Bio520F18

BIO 520 Bioinformatics
TITLE: Beginning Perl for Bioinformatics
Instructor: Dr. Jeramiah J Smith

BIO 520
Bioinformatics
Instructor: Dr. Jeramiah J Smith
Office Address: 311 TH Morgan Building
Email: jjsmit3@uky.edu
Office Phone: 257-0124
Office Hours: Tuesday 1:00 to 2:00 PM and by
appointment
Course Description:
BIOINFORMATICS
Prerequisites:
BIO 315 or BIO 304 or BCH 304 or BCH 401 or BCH 501 or BCH 502 or BIO 510 or consent
of instructor.
Student Learning Outcomes:
After completing this course, the student will be able to:
1. Interact with the terminal, install and use programs.
2. Perform analyses of large datasets (millions to billions of sequences).
3. Write and edit simple programs/scripts (e.g. Perl, bash)
Course goals or objectives: To achieve proficiency on computational analysis of large
biological datasets
Required Materials:
· TITLE: Beginning Perl for Bioinformatics
· AUTHOR: Tisdall
· COPYRIGHT YEAR: 2001
· PUBLISHER: O'Reilly & Associates
· ISBN: 9780596000806.
Course Assignments
Class Participation 100 points total
3 Quizzes 150 points total
1 Pre-proposal Presentation 50 points
1 Written Assignment (midterm) 100 points
1 Final Project 100 points
Total 500
Summary Description of Course Assignments
Class Participation
All students are expected perform the exercises covered in each in class. Because
teaching someone else is the best way to learn, students that finish early are
expected to assist those that have not yet completed their exercises (BUT, do not
do it for them).
Pre-proposal Presentation - A 10 minute presentation outlining the basic
biological question you are interested in, the specific dataset(s) you plan to
analyze and the analyses you plan to perform (what you hope to learn and why).
Notes:
A - if you are planning to analyze a dataset of you own that is yet to be
sequenced, you must provide an alternate dataset.
B - You may NOT use microarray data as your primary data source,
although microarrays analyses may be used to assess or complement other
analyses.
Written Assignment (due by 09/28/2018)
Written assignments should be prepared in the following format:
1) a brief abstract that outlines the biological question you are interested in. (1.5-
2.5 pages, single spaced 12-point font). You should include images, these do not
count to page limits.
2) list of specific datasets that you will use, including A) links to datasets on NCBI
on another server (or MD5 checksums for your own sequence data), B) Molecules
targeted for sequencing (DNA, RNA, mRNA, protein …), C) the type of sequencing
(paired-end, single-end, etc), D) sequencing chemistry used to generate the
dataset(s), E) numbers of reads/entities for each sample.
One concise supporting image (with title and legend) is strongly encouraged and
may be embedded in text or placed at the end of the document, these need not
count toward the page limit and should not be excessively large.
* IF YOU ARE PLANNINIG TO ANALYZE A DATASET OF YOU OWN THAT IS YET
TO BE SEQUENCED, YOU MUST PROVIDE AN ALTERNATE DATASET.
* You may NOT use microarray data as your primary data source, although
microarrays analyses may be used to assess or complement other analyses.
Presentation
All students will give an oral presentation, related to an analysis of a dataset of
their choosing (agreed upon by student and instructor). Presentations should be
30-35 minutes in length, with an additional 5 minutes for group discussion.
A successful presentation should minimally address the following questions 1)
why were the analyses performed done [why is it relevant?], 2) how were the data
generated/analyzed, 3) what are the biological insights gained? 4) Discuss caveats
and future directions.
Course Grading
Grading scale for graduates and undergraduates:
90 – 100% = A
80 – 89% = B
70 – 79% = C
60 – 69% = D
0 – 59% = F
Final Exam Information
Will be replaced by a final presentation and written assignment
Mid-term Grade (for 100-400 level courses, and for undergraduates in 500 level
courses)
Mid-term grades will be posted in myUK by the deadline established in the
Academic Calendar (http://www.uky.edu/Registrar/AcademicCalendar.htm)
Course Policies:
Submission of Assignments:
Presentations are expected to be presented orally. Written assignments may be
emailed to the instructor (single spaced, 12 point font). Written assignments
are due on or before 09/22/2017.
Attendance Policy.
Students are expected to attend and participate in all classes. See below for
further detail.
Excused Absences:
Students need to notify the professor of absences prior to class when possible.
S.R. 5.2.4.2 defines the following as acceptable reasons for excused absences: (a)
serious illness, (b) illness or death of family member, (c) University-related
trips, (d) major religious holidays, and (e) other circumstances found to fit
“reasonable cause for nonattendance” by the professor.
