Course Information

Course Number and Title: CS 642 Bioinformatics Research
Location: Harney Science Center 235
Schedule: M W 4:45-6:25pm
Class email list: go to

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

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.


Tentative schedule of progression of the course with due dates.


Bioinformatics Resources: research papers, textbooks, software, slides
There is no required text for this class. Bioinformatics texts are listed in Bioinformatics Resources


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.