be

1. A Cover Page with name and afiliation and a project summary of no more than 200 words

2. A Project Description, which is limited to 5 single-spaced pages including figures and tables. Font should be 12pt Times New Roman or equivalent. The main body of the proposal should present, in sufficient detail to permit evaluation, a description of the project, including:
a. Introduction: background to your proposal; any work on the subject, published or unpublished, especially studies using molecular genetics
b. Specific statement of aims and objectives
c. Methodology: sample collection, molecular methods, data analysis and interpretation
d. Broader significance: how does addressing the aim help in a broader context (e.g. conservation, management, engineering, etc)

4. A Timeline of work to be carried out, which should indicate how long you think each step is going to take. Bear in mind that you will only have 6 weeks to carry out the work. If you plan to carry out only part of your work in the course, your proposal timeline should identify this part and provide an estimate for the time needed to carry out the remaining work.

5. A budget detailing costs for general consumables, primers, and MegaBace runs (see example and list of costs of commonly used items). All items that are 'included with limitations' (see course fee page) in the course fee should be included in the budget.

6. References - as many as you need, but at least 10-15.

The instructor will be available during labs and by appointment to help with the proposal preparation and with the interpretation of published research. Here is also an example of a proposal - this one is rather ambitious, because it actually was a (funded) research proposal in my old lab (Hull, UK), but it should give you an idea how things should be structured. Contact me if there are any questions or problems.

Proposals are due at the end of week 2 (Friday, Jan 16, 2004). Submit your proposal as MSWord file by e-mail from your own e-mail account.

Proposal Review

Research Proposals will be distributed by e-mail to two students for anonymous peer review - that means that everybody in the class will get two proposals to review. The main idea of these reviews is for you to obtain feedback on your own proposal, and to learn about reading, evaluating and commenting on other people's work - you will be asked to do that frequently in your scientific career.

Reviews should not be longer than 2 single-spaced pages and are due by the end of week 3 (Friday, Jan 23, 2004). If you wish to remain anonymous to the proposal author you may do so, but I would encourage discussion among you.

Review Guidelines

• Peer reviews will not affect the grade of the proposal, so don't feel that you have to be overly positive to save your classmate's grade.
• Review the proposal as you would like to have your proposal reviewed - be constructive and helpful. Be polite - criticize, but stay constructive, and don't be rude
• First read the entire proposal without commenting; resist the tempation to provide specific comments straight away. then read it again and comment
• Think about the big picture - although grammatical and stylistic comments are useful, comments on scientific content are most relevant.
• Most funding bodies provide only very sketchy forms guiding the review. Below are some criteria for your review - you should try to comment on each of these, but do not feel obliged to be equally detailed about each point. Also, have a look at the Proposal Review Guidelines page of the University of Massachussetts, but don't worry about the applicant's qualifications - that's why you are in this class!
• If you wish to remain anonymous, do not edit the MSWord file sent to you (the edits will show your name).

• Significance and originality of proposed work
• Review of project background and current knowledge
• Statement of specific aims
• Presentation and detail of molecular methods
• Suitability of molecular techniques
• Strengths of Proposal
• Weaknesses of Proposal
• Clarity of presentation
  

I will add my own comments to the reviews to provide feedback on your proposals. You should use this feedback for your project, and for the final report.

Lab Notebooks

Each student should keep a lab notebook that records each day's activities. The lab notebook should be well organized and neat enough that someone else (not previously familiar with the work) could interpret what was done. You rarely write down too much, but it can easily happen that you want to go back to specific details of an experiment and haven't made a note of an important detail. In particular, you should note down which protocols you used, any deviations from that protocol, and any errors or mishaps. Consider that you may want to go back to your notebook years or even decades later. Some useful guidelines on writing lab notebooks can be found here.

You may show your lab book to the instructor along the way to see whether you are noting down the right amount of detail. We will collect and grade lab notebooks twice during the quarter.

Lab Participation

The class will be open access (that means, you have access to the lab within the building opening hours, 8am - 5 pm), but we will expect students to attend the lab sessions on Tuesday and Thursday. We also expect you to participate in experiments, and to make efforts to get your own project to work.

Discussion Participation

We will meet weekly on Tuesday (13:30) in room FTR 103, where we will discuss progress and any upcoming problems as a group. These sessions are only useful if students participate in the discussion, ask questions and suggest solutions. At some point around the middle of the quarter, we will hold a lab meeting in room FTR 103, in which each student will informally present his/her project and progress to date. Participation in this discussion will also be part of the Discussion Participation grade, which in total will count for 15% of the grade.

Presentation

At the end of quarter students will present the results in a short (10-12 min) presentation on their work using powerpoint or overheads. This presentation should include the aim of the project, molecular methods used, results to date, interpretation and further plans. This presentation will count for 10% of the grade. Constructive criticism by other students will count towards the discussion participation grade. See also workshop program.

Report

In the final week, students will submit short written report based on their proposals and lab notebooks. This report should be structured like a scientific paper (Abstract, Introduction, Material & Methods, Results, Discussion, References), and should present, in sufficient detail, the methods used, all the results and their interpretation as well as suggestions for further work. Reports should consider comments made on proposal, during the class and after the presentation. Maximum length of this report is 8 single spaced pages, excluding abstract and references (though it can be much shorter). This final report counts for 20% of the grade. Have a look at the 'How to write a scientific paper' page of Bates College.

Late work

All assigments have to be e-mailed to me from your own account by the deadline. Late work will incur a penalty of 10% a day. If you have problems finishing your assignment, come to me and discuss it.