Syllabus for Experimental Biology Lab Analysis of Biomedical data BSC 3402L-05 Spring 2014 David Houle

Transcription

1 Syllabus: Analysis of Biomedical Data Spring p. 1 Syllabus for Experimental Biology Lab Analysis of Biomedical data BSC 3402L-05 Spring 2014 David Houle TIME: T, Th. 2-4PM PLACE: King 1058 Instructor: David Houle Office: King 4063 phone: Office hours: M 11:30-12:30, T 4-5, Th 9:45-10:45 dhoule@bio.fsu.edu Research home page: Departmental home page: TAs David Aponte Office King 4055 Office hours TBA Phone daponte08@gmail.com questions to arrange other meeting times, or let us know of issues you have. Questions with answers of few words will be answered promptly. If you would like to go over more complicated questions please come to office hours, or arrange to meet with us at another convenient time. This syllabus lays out the basic procedures and policies that I will use to run this course. You should read all of the materials here. I will assume that all of you are familiar with these materials. I especially call your attention to the policies on late assignments, missed examinations, and the FSU honor code. Course Information The Blackboard site ( is how I will provide information to you about this course. Check this site regularly for information about such things as the schedule, assignments, etc. Most written material will be in pdf format. You will need a copy of Adobe Acrobat to view and print these pdf files. You can get a free copy from Adobe. If you do not know how to use the Blackboard site, please see us to learn how. If you are unable to use the internet for some reason we may be able to arrange alternative ways to get you the course material.

2 Syllabus: Analysis of Biomedical Data Spring p. 2 Description This course will use in-class exercises and discussion, some lectures, plus assigned readings and web-based material to teach you about how to read biomedical research, rate the quality of what you read, and to synthesize what you learn into a quantitative summary. I expect that students will attend class. Graded work will be participation in informal class exercises and discussions, three formal prepared class presentations, and written papers. Objectives Scientific knowledge is communicated in peer-reviewed papers in journals. One key skill necessary to take advantage of this accumulated knowledge is to be an intelligent reader of scientific papers. A second important, but less used, skill is to understand the strength of evidence accumulated in many paper on a specific topic. A third key skill is communicate what you know to a scientific audience. By the end of this course I expect students to be able to read and understand typical scientific papers, and to quantitatively summarize the evidence in them. I expect you to demonstrate these skills in oral and written presentations of your independent review on a biological or medical topic. Prerequisites Biological Science I and II, BSC 2011/2011L; Calculus or other math course. If you have had a statistics course, such as STA 2171: Statistics for Biology, you will have a leg up. Reading Readings of scientific papers will be assigned. Course work and grading This is the first time that I am teaching this course, so I want some details of my plans to remain flexible. The proportion of the grade that will be assigned based on each of the following major components will remain as presented, but I may decide to add or subtract specific assignments on this list.

3 Syllabus: Analysis of Biomedical Data Spring p. 3 Category Assignment Assignment grade Category grade In class discussion, informal Contributions to discussions, 18% presentations, Group project summarizing readings, literature searches, statistics, etc. Group project contribution 8% Total 26% Digital presentations Summary of paper for Group 4% project Proposal for Independent project 8% Final Independent project 14% Total 26% Written papers Summary of paper for Group 4% project Proposal for Independent project 8% Critiques of proposals 4% Completed Independent project 13% Critiques of projects 4% Revised Independent project 15% Total 48% The Group project will be a systematic review and meta-analysis that the class will perform together. We will pick a topic, refine that to a specific question, review the literature, decide on inclusion criteria, rate the quality of each paper, synthesize the results with a meta-analysis, then write up our results. In your Independent project, you will perform the same steps on a topic of your own choosing. You will give two presentations on your project one of a proposal, the second on your finished project. You will hand in three papers for this project your proposal, your completed project, and your revision of this project. As the term goes on, I will post additional information on these assignments section of the Blackboard site. Assignment Policy Work for this class should be produced by you, explicitly for this class. I expect you to observe the FSU Honor Pledge. It is particularly important for this class that you honestly present the facts you learn from the scientific literature. If you are having trouble finishing your assignment, come and talk to us about this before the due date, so we can talk about a possible exception to due dates. All problem sets and papers will be due by the BEGINNING of class on the due date. If you

