HomeMy WebLinkAboutBIO-211Bergen Community College
Division of Mathematics, Science, and Technology
Department of Biology and Horticulture
Introduction to Bioinformatics (BIO-211)
General Course Syllabus
Spring 2016
Course Title: Introduction to Bioinformatics (BIO-211)
Course Description: This course is designed to give students both a
theoretical background and a working
knowledge of the techniques employed in
bioinformatics. Emphasis will be placed on
biological sequence (DNA, RNA, protein)
analysis and its applications.
Prerequisites: BIO 101 General Biology I and BIO 210
Introduction to Biotechnology
General Education Course: No
Course Credits: 3.0
Hours per week: 4.0: 2 hours lecture and 2 hours lab
Course Coordinator: John Smalley
Required Textbook; Practical Bioinformatics, 1st ed., Agostino,
M., Garland Science, 2013
Required Lab Manual: None
Student Learning Objectives
The student will be able to:
1. Students will become familiar with a variety of currently available genomic
and proteomic databases. Assessment will be based upon performance on
computer assignments and exam questions.
2. Students will be able to search and retrieve information from
genomic and proteomic databases (e.g. GenBank, Swiss-Prot), and to
analyze their search results using software available on the internet
(e.g. BLAST, ClustalW). Assessment will be based upon performance on
computer assignments and exam questions.
3. Students will learn how to compare and analyze biological
sequences and how to interpret the results of their analyses. Assessment
will be based upon performance on computer assignments and exam questions.
4. Students will learn how to construct phylogenetic trees based
on biological sequence data. Assessment will be based upon performance
on computer assignments and exam questions.
5. Students will be able to locate consensus sequences,
genes and open reading frames within biological sequences. Assessment
will be based upon performance on computer assignments and exam questions.
6. Students will become familiar with the principles and
applications of microarrays. Assessment will be based upon performance
on exam questions.
7. Students will be able to perform elementary predictions
of protein structure and function. Assessment will be based upon
performance on computer assignments and exam questions.
8. Students will be able to perform elementary comparative genomic analysis.
Assessment will be based upon performance on computer assignments and exam questions.
9. Students will use the scientific method of inquiry, through the acquisition of scientific knowledge.
10. Students will use computer systems or other appropriate forms of t echnology to achieve educational and personal
goals.
Student Assessment Tools:
The above student learning objectives will be generally assessed or evaluated by instructors
using a variety of assessment instruments including lecture exams, laboratory exams, quizzes,
laboratory reports, written reports, presentations, projects, etc. The decisions concerning the
type or types and number of instruments that are used in a specific section of the course will be left
to the instructor of that section. This information, when given by the instructor should be recorded
by the student in the Student Assessment Section of this document.
Course Content (Lecture):
Week 1 Introduction, Review of DNA replication, transcription, and translation, Genome
organization
Week 2 Review of molecular biology methods
Week 3 Introduction to DNA and protein databases, data
storage, file formats, information retrieval
Week 4 Database queries, sequence retrieval, Creation of
restriction endonuclease maps
Week 5 Dot plots, Sequence alignment, Local alignment, Global
alignment, Multiple alignments
Week 6 Sequence alignments continued, Alignment scores,
Statistical significance of database searches
Week 7 Genetic distances, Distance based phylogenies, Phylogenetic tree construction
Week 8 Phylogenetic tree construction continued, Character based phylogenies
Week 9 Consensus sequences, Finding genes and open reading
frames in DNA sequences
Week 10 Microarrays and the transcriptome
Week 11 Microarray analysis and applications of microarrays
Week 12 Introduction to proteomics
Week 13 Prediction of protein structure and function
Week 14 Prediction of protein structure and function continued, Comparative genomics
Week 15 Comparative genomics continued, Future directions of bioinformatics
Course Content (Laboratory):
Week 1 Introduction to NCBI
Week 2 Navigating the NCBI website
Week 3 Performing keyword searches of the Online Mendelian
Inheritance In Man (OMIM), NCBI Taxonomy, NCBI Genome, and Swiss-Prot
Databases
Week 4 Sequence retrieval from genomic databases, Restriction
endonuclease mapping
Week 5 Comparison of sequences using Basic Local Alignment
Search Tool (BLAST), Interpretation of BLAST search results, Local
Alignment using L-Align
Week 6 Global Alignment using MatGAT, Multiple Alignment
using Clustal
Week 7 Construction of distance based phylogenetic trees
Week 8 Construction of character based phylogenetic trees
Week 9 Determination of consensus sequences, locating genes
(gene prediction) and open reading frames in DNA sequences
Week 10 Gene prediction II
Week 11 Prediction of protein structure and function I
Week 12 Prediction of protein structure and function II
Week 14 Comparison and analysis of whole genomes I
Week 15 Comparison and analysis of whole genomes
Student Assessment: Lecture Examinations %
Laboratory Component %
Student Project/Report %
Class Participation %
Other %
Total 100%
If you have a medical condition or develop a medical condition during this
semester, which prevents you from fulfilling the requirements of this course, you
must notify your physician. You and your physician must decide whether or not it
is appropriate for you to remain in this course. If the decision is to remain in this
course, please obtain a letter from your physician indicating that your continued
participation in this course is appropriate and present it to the Department Chair.
Faculty Addenda: As per individual faculty member
Lecture Attendance: As per instructor;
Lab Attendance: As per instructor;
Policy Concerning Late Assignments: As per instructor;
Policy Concerning Make-Up Testing: As per instructor;
Safety Information: As per instructor and assigned exercise;
College Policies:
Student Responsibility
Students will be held responsible for reading all pertinent information in college publications
regarding withdrawals, course drops, college deadlines, and tuition refunds. Students are
responsible for compliance with the rules and regulations as stated in college publications.
