Selected Topics in Zoology (Section 15716):
BIOL L506 (Z620) Fall 2015
Time & Location: Tu, Th 1:00p - 2:15p (Credits: 1.5); Ballentine Hall (BH) 118 (Tu), 107 (Th)
Instructors: Volker Brendel (205C Simon Hall; Tel.: 855-7074)
Tu, Th after class and by appointment.
Grades: will be determined as described below.
You will have access to networked computer terminals in class and will need such basic access outside of the classroom for assignments.
HTML version of this syllabus
SynopsisExtensive use of computing resources pervades all of modern biological and medical research. Bioinformatics is just one label for large-scale efforts to store and analyze data sets accumulating from both community and individual laboratory projects. This course provides a brief hands-on (keyboards and optical mouse) introduction to databases, Web servers, and workflow management systems that are widely used by biologists, independent of their particular research focus. The emphasis is on brief introduction, as the number of available databases (see 2012 NAR Database Summary Paper Category List) and Web services (see 2012 NAR Web Server issue and the Bioinformatics Links Directory) is overwhelming. Thus, out of necessity, we cannot cover the topic comprehensively. Rather, we will (collectively) seek to highlight and document use cases at selected sites, with the intent of developing appreciation of general principles and skills. An explicit goal of the class is to encourage students to eventually further develop their facility with bioinformatics and computational biology approaches, as taught in more advanced courses at IU.
PrerequisitesThis class is directed at first-year graduate students in the Biology Ph.D. program. Participants are expected to have passed the introductory BIOL L585 Molecular Genetics course. Enrollment preference will be given to students required to take this course.
Classes will be taught in a computer lab. Students are required to be familiar with basic computer operational skills, although no programming language knowledge will be assumed. Some class messages and materials may be shared through our Oncourse site in addition to these web pages and our course Wiki pages, and students are required to regularly check these relevant communication channels.
IU is committed to Creating a Positive Environment for teaching and learning. If you have any concerns or suggestions, please let the instructor know.
AssignmentsEach class period will cover a particular Bioinformatics2Go resource, to be announced on the class schedule. Students are expected to prepare for class by completing posted assignments prior to the class period. It is anticipated that each of these assignments will require about 3 hours of work outside the classroom. Each class period will begin with a review of the particular resource and a discussion of the completed assignments. Subsequently, students will be asked to solve more complex problems on the resource and document their approach and solution on dedicated course Wiki pages. Both in class and as part of the homework assignment, there will be randomized peer-review of the students' Wiki pages.
GradingGrades will be based on in-class participation and performance (30%) and an individual project (70%). Individual projects will be assigned after class on Thursday, Oct. 23, and will be due by Tuesday, Nov. 4, 23:59pm.
There is no textbook for the class. Students are highly encouraged to develop basic computer programming/scripting skills. There are a large number of online tutorials available on Linux, Perl, Python, R, specialized implementations such as Bioperl, etc. A particularly useful recently published text that serves both as a starting point and reference is "Bioinformatics Data Skills" by Vince Buffalo (O'Reilly, 2015).
Students are encouraged to review current research literature that provides many examples of application of the class topics. The following list provides a selection of relevant journals that are electronically accessible.