Introduction to Bioinformatics
Biology 416, 730C – Fall 2011
Class Meetings:
Meeting Time: 1:00-2:05 AM Mon., Wed.
Meeting Place: BHS 130
3 credits, 196, 197 and upper division course prerequisite
OUTLINE
A. INSTRUCTOR
B. COURSE PURPOSE AND OBJECTIVES
C. GRADING
D. COURSE MATERIALS
E. RESOURCES
F. POLICY
G. SYLLABUS AND IMPORTANT DATES
I reserve the right to modify course policies and content including grading.
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A. INSTRUCTOR
Professor: Dr. Martin Schiller
1Office Hours: Mon., Wed. 3:00 PM – 5:00 PM,
Office: WHI 118
Email: WebCampus
1Office
hours also by appointment through Webcampus if the student can demonstrate that all of the above times are
in conflict.
Interaction with instructor:
1.
2.
Only use web campus for email. I will not likely respond on my UNLV email account or
my office phone.
If you have more than two questions, do not email, come to my office hours
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B. COURSE PURPOSE AND OBJECTIVES
Course Purpose:
The Introduction to Bioinformatics class covers basic principles in Perl programming,
algorithms, databases, and use of many bioinformatics resorucesLaboratory exercised reinforce
these major themes with “hands-on” activities and individual/group learning exercises.
Attendance requires two lectures per week totaling 3 credits.
This course is designed to be on par with similar introductory courses at major
Universities in the US. The course material is designed to provide an overview in all major areas
of bioinformatics research. Because of the breath of material covered, the pace is demanding.
For that reason, it is essential that students be adequately prepared for this class and that they
allot sufficient time for study. It is strongly suggested that students complete the relevant
text readings prior to attending class. When preparing for lectures/exams and allocating
study time, consider the following:
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Student-faculty contact in and out of class is an important factor in student
motivation/involvement/success. In other words, students should not be afraid to ask
questions in class and during office hours.
According to education researchers, students learn only about 50% of what they read,
hear, and see (equivalent to reading the textbook and attending lecture). The most
effective learning strategy involves talking to the instructor and classmates about what
was presented from the lecture and the text, writing about it, relating it to past experiences
and applying it to daily lives.
A full-time course-load is a full-time job that requires 40 or more hours per week. This
class represents about 1/4 of a full course load, and thus requires that students set aside
about 10-15 hours per week to attend lectures, read the text, meet with study groups,
transcribe class notes, and STUDY. An effective strategy for doing well is to commit 2
hours of outside time to read the material and review the notes for each lecture.
This class will emphasize a conceptual and practical understanding of bioinformatics.
Successful completion of this course will require the ability to think logically and to apply basic
biological, computational, and mathematical principles to an understanding of biological systems
at the molecular, cellular, and organismal level.
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Learning Objectives:
Upon completion of this course, students should have a general understanding of:
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Simple programing in perl
The structure and querying of MySQL databases
Design principle for biological databases
Knowledge about biological databases and applications
The principles and applications of pairwise sequence alignment
The principles and applications of multiple sequence alignment
A basic understand of protein structure determination
Use of structure display and fitting tools
Knowledge of different types of algorithms used to solve bioinformatics problems
Understanding of the principles behind and use of Blast
Understanding of the principles behind building of use of applications to build
evolutionary trees based upon sequence similarity
Programs for analyzing gene expression arrays
Principles by the identification of proteins by mass spectrometry
Use of tools for DNA analysis involving cloning and subcloning
Available data on human variation and disease
Types of and tools for modeling biological networks
Tools to analyze sequence motifs
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C. GRADING
Grades are calculated from the following assessment in class:
Assessment
Labs (3)
Final Projects
Percentage of grade
60%
40%

Undergraduates will build a parser to
combine data for their project and perform a
set of SQL queries of their data.

Graduate students perform the same task, but will have an additional project to be
announced in class,
-------------------------------------------------------------------------------------------------------------------Final Project:
Students will be required to compete a final project that involves some programming and use of
the program to produce a desired outcome. Graduate students will be required to do a more
extensive project.