Absence of Instructor
Students are expected to wait twenty minutes for a faculty member to come to class. If at the end
of twenty minutes, the faculty member does not come, the students should sign an attendance
sheet, which indicates the course, date, and time. A student should deliver the attendance sheet to
the divisional office (A304) if between 9:00 a.m. and 5:00 p.m. or to the Evening Office (C107) if
before 9:00 a.m. or after 5:00 p.m. Students cannot be penalized by faculty for not waiting longer
than twenty minutes.
Academic Dishonesty and Plagiarism
Bergen Community College is committed to academic integrity – the honest, fair and continuing
pursuit of knowledge, free from fraud or deception. Students are responsible for their own work.
Faculty and academic support services staff will take appropriate measures to discourage
academic dishonesty. Plagiarism is a form of academic dishonesty and may be a violation of U.S.
Copyright laws. Plagiarism is defined as the act of taking someone else’s words, opinions, or ideas
and claiming them as one’s own.
Consequences of Violations Academic Integrity
A. Instructor’s Sanctions for a Violation
The faculty member will determine the course of action to be followed. This may include:
• Assigning a failing grade on the assignment;
• Assigning a lower final course grade;
• Failing the student in the course
• Other penalties appropriate to the violation;
In all cases, the instructor shall notify the Vice President of Student Services of the violation and
the penalty imposed. The student has the right to appeal the decision of the instructor to the
appropriate department head.
B. Institutional Sanctions for Violations
When a violation of academic integrity has been reported regarding a student, the Vice President
of Student Services may impose disciplinary penalties beyond those imposed by the course
instructor, which may include suspension or dismissal from the College. The student shall have the
right to a hearing before the Vice President of Student Services or a designated judicial affairs
committee. Judicial procedures governing violations of academic integrity are contained in the
student handbook.
Class Attendance
All students are expected to attend punctually every scheduled meeting of each course in which
they are registered. Attendance and lateness policies and sanctions are to be determined by the
instructor for each section of each course. These will be established in writing on the individual
course outline. Attendance will be kept by the instructor for administrative and counseling
purposes.
Eating and Drinking
Eating or drinking in classrooms, lecture rooms, laboratories, gymnasium, swimming pool, or
passageways is forbidden. Covered beverages only are permitted in the library. Eating and
drinking are permitted in cafeteria and vending areas only.
Learning Assistance
Henry and Edith Cerullo Learning Assistance Center
The Tutoring Center, English Language Resource Center, Math Walk-In Center and Writing
Center are collectively known as the Henry and Edith Cerullo Learning Assistance Center. The
Cerullo Learning Assistance Center is located in the Pitkin Education Building, in Room L-125.
The telephone number is (201) 447-7489. The Learning Assistance Center, staffed with peer and
professional tutors, offers free individual and group tutoring, supplemental instruction, and online
tutoring for subjects offered at the College. The Center provides alternative approaches to problem
solving and organizational skills. Tutors help clarify classroom lectures and textbooks and help
students prepare for exams. These services build student self-confidence and reduce fear of
failure. The Center is equipped with the latest technology and software, including tapes, books,
review sheets, exercises and software.
Services for Students with Disabilities
Bergen Community College aims to create inclusive learning environments where all students
have maximum opportunities for success. Any student who feels he or she may need an
accommodation based on the impact of a disability should contact the Office of Specialized
Services at 201-612-5269 or via email at ossinfo@bergen.edu for assistance.
Sidney Silverman Library
Main Building, Pitkin Education Center, L-wing, 2nd Floor.
Paramus Library Hours: (201) 447-7131 or visit http://www.bergen.edu/library/calendar/gcal.htm
Paramus Service Desk: (201) 447-7970
Meadowlands Location: 1280 Wall Street, Lyndhurst 2nd Floor
Meadowlands Library Hours: http://www.bergen.edu/library/calendar/gcal.htm
Meadowlands Service Desk: (201) 301-9692
www.bergen.edu/library
Testing Services
The Bergen Community College Office of Testing Services (OTS) is located in Room S-127. OTS
serves the college community by identifying, developing, procuring, administering, processing,
and/or evaluating examinations, which meet a variety of administrative and instructional needs. To
contact the OTS, please call (201) 447-7202. The Office of Testing Services administers makeup
tests as a service for students who, for compelling and exceptional reasons, have missed a
scheduled classroom examination. Students must receive prior permission from and make
arrangements with their course instructors to take these examinations, under specific conditions, in
the Office of Testing Services, Room S-127.
WebAdvisor
WebAdvisor is a web interface that allows students to access information contained in Datatel’s
Colleague, the administrative database used by Bergen Community College. Students may use
WebAdvisor to register for classes, to pay tuition and fees, to view their class schedules, to check
grades, to check on progress toward degree requirements, etc. WebAdvisor accounts are
available for all students enrolled in credit programs. New students are strongly encouraged to
attend an in-person registration or advisement session before using a WebAdvisor account.
Eligible students without WebAdvisor user names and passwords may access their WebAdvisor
account by going to go.bergen.edu and selecting “I’m new to WebAdvisor.” Then, follow the on-
screen directions. Check the WebAdvisor FAQ for answers to common questions, such as how to
reset your password. Students must have a valid e-mail address on file with the College to use
WebAdvisor