Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016
RAMAPO COLLEGE OF NEW JERSEY
School of Theoretical and Applied Science
Lecture & Lab Integrated
(Spring 2016) Syllabus (4 Credit Hours)
Note: This course will include a minimum of five (5) hours of independent hands-on project activity outside of the classroom
Instructor :
Paramjeet S. Bagga, Ph.D.
Professor of Biology Room ASB-426
& Convener of Bioinformatics
Office: G-418
(201) 684-7722, pbagga@ramapo.edu
Website: http://pages.ramapo.edu/~pbagga/
Office Hours :
M/R 12:45 – 1:00 PM & 5:40 - 6:55 PM
Or by appointment
Class Meets:
R at 2:00 to 5:30 PM
Course Pre-requisite : BIOL 331.
IMPORTANT DATES:
Feb. 18 : First Exam
Mar 31 : Second Exam
Apr 8 : Final day to withdraw
Apr. 28 : Final Project Report Due
May 5 : Final Exam ( 1:00 – 4:20 PM )
Background and Scope:
The interdisciplinary field of Bioinformatics, that uses computational techniques to help frame and resolve biological problems, has become an essential component of modern life sciences. Bioinformatics is employed to manage the vast amount of biological information, especially the data being produced by the Human Genome Project and sequencing endeavors of yeast, mouse, fruit fly and many other genomes. The management involves gathering, storing, analyzing and integrating data that can then be used for gene discovery, molecular modeling, drug design and much more. Bioinformatics can be applied to study structure and function relationships of proteins, and also to assign identities and functions to newly discovered genes.
Many Bioinformaticians are working on modeling the complex biochemical pathways, studying gene expression profiles and designing genetic medicines that were not possible before.
Bioinformatics is a young science and in great demand. Therefore, there is an unprecedented worldwide need for trained bioinformaticists at present. Modern biology and related sciences are increasingly becoming dependent on this new technology.
With this technological revolution now among us, it is imperative that scientists-in-training acquire the modern skills of
Bioinformatics.
An undergraduate course in Bioinformatics could be challenging for students. However, relative newness of the subject and the powerful capability to resolve problems of yet untamed scientific disciplines with the aid of latest computer technology will fascinate the students. In addition, enhanced marketability and better preparation for higher studies and research careers will amply reward their efforts.
Course Description:
The Bioinformatics course is designed to provide hands-on introduction to this emerging technological science for students of Bioinformatics, Biology, Biochemistry, health sciences, computer science and other related fields. In this course, students will learn about the major issues concerning representation, analysis and application of biological, molecular and biochemical information, especially from computational point of view. This course consists of integrated lecture and laboratory.
The course will be taught in an Internet equipped computer lab. It contains exercises to acquaint the students with the latest Internet based as well as commercial bioinformatics tools and resources for studying biological information and a variety of biological data analysis. All the students will present seminars and work on an end-of– semester research project as part of the course requirements.
The lectures of the course will mostly focus on introduction to various computational methods for solving problems in genome and protein analysis. Strengths and limitations of each method will also be discussed. Some of the topics to be covered in the lectures are: Fundamentals of Gene Structure and Function, Database Searches, Molecular
Sequence Analysis, Genomics, Gene Identification, Proteomics and Structure-Function Predictions.
No programming skills required. However, prior exposure to personal computers, e-mail, and the Internet is essential .
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Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016
Course Goals:
Upon successful completion of this course, the student should demonstrate:
1.
Integrated knowledge and technical skills gained from diverse scientific disciplines of biochemical, computational and life sciences; understanding key problems, possible solutions, and latest advances in bioinformatics.
2.
Understanding of the process of scientific inquiry, preparation for research, problem solving skills, data analysis and interpretation of results.
Course Objectives:
After successfully completing the bioinformatics course, the students will be able to:
1.
Show familiarity with concepts of Bioinformatics and its applications, Genomics and Proteomics.
(Exams 1-3; Lab week 1)
2.
Demonstrate basic understanding of the design, applications and significance of biological databases;
Extract, evaluate and manipulate relevant data from large biological data sets.
(Exam 1; Labs weeks 2-7)
3.
Develop basic understanding of computational methods and tools including: gene identification, sequence comparisons, and structure-function predictions.
(Exams 1-3; Labs weeks 8-11, 13-15; Project)
4.
Demonstrate the capability of making scientific observations, develop appropriate hypotheses and design experiments to test the hypotheses. Be able to validate and quantitatively analyze the results obtained from the experiments, interpret the outcomes and make inferences. Write logical and cohesive scientific reports.
(End of the semester lab project)
Required Text – Fundamental Concepts of Bioinformatics. D.E. Krane & M.L. Raymer. Benjamin
Cummings. 2003. ISBN: 978-0805346336 (This text is referred to as KR in rest of the syllabus).
Optional Recommended Texts :
1.
Bioinformatics and Functional Genomics.
3 rd Edition. Jonathon Pevsner. John Wiley & Sons, Inc.
2015. ISBN: 978-1-118-58178-0 ( Highly Recommended.
Will be used to supplement some lectures .) (This text is referred to as JP in rest of the syllabus).
2.
Practical Bioinformatics.
Michael Agostino. Garland Science. 2013. ISBN: 978-0815344568
( Highly recommended. Will provide support for many labs). (This text is referred to as MA in rest of the syllabus).
3.
Exploring Bioinformatics: A Project-Based Approach.
Clair and Visick. Jones & Bartlett. 2015.
ISBN: 978-1284034240 ( A practical approach for learning Bioinformatics. For beginners )
Additional Recommended Books for Supplemental Reading:
(In the decreasing order of utility for this course)
1.
Bioinformatics: A Practical Guide to the Analysis of Gene and Proteins.
3 rd Edition. Andreas D.
Baxevanis and B. F. Ouellette. John Wiley & Sons, Incorporated. 2009. ( Highly Recommended.
Will be used to supplement some lectures .) (This text is referred to as BO in rest of the syllabus).
2.
Essential Bioinformatics . Jin Xiong. Cambridge University Press. 2006 (print) 2013 (Kindle).
( Recommended for the beginner )
3.
Genomics, Proteomics, & Bioinformatics. 2 nd Edition. Campbell and Heyer. Cold Spring Harbor
Laboratory Press and Benjamin Cummings. 2006. ( Great resource for Genomics ).
4.
Understanding Bioinformatics. M. Zvelebil & J.O. Baum. Garland Science. 2008. (Recommended for advanced learners)
5.
Bioinformatics: Sequence and Genome Analysis . 2 nd Edition. David W. Mount. Cold Spring Harbor
Laboratory Press. 2012. ( An excellent source for bioinformatics-algorithms )
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Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016
Topics
1. Introduction
Understanding Gene Structure and Function
2.
3.
Storage and Expression of Genetic Information
Structure and Function of Proteins
(Week 1; Handout, JP: pp 3-7)
(Self Reading Assignment; KR: Chapter 1)
(Self Reading Assignment; KR: Chapter 1)
4. Molecular Structure of Eukaryotic and Prokaryotic Genes
Data Search and Sequence Comparisons
5.
6.
Sequence Alignment methods
Database Searching methods
(Weeks 1 & 2; Handout)
(Weeks 2 & 3; KR: pp34-38)
(Week 4; KR: pp48-51, BO: pp302-322, Handout)
7.
Structure Prediction
8.
9.
Multiple Sequence Alignments
Basic concepts
Methods for Secondary Structure prediction
(Week 4; KR: pp52-53, Handout)
(Week 5: First Exam)
(Self Reading Assignment; KR: pp13-15, 156-160, Handout)
(Week 6; KR: pp160-164, Handout)
10. Tertiary and Quaternary Structure
11. Protein folding models and Structure prediction
12. Prediction of RNA Secondary Structures
(Week 7; KR: pp164-167, Handout)
(Week 7 & 8; KR: pp167-174, Handout)
(Week 8; KR: pp175-176)
( Week 9: Spring Recess )
Genomics
13. Introduction to Genomics
14. Prokaryotic Genomes and Gene Recognition
(Week 10; Handout)
(Week 11: Second Exam)
(Week 12; KR: pp118-127)
15. Eukaryotic Genomes and Gene Recognition
16. Gene Expression analysis and Microarrays
(Week 13; KR: pp127-143, 148-151)
(Week 14; KR: pp143-147, Handout)
Proteomics
17. Proteome, Protein Classification, and Techniques (Week 15; KR: pp180-187, 191-197, Handout)
18. Post Translational Modification and other predictions
19. Inhibitors, Drug Design and Ligand Screening
(Week 15; ; KR: pp197-203)
(Week 15; KR: pp187-191)
(Week 16: Final Exam)
*Notes:
1.
This is a very tentative sequence of topics to be covered. Modifications will be made as and when necessary to the order and dates of topics to be covered during the semester. Modifications, if any, will be announced in the class or posted on the course web site.