4 Syllabus: Analysis of Biomedical Data Spring p. 4 come to class late when an assignment is due, your assignment is late. You will lose 20% of the possible grade for a late paper, and 5% per day after that. Calendar This schedule is tentative and subject to change. Month Day Topic Assignment: Readings Jan. 7 Types of papers Reading papers. Group project ideas. Chapter 3: How to read a Paper. Sui, X., M. J. LaMonte, J. N. Laditka, and et al Cardiorespiratory fitness and adiposity as mortality 9 predictors in older adults. JAMA 298: Quality of a paper. Seralini et al. paper. Group project ideas. Chapter 4: How to Read a Paper. Seralini, et al Food and Chemical Toxicology 50: More on Seralini et al. Defining a question: Literature searches. Group project definition Basic statistics Group project refinement Presentation of Paper summaries Arjo et al Transgenic Research 22: Panchin Food and Chemical Toxicology 53: 475. Seralini, et al Food and Chemical Toxicology 53: Breast cancer readings, assignment Guyatt, et al Users guides to the medical literature.2. How to use an article about therapy or prevention. Are the results of the study valid? JAMA - Journal of the American Medical Association 270: Levine, et al User s guides to the medical literature.4. How to use an article about harm. JAMA- Journal of the American Medical Association 271: Paper summary, written and oral Basic statistics Feb. 4 Statistics experiments 6 Quantifying Effect sizes Group project 11 Meta-analysis Group project 13 Meta-analysis 18 Group project activities Group project 20 Group project activities 25 Finishing the group project Group project 27 Consultations Independent project proposal March 4 Consultations 6 Consultations Critiques of proposals Spring Break Independent project proposal Proposal presentations 18 presentations Independent project proposal Proposal presentations 20 presentations 25 Independent project proposal Proposal presentations

5 Syllabus: Analysis of Biomedical Data Spring p. 5 presentations 27 Consultations April 1 Consultations 3 Consultations 8 Consultations 10 Completed projects due 15 Final presentations Final presentations 17 Final presentations Final presentations 22 Final presentations Final presentations 24 Final presentations Final presentations, Critiques of final projects 30 Revised projects due Honor Code I expect you to be familiar with and adhere to the University's academic honor code as described in the FSU Student Handbook. Any claim of ignorance of the honor code is unacceptable. The Academic Honor System of The Florida State University is based on the premise that each student has the responsibility to: Uphold the highest standards of academic integrity in the student's own work, Refuse to tolerate violations of academic integrity in the University community, and Foster a high sense of integrity and social responsibility on the part of the University community. The FSU Undergraduate Bulletin details the Honor Code. Plagiarism The vast majority of Honor Code violations that I deal with are plagiarism. Please note the following description of plagiarism from the FSU Academic Honor Code Presenting the work of another as one's own (i.e., without proper acknowledgement of the source). Typical examples include: Using another's work from print, web, or other sources without acknowledging the source; quoting from a source without citation; or using facts, figures, graphs, charts or information without acknowledgement of the source. Honor Code Violations Violations of the Honor code will be penalized severely, including the possibility of receiving a failing grade in the course. I do report all violations of the Honor Policy to the Dean of Faculties I am required to do so. If you are found to have committed such a violation, it will become part of your academic record. Students with disabilities

6 Syllabus: Analysis of Biomedical Data Spring p. 6 Students with disabilities needing academic accommodations should first of all let me know of your limitation, and suggest ways that we can help you surmount them. Formally, for the University procedure, you should: Register with and provide documentation to the Student Disability Resource Center (SDRC). Bring a letter to the instructor from the SDRC indicating you need academic accommodations. This should be done within the first week of class. For more information about services available to FSU students with disabilities, contact the Student Disability Resource Center 874 Traditions Way 108 Student Services Building Florida State University Tallahassee, FL (850) (voice) (850) (TDD) sdrc@admin.fsu.edu This syllabus and other class materials are available in alternative format upon request.