Labs:
Students will attend 3 laboratories where they will use bioinformatics tools or will learn to
program simple programs.
Finally, students are reminded that it is their responsibility to fill out the necessary forms
to drop this class. A failure to attend classes and exams does not result in an administrative drop.
Failure to drop a class usually results in an “F” being recorded on the student’s transcript.
If I made a mathematical grading error, please bring it to my attention immediately, but I
will not award points for any other reason. Please do not email or call with requests for
grades as I will not reply.
Final course grades are based on the combined numerical. Letter grades will not be assigned to
individual examinations. To evaluate your performance as the semester progresses, the
following cutoffs can be used: 90% and above is an A, 80% and above is a B, 70% and above is
a C, 60% and above is a D, below 60% is an F
Students should not expect the grades to be CURVED!
Remember that the early-drop deadline is September 2, 2011 at 5:00 PM. The latedrop deadline is November 1, 2011 at 5:00 PM.
Incomplete grades:
Incomplete grades are only issued under very extenuating circumstances. Such instances
include a debilitating illness or a family emergency. The student must make arrangements with
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the instructor, and the instructor must agree to the conditions for the incomplete and how it is to
be remediated before the end of the semester when grades are to be submitted. It is then the
responsibility of the student to fulfill the conditions to remove the incomplete grade. Typically
the student will fulfill the conditions for removing the incomplete by the end of the subsequent
semester. Failure to do so will automatically cause the incomplete to be converted to an F. An
incomplete grade cannot be used to “rescue” a poor or failing performance in the course because
according to University policy, a student must have completed 2/3 of the course with a passing
grade to be eligible for this option.
Class Attendance of Lectures:
Attendance of the lecture classes is strongly recommended. Past experiences and
analysis of data from other classes have demonstrated a strong correlation between students who
do well in the course (receive an A or a B) with those who attend the lecture classes regularly. In
addition, lecture exams will be based almost, but not entirely on the material presented in class.
The required reading of the textbook is designed to clarify concepts and provide more
background information. Most lectures will follow the book closely, but often newer and more
relevant material will be provided in class that is not available in the book. A student should
come to class and take good notes using the outline option of note taking.
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D. COURSE MATERIALS
Required Materials:
1. Access to a networked computer for accessing WebCampus is required. Access to Adobe
Acrobat software (for opening PDF files) is also required. Adobe Acrobat is available as a
free download for UNLV students.
2. Lecture text: Bioinformatics and Functional Genomics 2nd ed. Johnathan Pevsner. Wiley
3. The NCBI handbook Jo McEntyre and Ostrell, National Center for Biotechnology Information,
Free at http://www.ncbi.nlm.nih.gov/books/NBK21101/
Visit Wiley.com to save 20% on Bioinformatics and Functional Genomics textbook. When
you checkout, please enter code VA341 in the Promotion Code field and click the Apply
Discount button
BOOKS FOR CLASS
Abbreviation Title
BFG
Bioinformatics and Functional Genomics
BPB
Beginning Perl for Bioinformatics
ABN
Analysis of Biological Networks
Authors
Johnathan Pevnser
James Tisdall
Bjorn Junker and Falk
Schreiber
IRDT
An Introduction to Relational Database Theory
Hugh Darwen
* you should purchase the first book. Others are ebooks on webcampus
Additional (Non-Required) Materials:
Students are also encouraged to seek out online resources and You-tube videos to
supplement their learning.
WebCampus: WebCampus will be used in this course to list the syllabus, announcements,
lecture notes, and grade distributions. It will also be used to report grades and for e-mail
correspondence between students and the instructor. Complete lecture notes will usually be
posted 24 hours AFTER each class in PDF or PowerPoint formats. Audio recordings of the
lecture will also be provided. Complete notes are only available after each lecture to encourage
an “active learning” experience. Educational studies have demonstrated that students do best
when they listen to lectures and take notes in class.