2.
The above sequence of topics may differ from that of the text-book (s). The assigned text-book(s) are written to serve the needs of students at various academic levels. Above topics have been very carefully picked by the instructor in order to design a package that suits the academic level and specific needs expected of the students registering for this course.
3.
Since this is a rapidly progressing science and discoveries are made almost everyday, the text needs to be supplemented by the latest information from time to time. Students will be provided handouts, prepared from latest articles relevant to this course, in order to keep them up to date with the developments in the field. Whenever possible I will also post relevant scientific articles, news etc. on my website ( http://pages.ramapo.edu/~pbagga/ ).
Students are also required to frequently check out the " Bioinformatics Resources on the Internet "
( http://pages.ramapo.edu/~pbagga/binf/binf_res/binf_int_res.htm
) on my website.
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Instructor: Dr. Paramjeet S. Bagga
Week
Bioinformatics BIIN 430 Syllabus: Spring 2016
Schedule of Laboratory Exercises
Date
Exercise
01/21/16
01/28/16
02/04/16
Introduction to Bioinformatics, non-commercial and commercial Bioinformatics Resources.
(JP: pp13-45)
Introduction to NCBI-Entrez System: GenBank, Protein, RefSeq and PubMed databases
(MA: pp23-27, 30-32)
Exploration of Genomic Information: Entrez Gene, Human Ensembl, MGD, HGNC, and
Gene Ontology databases: Student presentations
02/11/16
Analysis of Genomic Variations: SNP, OMIM, and HGMD databases: Student presentations
02/18/16
02/25/16
03/03/16
Regulated Gene Expression: EPD Database: Student presentation
FIRST EXAM
Information Retrieval and Analysis of Proteins: UniProt and HPRD databases:
Student presentations
Protein Structure/Function relationships: Pfam, ProDom, and Conserved Domains databases:
Student presentations
03/10/16 Self-Study: Vector NTI Advance (Informax) package.
9
10
11
12
03/17/16
03/24/16
03/31/16
Spring Recess
Sequence comparisons: Global and Local Alignments; Multiple Sequence Alignments.
Database Searching. (MA: Ch.4, Ch.11)
Protein Structure/Function Predictions: Secondary Structure, Hydrophobicity and Functional
Domains. SECOND EXAM
04/07/16
Proteomics Tools, Protein Sorting and cellular localization prediction .
13 04/14/16 Self-Study: Vector NTI Advance (Informax) package.
04/21/16 Protein Structure Analysis: Structure databases 14
15 04/28/16 Gene Identification Methods. Final Project Report Due
16 05/05/16 Final Exam ( 1:00 – 4:20 PM )
Note: This is a tentative sequence of exercises to be covered. Modifications will be made as and when necessary during the semester. Modifications, if any, will be announced in the class or posted on the web
(http://pages.ramapo.edu/~pbagga/).
Lab Notebooks :
Often your lab book / manual / handout give you all the information you need but you must interpret your own data . You are required to maintain a laboratory notebook for this course. All of your data obtained in this laboratory is to be recorded in your notebook.
1. Purchase a laboratory notebook with the following characteristics:
- Pages approximately 8 1/2 by 11" (not composition book size).
Bound permanently--not tear-out or loose-leaf. Ring-bound is fine.
2.
3.
4.
5.
6.
-
- ALL Pages numbered.
Write your name in your notebook in a prominent location.
Save first one or two pages for the Table of Contents.
Make all entries in ink. If you need to add pages from other sources (like printouts of graphs, handouts, etc .), tape or paste them into the notebook securely. No stapling please.
Begin a new experiment on a new page.
For each experiment, use the following headings.
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Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016
7.
Title - A one-sentence meaningful description of the experiment.
Date - List the date you performed the experiment.
Objective - One or more sentences (bullets would be ok) describing the purpose of the experiment.
Background – General information about the concept that you are testing.
Tools - List all tools and databases used. Provide their locations (url etc.)
Methods/Protocol - List the steps to be followed, being as specific as possible.
Results -
Include all necessary data obtained (tables, graphs, drawings, printouts etc .) Tape into this section of your notebook printed results from computations, graphs, etc . DO NOT USE
STAPLES.
Discussion &Conclusions – A thoughtful interpretation of your results. What did you demonstrate?
