Syllabus
Course Information
Course Number and Title: CS 642 Bioinformatics Research
Location: Harney Science Center 235
Schedule: M W 4:45-6:25pm
Website:http://www.cs.usfca.edu/~pfrancislyon/courses/642/syllabus.html
Class email list: go to groups.cs.usfca.edu
Instructor: Patricia Francis-Lyon
Email: pfrancislyon (at) cs (dot) usfca (dot) edu
Phone: (415) 422-2810
Office: Harney Science Center 542
Office Hours: M 9:15-10:15 am, 1-3 pm; 6:30-9 pm (or if SLS speaker, then 7:30 - 10 pm), W 1-3 pm; F 1-2 pm; Also by appointment
Learning Outcomes
- Students will gain experience in the field of bioinformatics by either undertaking a research project in the field
or creating a tool for use by the scientific community.
- Students will gain understanding of bioinformatics subject matter while creating computational and algorithmic solutions that are of value to biologists and chemists.
- Students will gain experience in the verbal and written presentation of their work to others.
While no prior coursework in bioinformatics is assumed, to succeed in this class you must be willing to
come up to speed in the background knowledge necessary for your project.
Schedule
Tentative schedule of progression of the course with due dates.
Resources
Bioinformatics Resources: research papers, textbooks, software, slides
There is no required text for this class. Bioinformatics texts are listed in Bioinformatics Resources
Grading
Choose Option 1 OR Option 2
Option 1 is Creation of a Software Tool for a Sponsor
Option 2 is Academic Research
| 1. Develop Software Tool | 2. Academic Research |
| % | Assignment | % | Assignment |
| 5% | weekly status reports | 5% | weekly status reports |
| 10% | Topics | 10% | Topics |
| 25% | status reviews (3):
Status Review 1 (8%)
Status Review 2 (9%)
Status Review 3 (8%) |
25% | status reviews (3):
Status Review 1 (8%)
Status Review 2 (9%)
Status Review 3 (8%) |
| 10% | final documentation (10%) |
20% | drafts* (4):
draft Intro(5%)
draft Methods(5%)
draft Discussion (5%)
figure, draft Conclusion (5%) |
| 10% | Project Specification | 5% | Research Proposal |
| 10% | presentation | 10% | presentation |
| 5% | test suite, figure | | |
| 15% | final project quality | 15% | final project quality |
| 10% | final deliverables | 10% | final paper |
* A poster pesentation at a conference may substitute for the paper and all drafts
weekly status reports should take about 10-15 min for you to write, and up to 5 min for me to read.
They should contain a list of what you've accomplished for the week, and any problems you've identified or solved.
They should include amount of time you put into each task. (You are expected to spend an average of 15+ hours per week on your project, but will have some class time to work with your team.)
Weekly reports and emails to sponsors are due on Blackboard Sunday night, beginning Feb 3rd.
Please upload a description of your project and list of team members Mon Jan 28th.
Mapping to Letter Grade
100 - 93.0 : A
92.9 - 90.0 : A-
89.9 - 87.0 : B+
86.9 - 83.0 : B
82.9 - 80.0 : B-
79.9 - 77.0 : C+
76.9 - 73.0 : C
72.9 - 70.0 : C-
69.9 - 67.0 : D+
66.9 - 63.0 : D
62.9 - 60.0 : D-
59.9 - 0 : F
Late Policy
Students are responsible for meeting all assignment and project deadlines. In general, late work will not
be accepted. If an emergency arises and you are unable to meet a deadline, please notify the instructor
beforehand to avoid a grade penalty.
Students are responsible for keeping backups of written assignments and project files until the course is
over. Extensions will not be granted for lost work.
Academic Honesty
Academic Honesty
We will adhere to the University's Student Academic Honesty Policy.
In this course you must do your own work, unless you credit others for their contribution.
There will be absolutely no copy-pasting of the work of others unless contained in quotation marks and properly referenced. Non-quoted ideas of others must be paraphrased by you and cited.
If you are part of a team, and do not contribute your share to the team effort you will not earn the same grade as those who do contribute, your grade will be lowered.
Note: This syllabus is subject to change.