A WebCampus page has been created for this course. Login instructions are available at
http://webcampus.nevada.edu. In addition to providing notes, WebCampus provides a
confidential means of communicating with your instructor and for viewing grades. Please note
that the instructor is not responsible for, and will not answer e-mails using servers outside the
WebCampus system. Using WebCampus insures that a student's e-mail is not blocked by spam
or lost in other mailboxes. Students who are having problems using WebCampus should call the
Student Computing Support Center (895-0761) to immediately report problems.
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E. RESOURCES
Disability Assistance:
The Disability Resource Center (DRC) coordinates all academic accommodations for
students with documented disabilities. The DRC is the official office to review and house
disability documentation for students, and to provide them with an official Academic
Accommodation Plan to present to the faculty if an accommodation is warranted. Students should
provide faculty with their official Academic Accommodation Plan to receive special
accommodations.
UNLV complies with the provisions set forth in Section 504 of the Rehabilitation Act of
1973 and the Americans with Disabilities Act of 1990, offering reasonable accommodations to
qualified students with documented disabilities. If you have a documented disability that may
require accommodations, you will need to contact the DRC for the coordination of services. The
DRC is located in the Student Services Complex (SSC), Room 137, and the contact numbers are:
Voice (702) 895-0866, TDD (702) 895-0652, fax (702) 895-0651. For additional information,
please visit: http://drc.unlv.edu/.
Tutoring:
The School of Life Sciences operates a Biology Learning Center in White Hall, room 204.
If a question cannot be resolved at the tutoring center, should a student come to my office hours.
To be seen the student should bring the name of the tutor that they spoke at the tutoring center.
The hours of the Tutoring Center are Mon, Tues, Wed, Thurs 9AM – 4 PM and Friday 9AM – 2
PM.
The Academic Success Center (ASC) provides tutoring and academic assistance for all
UNLV students taking UNLV courses. Students are encouraged to stop by the ASC to learn
more about subjects offered, tutoring times and other academic resources. The ASC is located
across from the Student Services Complex, #22 on the current UNLV map. Students may learn
more about tutoring services by calling (702) 895-3177 or visiting the tutoring web site at:
http://academicsuccess.unlv.edu/tutoring/.
UNLV Writing Center:
One-on-one or small group assistance with writing is available free of charge to UNLV
students at the Writing Center, located in CDC-3-301. Although walk-in consultations are
sometimes available, students with appointments will receive priority assistance. Appointments
may be made in person or by calling 895-3908. The student’s Rebel ID Card, a copy of the
assignment (if possible), and two copies of any writing to be reviewed are requested for the
consultation. More information can be found at: http://writingcenter.unlv.edu/.
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F. POLICY
Classroom Conduct:
The University requires that all students behave in class and in libraries in ways that do
not interfere with the right of other students to learn or of instructors to teach. Behaviors such as
talking, texting, or reading newspapers or magazines during lecture, late and/or disruptive
arrival, early and/or disruptive departure, having a cell phone ring, or any other actions that
compromise the classroom learning environment is extremely rude. The instructor maintains a
zero-tolerance policy on these activities and will single the student out if they occur. Firsttime offenders may be embarrassed, but serial offenders face stiffer consequences, which may
include administrative ejection from the course. Students should be aware that they are not
anonymous in this class and that bad behavior will be rewarded as such.
It is important to remember that the instructor wants the students to do well in this class,
thus many extra benefits are provided (online outlines, posted lecture notes, extra credit points).
Students should visit office hours or make office appointments if they are having trouble
comprehending the course material or studying for exams. These problems, if corrected early,
can often help the student avoid receiving a grade that does not reflect his/her efforts and
expectations for the class.
Because this class encompasses so much material, it is important that it starts promptly at
8:30 AM. Please make every effort to come to class on time. If you MUST be late, please be
considerate of your classmates when entering the room after instruction has begun. Any person
who is not registered cannot attend lectures without written consent of the Instructor. This
includes children.
Academic Misconduct:
“Academic integrity is a legitimate concern for every member of the campus community;
all share in upholding the fundamental values of honesty, trust, respect, fairness, responsibility
and professionalism. By choosing to join the UNLV community, students accept the expectations
of the Academic Misconduct Policy and are encouraged when faced with choices to always take
the ethical path. Students enrolling in UNLV assume the obligation to conduct themselves in a
manner compatible with UNLV’s function as an educational institution.”