Remember, your notebook should allow another scientifically literate individual to understand what, why, and how you did a particular experiment. There should be sufficient detail to permit someone to duplicate your experiment.
Preparation for the Experiments: You are required to thoroughly prepare for the exercise to be performed in the lab. You should have all the information for preparation, either from the lab manual, in the form of handouts, syllabus or instructions provided to you in advance. There will be surprise quizzes before starting several experiments to make sure that you are prepared for the lab.
Presentations:
By the second week of semester, every student will be assigned topics for presentation. The goal of the presentations is to introduce important molecular biology/bioinformatics databases available freely on the Internet.
Each 15-20 minute presentation will start with a brief introduction of the data stored in the database. This should also include description of the data model and associated background information. The introduction should be followed by a hands-on tutorial that you will design. The tutorial should use one or two examples of typical queries in order to teach the following skills to the class:
1.
query the database and retrieve the information
2.
understand, analyze, evaluate (including statistical evaluation and/or mathematical confidence of the results) and interpret the retrieved information
3.
use it for further computations and/or analysis with other bioinformatics tools
You are required to provide a summary/outline of your presentation in the form of a handout (up to two pages only) for each member of the class. The handout should enlist all the steps in the tutorial in addition to an introductory paragraph, the URL where the database can be accessed and references (only in a standard format) that you consulted, and 2-3 problems for practice. Do NOT ‘copy’ and ‘paste’ information from ANY publication
(including websites) into your summary document. It will be treated as plagiarism.
Your presentation will be graded for: Introduction, Information Presented, Overall Clarity, Organization of the seminar, Ability to answer questions and Summary/Outline that you will provide.
Final Project: (Outside the classroom hands-on activity)
Towards the end of semester, you will be assigned a project which will utilize the methods learnt during the course. Each student/team in the class will be assigned a unique and novel protein sequence. The goal of your project will be to apply bioinformatics skills that you have acquired during the semester to predict the structure and function of this previously unknown protein. You will name the protein based on your findings and will also predict what type of diseases may result due to a mutation in this protein. This activity requires in excess of five (5) hours of unmonitored research experience outside of the classroom.
The final project report will be graded by the instructor and will count significantly towards your final grade in this course. (See course grading policy below).
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Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016
The completed ‘ final project’ report is due for submission on the last day of the class (usually one week before the final exam). The detailed outlines for the
‘final project’
report can be accessed at: http://pages.ramapo.edu/~pbagga/binf/binf/binf_project_assignment.docx
. Briefly, the format is as follows:
Date . Date you started writing the report.
Title : Meaningful description of the experiment in one sentence .
Objective(s) : A concise statement(s) of the purpose(s) of the project.
Background: General information about the topic, the significance of the project and the sequence analysis based predictive methodology.
Tools
& Methods: Describe all the tools, software etc. that you used. Describe your experimental approach.
Provide sufficient background information about all the predictive methods that you used.
Results : Include and describe all necessary data obtained.
Discussion : A thoughtful interpretation and analysis of the results obtained. Compare information obtained by different methods, put ‘two and two’ together.
Conclusions: Final conclusions and major findings of the project.
References : Cite sources ( do not use encyclopedias ) used in the writing of your project report. The references should be provided in a standard format only. To learn how to cite references correctly, visit: https://owl.english.purdue.edu/owl/
Late report submission could result in 10% penalty per day.
Course Requirements and Policies

