Bioinformatics Workshop 2013

Summer Bioinformatics Biology (BIOL 470.83/790.86, Spring 2013) Instructors: Che Martin & Slav Kendal Room:1000G HN (10th Floor, North Building Hours: Tues & Thur 11:30 am-15:00 Office Hours: Room 830 HN; Tuesday 3-5pm or by appointment Contacts: Mr Martin: cmartin@gc.cuny.edu; Mr Kendal: skendall@hunter.cuny.edu

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Course Description

Background

Biomedical research is becoming a high-throughput science. As a result, information technology plays an increasingly important role in biomedical discovery. Bioinformatics is a new interdisciplinary field formed by the merging of molecular biology and computer science techniques.Today’s biology students must therefore not only learn to perform in vivo and invitro, but also in silico research skills. Quantitative/computational biologists are expected to be in increasing demand in the 21st century.

However, the technical barrier to enter the field and perform basic research projects in a bioinformatics lab is daunting for most undergraduate students. This is mainly due to the multidisciplinary nature of quantitative biology, which requires understandings and skills in chemistry, biology, computer programming, and statistics. The Hunter Summer Bioinformatics Workshop aims to introduce bioinformatics to motivated undergraduate and high school students by lowering the barrier and dispensing the usual pre-requisites in advanced biology/chemistry courses as well as entry-level programming/statistics courses. The Workshop does not assume prior programming experience.

The workshop DOES NOT

• Replace existing advanced bioinformatics courses such as BIOL425 and STAT 319
• Teach advanced bioinformatics programming skills (e.g., advanced data structure, object-oriented Perl, BioPerl, or relational database with SQL), which are the contents of BIOL425
• Teach in-depth statistics or the popular R statistical package, although probabilistic thinking (e.g., distributions of a random variable, stochastic processes, likelihood, clustering analysis) is at the core of all bioinformatics analysis (STAT 319 teaches these topics)

To learn these advanced bioinformatics topics and skills, motivated students are encouraged to enroll in one of the Five Bioinformatics Concentrations of at Hunter. The QuBi program prepares the students for bioinformatics positions in a research lab or a biotechnology company.

Contents

This course will introduce both bioinformatics theories and practices. Topics include: database searching, sequence alignment, and basic molecular phylogenetics. The course is held in a UNIX-based instructional lab specifically configured for bioinformatics applications. Each session consists of a first-half instruction on bioinformatics theories and a second-half session of hands-on exercises.

Learning Goals

Students are expected to be able to:

• Approach biological questions evolutionarily ("Tree-thinking")
• Design efficient procedures to solve problems ("Algorithm-thinking")
• Manipulate high-volume textual data using UNIX tools, Perl and Relational Database ("Data Visualization")

Textbook

St.Clair& Visick, (2010). Exploring Bioinformatics: a Project-Based Approach. Jones and Bartlett Publishers, Sudbury, Massachusetts, Inc. (ISBN 0-978-7637-5829-5)

This book should be available through several popular retailers and resellers online.

Grading & Academic Honesty

Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records and official documents) as serious offenses against the values of intellectual honesty. The College is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.

Student performance will be evaluated by weekly assignments and projects. While these are take-home projects and students are allowed to work in groups, students are expected to compose the final short answers, computer commands, and code independently. There are virtually an unlimited number of ways to solve a computational problem, as are ways and personal styles to implement an algorithm. Writings and blocks of codes that are virtually exact copies between individual students will be investigated as possible cases of plagiarism (e.g., copies from the Internet, text book, or each other). In such a case, the instructor will hold closed-door exams for involved individuals. Zero credits will be given to ALL involved individuals if the instructor considers there is enough evidence for plagiarism. To avoid being investigated for plagiarism, Do Not Copy from Others & Do Not Let Others Copy Your Work.

The grading scheme for the course, is as follows (Subject to some change. You will be notified with sufficient time):

• Assignments (50%): 6 exercises (10 points each).
• Final exam (40%)
  • test
• Classroom Q & A (5%): Read the chapters before lecture.
• Attendance (5%): 1-2 absences = -2.5%. More than 2 = -5%.
• Email help: Include course code ("BIOL470", or "BIOL790") in the subject line