Please take a moment to review this syllabus. It contains important information about grading, academic honesty, and privacy guidelines.
PREREQUISITES
This course is designed for students who have a basic understanding of biology and who have already taken their first steps programming (although we have found that our materials engage experienced programmers as well).
TIME COMMITMENT
4-10 hours/week .
COURSE DEADLINES
This course is self-paced - you can access all course materials when the course begins, and assignments do not have due dates. You can complete course material at any time before the course end date.
Course content
Welcome! A brief introduction to the course and its logistics.
Week 1: A Journey of a Thousand Miles. . . What does a cryptic message leading to buried treasure have to do with biology? Many cellular processes are encoded as "secret messages" within an organism's DNA. But how do we decipher these messages?
Week 2: Finding Replication Origins. We examine the details of DNA replication and apply these details to design an intelligent algorithmic approach to find the replication origin in a bacterial genome.
Week 3: Hunting for Regulatory Motifs. Your cells "tell time" and maintain your circadian clock by turning genes on and off during the day in set patterns. This brings us to a different kind of "secret message" problem in biology: how do we find the motifs hidden in DNA that switch on genes? We develop introductory algorithms for motif-finding in genes.
Week 4: How Rolling Dice Helps Us Find Regulatory Motifs. We see how to improve upon these motif-finding approaches by designing randomized algorithms that can "roll dice" to find motifs and perform quite well in practice.
Week 5: Finishing Up
- Bioinformatics Application Challenge: Motif-Finding. We use popular software built on the motif-finding algorithms that we learned to hunt for motifs in a real biological dataset.
- End-of-the-Course Assessment. In an end-of-the course assessment, we will ask you to answer Course Review questions. This will give you the opportunity to let us know how the course went for you. This assessment will provide data for our research study and will help us improve our courses for future learners.
Grading
- Interactive Textbook code challenges - 60% (15% each week).
- Quizzes - 20% (5% each week)
- Application Challenge - 10%
- End-of-Course Assessment - 10%
Each problem or quiz question is worth a number of points as indicated. Questions in the Application Challenge are mostly Open Response, and you will be asked to evaluate your own answers after submission. We are encourage you to provide your opinion or feedback for these questions.
Questions in the End-of-the-Course Assessment are intended to check your understanding of the material, and will be evaluated by instructors.
Certification
The passing grade for this course is 70%. You can find your current score on the Progress page.
EdX provides certificates to those who have passed the course and verified their identity. If you achieve a passing grade in this course you are eligible for a Verified Certificate. Your certificate will indicate you have successfully completed the course, but will not include a specific grade.
You can find out more about self-paced courses and certification at the EdX Learner's Guide.
Academic Honesty
All assignments in this course are subject to the edX Terms of Service & Honor Code. As such, your answers should be your own and should not be taken from other students, or from the rubric in previous sessions. Violations of the honor code will be taken seriously.
Contacting Course Staff
Course staff can be contacted on the discussion boards, by creating a new post with the word [STAFF] in the title. Issues will generally be addressed within 24 hours. Please use this for technical matters only, not for questions about the course's science content.
Research
In this class, we are conducting a learning experiment, which means that not all students will see the same questions or learning materials, or see them in the same locations.
By registering as an online learner in our open online courses, you are also participating in research intended to enhance UC San Diego instructional offerings as well as the quality of learning and related sciences worldwide. In the interest of research, you may be exposed to some variations in the course materials. UC San Diego does not use learner data for any purpose beyond the University's stated missions of education and research. For purposes of research, we may share information we collect from online learning activities, including Personally Identifiable Information, with researchers beyond UC San Diego. However, your Personally Identifiable Information will only be shared as permitted by applicable law, will be limited to what is necessary to perform the research, and will be subject to an agreement to protect the data. We may also share with the public or third parties aggregated information that does not personally identify you. Similarly, any research findings will be reported at the aggregate level and will not expose your personal identity.