Preparation: This course has required prerequisites ( BIOL 331 ). I expect that you have a thorough understanding of fundamentals of Biology & Chemistry, and Genetics. No programming skills are required; however, prior exposure to personal computers, e-mail, and the Internet is essential. If you don't fulfil ALL of the above requirements talk to me immediately.

In addition, it will be helpful if you are familiar with basic concepts of Molecular Genetics.

I expect that you will pay serious attention to the lecture in the class and read the lecture material before and after the class. Most of my lectures will start with a review of previous lecture. During this you will be encouraged to ask me questions. After answering your queries I will also ask questions to the class.

You are highly recommended to bring your textbook(s) to every class . Some lectures will be presented with the help of overhead-projections, slides or computer presentations. Frequently, the materials presented will be not from the book. Whenever possible, I will provide handouts, announce the source, reserve it in the library for students, or post it on my Web-site. Please do not start copying the lecture-outline presented to you on the screen.
All the lecture-outlines will be provided as handouts or posted on my Web-site. You are, however, encouraged to take detailed additional notes for the class discussions.

Attendance Policy: PLEASE ARRIVE ON TIME TO CLASS. The class will begin promptly at the designated time. I will take attendance before most classes. If you come in to the class late (after your name has been called, or the lecture has already begun), you will be marked absent.
However you are still encouraged to attend the lecture. If you are late, try to enter the class quietly and take a seat close to the door where you have entered. If you need to, please go to the restroom before coming to the class or during the designated break.
As far as possible, please do not disturb the class for a restroom visit during the lecture.

Participation: You are required to attend All the classes and be present for All the exams and other class activities. Since on several occasions the information discussed in this class will be from outside the book, and since the exams are mostly based on materials covered in the class, absences are expected to result in poor performances in the exams. Each unexcused absence could result in 5% penalty for the final grade.
Two unexcused absences could result in ‘F’ grade for the course. (College policy states that students must notify faculty within the first three weeks of the semester if they anticipate missing any classes due to religious observance.)

You are required to turn off the cell phones while in the class. Alternatively, you may switch the ringer to vibration or quiet mode.
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Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016

All assignments must be submitted on time and must be legible. Late submission will result in 10% penalty per day.

This class requires that you have an e-mail account and have access to the Internet. In accordance with
College policy, I will use your Ramapo College email address (@ramapo.edu) to communicate with you about all course-related matters. From time to time I will provide Internet information pertinent to the course.
I will also post important messages for the entire class on my Website. You are required to look at the
" Bulletin Board " ( http://pages.ramapo.edu/~pbagga/bulletin_board.htm
) on my Website before coming to each class . I will also try my best to notify you about our cancelled or late classes during rough weather via the
Bulletin Board.

