BI 7543 Bioinformatics Ii: Protein Structure, Credits: 3.00
Course Syllabus Grading Policy
Hello Class,
Based on my experiences the last few semesters I have made certain changes in
reagards to the grading policy and structure of the course. So with that said:
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- Homework Assignments (1 every week)
----------------------25% - Reading Assignments (1 every week)
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- Student Journal (Daily Documentation)
- Final Project. More information on this when the time comes
Homework Assignments:
Every Tuesday you will submit your homework assignment and every Tuesday you
will get your new assignment. It is absolutely necessary of course in the case where
it applies that you site all sources and give credit where credit is due. A failure to do
so will result in that assignment not being accepted. I am very lenient in that you
can return a homework assignment as many times as you want until you get a grade
you are satisfied with.
Reading Assignments:
Every week you will be required to find and summarize in one page an article which
shows the application of what we are learning that particular week. Take this as an
opportunity to explore the vast field of proteomics and find topics which are really
interesting to you. This will help greatly when it comes down to picking a final project
Student Journal:
Every time you read something on the course site or an article for the reading
assignment I would like you to make a summary of it. This is a rally informal affair.
Basically let me walk you through the steps of doing documenting your student
journal.
Click the Drop box tab, Select journal Then click on the link add new entry. If you
have followed me so far this is what you should see:
For the Title enter the Week, for instance if this is the first week you would write
Week One Student journal Entry 1. There can be more than one entry in a week as
many as you would like. For the Entry, I want you to explain in your own terms
what you have learned and what you have taken from this lecture or section of the
lecture that you have written.
This may seem tedious and it may seem a lot to do but this will really help
your understanding of this course. Some subjects are not easy to grasp the first and
second or even third time around. When I took this course myself, many moons ago
this is what I used to help me remember everything and full understand the subtle
point made throughout the lecture. In your journal you can leave me a question or a
request to explain something that isn’t so clear yet. Then I will know what you have
read through and where do you stand in your digestion of the material and be able to
as thoroughly as possibly answer your questions
Sample Journal entry:
Paquiot, David
TITLE: Week 1, Entry 1
ENTRY: I have recently read today sections 2 and 3 from lecture 4 about chaperonin
subunits GroES and GroEL. I am starting to understand the mechanism of how these
two subunits dissociate and associate. I also understand that these chaperonins
unfold proteins and fold them back again. What is not as of yet clear to me is what
about the inner cavity of the protein with all its combined units allows this to happen.
Tomorrow I will continue to work through this problem.
Grading Criteria
When I am grading your assignment I am looking for somehtign thats shows me that
youa re not parroting information back to me, that you really understand the topics.
Understanding the topic is great and initially the first few weeks I will be looking to
see if you are understanding the topics. Afterward I want you totake it further and
apply what you have learned in the weeks previous. SHow me you are learning and
thinking.
35 Final project
15 Article Summaries
25 Homework Assignments
25 Students Log
Course Description
This course is an intensive course. It isnt easy initially but towards the end of the
course you will all be very proficient in your understanding of proteomics. There will
be homework and reading assignments one per week. This is to help you see a real
world application to what we are studying. I am here all the time to help so take
advantage and make a sincere effort . We are not born knowing everything so
questions will always be happily accepted.
Course Objectives
The Course objectives are simple and straightforward with your hardwork these
objective can be obtained.
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1. Give you a great platform for your further studies in proteomics
2. Try to introduce you to as many different aspects of proteomics as possible
3. Have you well versed with what is being done in the field currently
4. Learn the basics of how scripting languages are used in Bioinformatics
through having your learn and work with PERL and PYTHON
The New Plan for this Semester.
Week
Week
Week
Week
Week
Week
Week
Week
Week
Week
1
2
3
4
5
6
7
8
9
10
Week 11
Week 12
Week 13
Week 14
Lesson 1 Basic Introductory Information
Lesson 2 Structural Proteomics: Alpha Helices and Beta Sheets(1)
Lesson 3 Structural Proteomics: Alpha Helices and Beta Sheets(2)
Lesson 4 Structural Proteomics: Alpha /Beta Structures
Lesson 5 Structural Proteomics: Beta Structures
Lesson 7 Structural Proteomics: Folding and Flexibility
Lesson 8 Proteomics 101: Substitution matrices and protein Databases
Lesson 9 Proteomics101: Protein Databases
Lesson 10: Methods in Proteomics: Mass Spectroscopy
Lesson 11: Special Topics" Special Uses Further Bioinformatics Studies
and Uses of PERL and Python
Lesson 12: Special Topics: Prediction, Engineering and Design of Protein
Structures
Lesson 13 : Introducing Databases and proteomics (1)
Lesson 14 : Introducing Databases and proteomics (1)
Review and Final Project
Course Policies and Procedures
Firstly timely submission of materials is of utmost importance as you all have 7 days
in which to read your articles, your lessons and the do the homework assignments.
Points will be deducted for every week your particular assignment is late. It doesnt
matter if you are the next best science writer late papers will cost you. Secondly
everything you send in will be read carefully so please to avoid problems please do
not copy from your fellow classmate. Make a sincere effort! If there is something you
don't understand feel free to ask! Thirdly try to really keep a steady pace with the
lessons. Especially with the structural proteomics material. It needs to be slowly
digested. Procrastination will show itself on what you hand in.
Textbook(s)
Brief Note on the texts used:
Many different texts were consulted to create this course for you. These texts are
listed below. Though you do not have to purchase these texts for this class I would
recommend that in the long run you purchase or peruse at length any one of these
books as they have proven , at least for me, to be a great resource in and out of the
classroom
Recommended: Introduction to Protein Structure -- Carl Branden & John Tooze
Garland, Second Edition
Recommended: Bioinformatics Sequence and Genome Analysis -- David W.
Mount
Cold Springs Harbor Laboratory Press
Recommended: Developing Bioinformatics Computer Skills -- Cynthia Gibas
and Per Jambeck
O'Reilly