Students and faculty will develop and share professional interests while discussing current trends and developments in bioinformatics and biotechnology. Students will develop and then assess literature reviews.
| Meeting Location: | WAL-4560 |
| Meeting Time: | MWF 12-12:50pm |
| Credits | 3 |
| Instructor: | Michael Osier |
| Office: | 08-1338 |
| Instructor Schedule | Schedule |
| Email: | mvoscl@rit.edu |
Under certain circumstances, the instructor may have to alter course requirements, assignment deadlines, and grading procedures; and the university may have to alter the academic calendar.
| Week | Topic | Slot A | Slot B | Slot C |
|---|---|---|---|---|
| Week 1 - Aug 25 | Introduction and Background | Course Introduction/Organization | Sample review - Reading Beta | Schedule readings presentations |
| Week 2 - Sept 1 | Article anatomy | No class Monday | Structure of a scientific article - Kesel et al. | Background/Introduction |
| Week 3 - Sept 8 | More anatomy | Results | Results - what goes into a good figure or table? | Discussion |
| Week 4 - Sept 15 | Dissection | Materials/Methods and Abstract | Readings A - Sample research papers | Readings B - Sample review articles |
| Week 5 - Sept 22 | Genomics | Readings C - Short-read sequencing | Readings D - Long-read sequencing | Readings E - Assembly/Alignment |
| Week 6 - Sept 29 | Transcriptomics | Readings F - Genomics/transcriptomics/proteomics | Readings G - RNA Seq | Readings H - Single cell sequencing |
| Week 7 - Oct 6 | Literature review - Vaccine trials | Literature background checks | Half-time, team formation and brainstorm | Readings I - Phase 1 and 2 trials, Team topics due |
| Week 8 - Oct 13 | Treatment development - Vaccine trials | No class Monday | Readings J - Phase 3 and 4 trials | Readings K - Covid vaccine trials |
| Week 9 - Oct 20 | Renewable energy | Readings L - Ethanol production | Readings M - Rapid crop growth | Readings N - Algal engineering |
| Week 10 - Oct 27 | Proposal development | Faculty team review | Deeper background literature searches | Faculty team review |
| Week 11 - Nov 3 | Agricultural biotechnology | Readings O - Drought tolerance | Readings P - Salt tolerant rice | Readings Q - Pest resistance - Online |
| Week 12 - Nov 10 | Peer evaluations | Peer evaluations - reviews due Sunday at the end of this week at midnight | ||
| Week 13 - Nov 17 | Revision | Faculty breakout to discuss peer evaluations | Current challenges in biology | Team revision breakout discussions |
| Week 14 - Nov 24 | Revision | Online activity - Literature review cleanup - revisions due at midnight | Thanksgiving break | |
| Week 15 - Dec 1 | Peer re-evaluations | Peer re-evaluations - reviews due Friday at midnight | Current challenges in bioinfo and comp bio | |
| Week 16 - Dec 8 | Closure | Course discussion | Exam period - wrap-up, final reviews due | |
| Paper presentations | 30% | |
| Literature reviews | Literature searches | 8% |
| Article draft | 5% | |
| Peer evaluations | 7% | |
| Article revisions | 6% | |
| Faculty team reviews | 5% | |
| Peer re-evaluations | 7% | |
| Final articles | 12% | |
| Participation | 20% | |
| Total | 100% | |
|---|---|---|
| A | [95-100] | B+ | [86.7-90) | C+ | [76.7-80) | ||||
| B | [83.4-86.7) | C | [73.4-76.7) | D | [60-70) | F | <60 | ||
| A- | [90-95) | B- | [80-83.4) | C- | [70-73.4) | ||||
Paper Presentations and Discussion: Grades will be in-part based on presentations to the class and participation in discussions of the presentations. All discussion sessions will be divided evenly among students during the final lecture of the first week of the semester. If you cannot make the class in which they are assigned, please inform the instructor as soon as possible.
Students are required to speak with the instructor well before their presentation. This is intended to help you give the best possible presentation. Appointments must be at least one week (7 full days) in advance of the presentation date to give you sufficient time. Failure to meet with the instructor far enough in advance to discuss a paper will result in a 50% grade reduction for that presentation. Note that presentations are not necessarily in order by reading letter! Please pay attention to which week your presentations are.
Individual presentations will be evaluated by the class using a standardized scoring sheet. The final grade for that presentation will be determined by the instructor based on these evaluations and his own. Presentations are expected to cover the major points of the paper, as discussed with the instructor during the required meeting. Overlap with previous presentations, for the topic and for the student, should also be minimized.
Participation grades will be determined through a combination of attending class on time and for the full session, filling out scoring sheets for presentations, and instructor assessment of student engagement.
During the course, students will form teams to develop their own literature reviews of a relevant topic of interest and evaluate the reviews of other teams. Evaluations will be done by rubrics. Each literature review will go through a development process, with faculty guidance, and individual components to the final grade.
Literature reviews may not be historical reviews or purely clinical. There must be a bioinformatics component.
The final literature review should be 15-20 pages long, double-spaced. Citations will not count for or against the page limit. Excessive quotes and figures/tables are strongly discouraged.
Note that articles marked "[online]" are available from myCourses under Content.
For the first offense, anyone caught plagiarizing or otherwise cheating will receive a 0 (zero) on the assignment/exam, and be referred to the Head of the School of Life Sciences. In the event of a second offense, the student will receive an "F" for the course. If you have any questions about whether or not something constitutes plagiarism and/or cheating, please ask the instructor in advance. Duplicate submissions will also receive a grade of 0 (zero) for the first incident. In the case of especially egregious offenses, the instructor reserves the right to assign a grade of "F" for the course, as per RIT policy.
You are encouraged to work with each other in person and through discussion groups, but must in the end write your own work. Sufficient evidence of cheating on a workshop or homework will be treated the same as for plagiarism or cheating in any other part of the course. The assignments will be automatically checked for cheating.
Also be aware that for this course the use of AI will be cheating. Note that AI is faulty, and can give incorrect answers. So using AI doubles your risk. It also reduces your practice of the course material, which will set you behind for later assignments and other courses.
The legal use of distributed material is strictly limited to course activities, and not activity outside the course. The use of copyright protected material outside of this RIT course may be prohibited by law.
Unless written permission is granted by the faculty member, or a specific accommodation has been approved by the Disability Services Office, students are prohibited from recording lectures or presentations as audio or images/video.
Contents last updated 4/15/25