All exams and written assignments are to be done individually. Evidence to the contrary
will be deemed as academic misconduct. The instructor maintains a zero-tolerance policy on
academic dishonesty, which is a very serious offense that can result in expulsion from the course,
a grade of “F” for the entire course, and other possible disciplinary action. The minimum policy for
academic dishonesty will be an automatic failure in the course. I will also seek university wide sanctions
as appropriate including but not limited to requesting that a permanent indication of academic dishonesty
be included in your official transcript. If you feel that you must cheat to succeed in this course, please drop
the course immediately.
Additional information regarding UNLV’s policies on academic misconduct can be found
at (http://studentlife.unlv.edu/judicial/misconductPolicy.html). The following actions are
examples of academic dishonesty:
• Copying graded homework.
• Working together on a take-home test or homework when specifically prohibited by the
professor.
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• Looking at another student’s paper during an exam.
• Lending an i-clicker to another student to receive in-class credit.
• Using another student's i-clicker to help them receive fraudulent in-class credit.
• Looking at your notes when prohibited.
• Taking an exam out of the classroom (either in person or by using electronic means)
when prohibited.
• Giving your work to another person to be copied.
• Giving someone answers to exam questions during the exam.
• After taking an exam, informing a person of questions that appeared on the exam.
• Giving or selling a term paper or class work to another student.
• Copying homework answers from a textbook and handing them in for a grade.
• Quoting text or other works on an exam, term paper or homework without citing the original
source.
• Handing in a paper purchased from a term paper service or from the Internet.
• Handing in another person’s paper as your own.
• Taking a paper from an organization’s files and handing it in as your own.
• Passing information from an earlier class to a later class.
• Having someone take your test for you.
• Changing a graded paper and requesting that the paper be regraded.
• Transferring a computer file from one person’s account to another.
Plagiarism can take several forms. The most obvious form of plagiarism is the purchase of prepared
papers from another student or from commercial term paper companies and the submission of such
papers as one’s own work. Another example is using the words or ideas of another, from the Internet
or any source, without proper citation of the sources.
Copyright and Fair Use Laws:
The University requires all members of the University Community familiarize themselves with,
and follow copyright and fair use requirements. You are individually and solely responsible for
violations of copyright and fair use laws. The university will neither protect nor defend you nor
assume any responsibility for employee or student violations of fair use laws. Violations of
copyright laws could subject the student to federal and state civil penalties and criminal liability, as
well as to disciplinary action under University policies. To familiarize yourself with copyright and
fair use policies, the University encourages you to visit its copyright website at
(http://www.unlv.edu/committees/copyright/).
Sexual Harassment:
It is the policy of UNLV to maintain the University Community as a place of work and study
for staff, faculty, and students free of sexual harassment and all forms of sexual intimidation and
exploitation. The determination of what constitutes sexual harassment will vary with the particular
circumstances, but it may be described generally as repeated and unwanted sexual behavior, such as
physical contact and verbal comments or suggestions that adversely affect the working or learning
environment. Anyone who is subjected to offensive sexual behavior is encouraged to pursue the
matter through the Office of Diversity Initiatives (Tel. 895-3891). Contacts are confidential.
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Dangerous Weapons:
Dangerous weapons are not permitted on campus without the express written approval of the
Director of the Office of Public Safety. This policy applies to all persons on the UNLV campus,
except law enforcement officers in pursuit of their duties. Facsimile weapons are also banned.
Religious Holidays Policy:
Any student missing class examinations, or any other class or lab work because of
observance of religious holidays shall be given an opportunity during that semester to make up
missed work. The make-up will apply to the religious holiday absence only. It shall be the
responsibility of the student to notify the instructor no later than the last day at late registration of
his or her intention to participate in religious holidays, which do not fall on state holidays or
periods of class recess. This policy shall not apply in the event that administering the test or
examination at an alternate time would impose an undue hardship on the instructor or the
university, which could not be avoided. For additional information, please visit:
http://catalog.unlv.acalog.com/content.php?catoid=1&navoid=44&bc=1.
