Introduction to Bioinformatics - COIN81
COIN 81 Syllabus
Welcome to COIN81, Introduction to bioinformatics, and bioinformatics tools and databases. This course is taught online in Spring Qtr. 2009. This course is intended to provide an introduction to bioinformatics tools, databases, and techniques available through the World Wide Web. Students should have a background that includes molecular biology, and especially awareness of sequence comparisons as a technique for establishing similarities in protein homology, function, and first approach structure prediction.
This course follows a path that introduces bioinformatics databases, including a thorough tour of NCBI, followed by protein resources including UniProt and EMBL. You'll gain significant experience with BLAST as well as an introduction to protein structure visualization in these first two sections. The course then introduces Biology Workbench, a tool hosted by UCSD, and emphasis on working within a "problem domain". You'll apply phylogenetics to understanding HIV mutation, retroviral proteins, the emergence of SARS, and then a scenario based study of avian influenza. In the final third of the course, you will work on genomics and proteomics systems, studying SNPs, haplotypes, microarrays and gene expression. In the last two week, we'll introduce advanced topics including systems biology and pathways, and synthetic biology and digital cells. The final week introduces BioPerl and XML as optional topics for advanced study.
This course can be completed in 12 weeks with about five to ten hours of effort per week, including becoming familiar with technical papers and current scientific research in bioinformatics. The text book, Bioinformatics for Dummies, is really quite fun to read, and offers a gentle guide to bioinformatics databases and techniques. Students are welcome to send email as required before enrollment to see if this course is right for you.
Assignments
There are five assignments in this class, and one or more midterms that are linked from the assignments page. Each assignment focuses on a key area, and roughly correspond to NCBI, genomics, proteomics, phylogenetics, and metabolic pathways. You'll describe you rjourney through each assignment, and turn in 'artifact's as required. I grade soley based on effort, so please do not be intimidated by the scope of an assignment.
Assignments are due in 2 to 3 week intervals - some take longer, some take less. Stay on task and you'll do well. No assignments may be submitted after the final day of class (June 28th) and there are no incompletes possible for this class. Ask for help early if you get behind. Assignments must be turned in through ETUDES, but if they include graphics, can also be sent attachments in email. Please limit file size to less than 1 MByte (zipped files)
Grading
Grading is by cumulative points. Each assignment is worth 20 points, and each midterm is worth 25 points. Total points possible in the course are 150. A = 135 - 150 points B= 120- 134 points C= 105 - 119 points D= 90 - 104 points. F = anything less than 90 points.
Hybrid Lectures and Office Hours
We will likely have a hybrid lecture on Wednesday evening, where we will cover the lecture of the week. I don't have formal office hours for this course - but I do reply to email very fast all throughout the week. This is still a fairly new course - so let's have fun, and use these tutorials to expand your knowledge into your area of research interst. You will learn to use the Web to "Surf the Genome".
Textbooks
I am recommending two or three books for this course depending on your biology and computer science background. Bioinformatics for Dummies is great for all students, and is the "official" book for this course. Bioinformatics Computing from Prentice Hall adds a little more technical explanation to these tools. For the technically gifted or those desiring more of a CIS perspective, Sequence Analysis in a Nutshell by Darryl Leon is a great book. I own all three, and all add a piece of the puzzle in learning your way around these Internet resources.
Errata
I think that's it - but as this course grows and forms new topics (based on your inputs and suggestions), expect changes in this website, and your helpful comments and patience are both appreciated.