Students anticipating an absence for a major religious holiday are responsible
for notifying the instructor in writing of anticipated absences due to their
observance of such holidays no later than the last day in the semester to add a
class. Information regarding dates of major religious holidays may be obtained
through the religious liaison, Mr. Jake Karnes (859-257-2754).
Students are expected to withdraw from the class if more than 20% of the
classes scheduled for the semester are missed (excused or unexcused) per
university policy.
Verification of Absences
Students may be asked to verify their absences in order for them to be
considered excused. Senate Rule 5.2.4.2 states that faculty have the right to
request “appropriate verification” when students claim an excused absence
because of illness or death in the family. Appropriate notification of absences
due to university-related trips is required prior to the absence.
Academic Integrity:
Per university policy, students shall not plagiarize, cheat, or falsify or misuse
academic records. Students are expected to adhere to University policy on
cheating and plagiarism in all courses. The minimum penalty for a first offense
is a zero on the assignment on which the offense occurred. If the offense is
considered severe or the student has other academic offenses on their record,
more serious penalties, up to suspension from the university may be imposed.
Plagiarism and cheating are serious breaches of academic conduct. Each
student is advised to become familiar with the various forms of academic
dishonesty as explained in the Code of Student Rights and Responsibilities.
Complete information can be found at the following website:
http://www.uky.edu/Ombud. A plea of ignorance is not acceptable as a
defense against the charge of academic dishonesty. It is important that you
review this information as all ideas borrowed from others need to be properly
credited.
Part II of Student Rights and Responsibilities (available online
http://www.uky.edu/StudentAffairs/Code/part2.html) states that all academic
work, written or otherwise, submitted by students to their instructors or other
academic supervisors, is expected to be the result of their own thought,
research, or self-expression. In cases where students feel unsure about the
question of plagiarism involving their own work, they are obliged to consult
their instructors on the matter before submission.
When students submit work purporting to be their own, but which in any way
borrows ideas, organization, wording or anything else from another source
without appropriate acknowledgement of the fact, the students are guilty of
plagiarism. Plagiarism includes reproducing someone else’s work, whether it
be a published article, chapter of a book, a paper from a friend or some file, or
something similar to this. Plagiarism also includes the practice of employing or
allowing another person to alter or revise the work which a student submits as
his/her own, whoever that other person may be.
Students may discuss assignments among themselves or with an instructor or
tutor, but when the actual work is done, it must be done by the student, and the
student alone. When a student’s assignment involves research in outside
sources of information, the student must carefully acknowledge exactly what,
where and how he/she employed them. If the words of someone else are used,
the student must put quotation marks around the passage in question and add
an appropriate indication of its origin. Making simple changes while leaving
the organization, content and phraseology intact is plagiaristic. However,
nothing in these Rules shall apply to those ideas which are so generally and
freely circulated as to be a part of the public domain (Section 6.3.1).
Please note: Any assignment you turn in may be submitted to an electronic
database to check for plagiarism.
Accommodations due to disability:
If you have a documented disability that requires academic accommodations,
you must provide me with a Letter of Accommodation from the Disability
Resource Center (Suite 407 Multidisciplinary Science Center. Phone: 257-2754.
Email: dtbeach1@uky.edu).
Classroom Behavior Policies
No use of cellphones, or similar devices, during class. This includes audible
ringtones. Students are expected to be immediately-engaged by exercises and
discussions.
Guidelines for respectful dialogue: Discussions are a large part of the course
and differences in interpretation/opinion can be anticipated. It is expected
discussions will take place in a scientifically relevant and respectful manner.
Opinions presented should strive to be logical and/or be supported by citable
data.
Tentative Course Schedule
08/24/17 Introduction to computational biology and the terminal (blast), file structure
basics, data sources.
08/31/17 Introduction to machine commands and remote access installing and
compiling programs, sequencing technologies.
09/07/17 Pre-proposals Group 1 …. Introduction to machine commands and
remote access installing and compiling programs
09/14/17 Pre-proposals Group 2 ….Intro to assembling transcriptomes and
simple genomes Take Home Quiz.
09/21/17 Assembling transcriptomes and simple genomes
09/28/17 Transcriptional profiling and statistical analysis (from sequence data) Due
date for Written Assignment
10/05/17 Intro to programming in Perl I, Take Home Exercises / Quiz
10/12/17 Catchup of methods for primary data analysis.
10/19/17 Visualizing and interpreting genomic/ transcriptomic data
10/26/17 Visualizing and interpreting genomic/ transcriptomic data Take Home
Quiz
11/02/17
Makeup dates / help sessions
11/09/16 Class Presentations
11/16/16 Class Presentations
11/23/16 Thanksgiving Break
12/30/16 Class Presentations
12/07/16 Class Presentations