Rebelmail:
By policy, faculty and staff should e-mail students’ Rebelmail accounts only. Rebelmail
is UNLV’s Official e-mail system for students. It is one of the primary ways students receive
official university communication such as information about deadlines, major campus events,
and announcements. All UNLV students receive a Rebelmail account after they have been
admitted to the university. Students’ e-mail prefixes are listed on class rosters. The suffix is
always @unlv.nevada.edu.
Student conduct:
These policies are designed to limit student distractions during lecture periods and promote
respectful behavior among all members of the class.
1. To succeed in this course it is necessary to attend the lectures. Lectures will start on time,
please be in your seat and prepared to take notes. If for some unforeseen reason you arrive
late, please seat yourself quietly in a place that will not disturb other students. Lectures will
end on time, you are expected to stay until the class is dismissed.
2. Please turn off the ringer on all cellular phones and beepers.
3. If you have a question, please raise your hand to be recognized and ask your question.
4. Please avoid unnecessary wandering in and out of the room, it distracts others who are
trying to listen/take notes. Likewise do not engage in other distracting behaviors such as
reading a newspaper or conversing with your neighbor(s).
5. During discussion and other interactions, we will all treat each other politely and with
respect, especially when individuals disagree with each other.
Intellectual property:
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All PowerPoint lecture notes and audiotaped lectures are the intellectual property of UNLV and you
are permitted to use these for the class, but not allowed to distribute these materials to others unless
approved by the instructor of the class.
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G. SYLLABUS AND IMPORTANT DATES
Tentative Lecture, Lab, and Exam Schedule
Date
Jan
Feb.
Mar.
Apr.
May
Final
Reading (Chap.;
pp.)*#
Lecture topic
22
27
1.1: HISTORY OF BIOINFORMATICS
1.2 DATABASES pt.1
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1.3: THE BIOLOGICAL LITERATURE
3
5
10
12
17
19
24
26
3
5
10
12
17
19
24
26
31
2
7
9
14
16
21
23
28
30
5
7
12
20
1.4: ACESSING SEQUENCE DATA
1.5: PAIRWISE SEQUENCE ALIGNMENT I
1.6 NEXT GENERATION SEQUENCING - Murugapiran
1.7: BLAST - Murugapiran
No Class – Washington’s Birthday
1.8: ADVANCED BLAST- Murugapiran
1.9: MULTIPLE SEQUENCE ALIGNMENT- Murugapiran
SECTION 1 LAB; Due 3/7
SECTION 1 LAB; Due 3/7
2.1 BASIC PERL Interactive workshop pt. 1- Han
2.2 BASIC PERL Interactive workshop pt. 2 - Han
2.3 DATABASES pt. 2
No Class – Spring Break
No Class – Spring Break
2.4: MOLECULAR PHYLOGENY pt. 1
2.5 MOLECULAR PHYLOGENY pt. 2
2.6 RNA
2.7 GENE EXPRESSION
SECTION 2 LAB; Due 4/11
SECTION 2 LAB; Due 4/11
3.1 PROTEOMICS
3.2 PROTEIN STRUCTURE - NMR
3.3 PROTEIN STRUCTURE XRAY - Kleiger
3.4 PROTIEN STRUCTURE – DALI, VENN, Display
3.5 MOTIFS
3.6 MOLECULAR BIOLOGY TOOLBOX
3.7: BIOLOGICAL NETWORKS
SECTION 3 LAB
FINAL PROJECT Due by 5:00 PM
Grades due
*text book abbreviations are in the table of the course materials section
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IBA: 79-82
BFG: 2-38
BFG: 2: 38-40,
20:859-863
BFG: 2: 13-38
BFG: 3: 47-97
No Text Book
BFG: 4: 101-137
-BFG: 5: 141-176
BFG: 6: 179-210
BPB
BPB
IRDT
BFG: 7: 215-272
BFG: 7: 215-272
BFG: 8: 279-325
BFG: 9: 331-373
BFG: 10: 379-416
BFG:11:421-433
BFG:11:421-433
BFG:11:421-457
BFG:10:389-398
No Text Book
ABN
due 5/12