If you have any questions or need help, see me at office hours or e-mail me. I will usually be available outside my office hours as well. Do not hesitate to ask for help / guidance.
Exams
1.
There will be three class exams. The first two exams will each cover the material presented in the class (and materials assigned for self-study) up to that day. The last class examination will be given during the final exam period but will include All the material covered during the semester ( i.e
., the final exam will be cumulative ). In addition, the final project is considered as part take-home final exam .
2.
Each class exam will consist of a written part and a part where you will need the computer to solve problems.
3.
You are required to bring pencils for all exams.
4.
All electronic gadgets should be turned off and left in your bag during the exam. Theses include cell phones,
PDAs, iPods, MP3 players, IM gadgets, electronic watches that can be used to store information, transmit or receive any kind of signals etc. You are permitted to use your own calculator. You are not allowed to borrow a calculator from anyone else.
Graphics calculators are not permitted during the exam. If you need an electronic gadget for medical or another essential/special needs, please obtain permission from your instructor ahead of time.
5.
The first two exams will be returned to you promptly in class. The final exam will be kept in your instructor's office where you may come to review it on a date and time announced in the class during the final exam. At this time, you will also be able to look at your final calculated grades.
Your final grades will not be emailed to you . Unfortunately , all email and voice mail inquiries for finding out the final grades will have to be ignored. You will be able to see your grades online via your college account after the grading deadline.
6.
Make-up exams will not be given (except in rare circumstances of illness accompanied with a note from a physician or other documentary proof).
Make-up exams in these exceptional cases (if any) will be given during the last week of class or during the final exam period. Make-up exams are generally of higher difficulty level.
7.
Your exams will be re-graded if you think an error has been made in grading, but you must submit the exam and a written description of the error within one week of the day the exams are returned to you.
Extra-Credit Activities (optional)
You can choose one or more of the following activities to earn a maximum of 2% points towards your final course average as extra credit. ( None of these activities can be double counted for credit in another course ).
1. Journal Club Participation : The goal of TAS Journal club is to enhance awareness of the current research developments in specific scientific disciplines. Journal Club meets on Wednesdays at 4-5 PM in ASB 426. You can earn 1% point as extra credit towards your final course average for regular, active participation for the entire semester in this club. You will have to attend all the weekly meetings (attendance will be taken) AND demonstrate active participation in the discussions to earn this credit.
2. Journal Club Presentation: You can earn 1% point as extra credit towards your final course average by making a presentation in the Journal Club. For this presentation, you will need to pick a recent (published not more than 6 months ago) research article related to Bioinformatics , published in a standard peer-reviewed scientific research journal . News articles will not be acceptable. The article has to be a report of a hard core research project with original data generated, analyzed and interpreted.
The Journal club is not just about presentations. The purpose of presentation is, in fact, to initiate scientific discussions. Open discussions during and after the presentation are highly encouraged and anticipated. Up to 25 minutes of brief presentation will generally be followed by 25 minutes of
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Instructor: Dr. Paramjeet S. Bagga Bioinformatics BIIN 430 Syllabus: Spring 2016 discussion. Presenting student will be expected to initiate discussions by asking questions to the audience following their talks. In case all the students of this course cannot be accommodated in the Journal Club, two presentations of
20 minute each followed by 10 minute discussions for each of the respective presentations can be attempted. If this measure is still not enough to accommodate all students, an election may be held in the class to select the presenting students.
Academic Integrity/ Plagiarism /Cheating: There is a ZERO TOLERANCE policy for Plagiarism /Cheating or copying for this course. Students are expected to read and understand Ramapo College’s Academic Integrity
Policy, which can be found online in the College Catalog (http://www.ramapo.edu/catalog). Members of the
Ramapo College community are expected to be honest and forthright in their academic endeavors. Students who are suspected of violating this policy will be required to meet with the faculty member and will be referred to the
Office of the Provost. Plagiarizing in exams, assignments or other class activities are only some examples of the violation. Do not copy parts of the handouts into your notebook/report. Do not plagiarize / Cheat / Copy someone else's data or enter false data in your Lab Note Book or Reports. You will be penalized equally for copying as well as for allowing to be copied. If you performed the experiment in a group, you can share the raw data with your teammates but DO NOT SHARE YOUR INTERPRETATIONS/ GRAPHS/ CONCLUSIONS. If for some reason your experiment didn't work, talk to me; don't copy anybody else's data. ‘Copying’ and ‘pasting’ information from
ANY publication (including websites) is considered plagiarism.
It is highly recommended that you spend a minimum of two hours outside the class for each lecture hour spent in the class.
Course Grading:
Final grade will be based on your performance in class exams (67%; 22% each for exam I & II, and 23% for the final exam), presentations (15%) and the final project report (18%).
The final letter-grade for the course will be calculated out of 100% as follows:
A :   
C + :
 
C
    
  
C


    
 
D +
 
   
D
 
F: <
 
Participation in class discussions, attendance, all other assignments and progress made during the semester will be taken into consideration IF your grade is borderline.
The instructor may ask you to fill out an exit survey towards the end of the semester for assessment purposes.
If you need course adaptation or accommodations because of a disability that has been documented with the Office of Specialized Services, please make an appointment with me.
NOTE: I am allergic to most known fragrances. Please be considerate. I will sincerely appreciate if you maintain a safe distance from me in the class in case you are wearing cologne or a perfume. I will also appreciate if you don’t wear a fragrance when coming to see me in my office.
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