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CSCI 5931 -- Computational Bioinformatics

Updated January 17, 2009

Office and Addresses

Delta 171 Phone 281.283.3805
email: boetticher@cl.uh.edu
Secretary: Ms. Kim Edwards, Delta 161 281.283.3860

Class Hours

Monday 4:00 - 7:00, Delta 237.

Office Hours

Mon. 7 - 8, Tues. 5:30 - 7, Wed. 5:30 - 7, or by appointment. If the suite door is locked, then call my extension (last 4 digits) using the phone in the hallway.

Why Bioinformatics?

Consulting Resources Corporation expects the total worldwide employment numbers to increase to 750,000 by year 2011 (400,000 of those employed in biotech companies). Major worldwide recruiting firms are also certain of this kind of growth, but no one is willing to go on record about the specific areas of technology from which these jobs will be generated.

The biotechnology industry continues to break new ground, creating products and future jobs that will come from bursts of new technology development. To tens of thousands of worldwide biotech employees, it remains a fascinating and yet challenging industry for a career.

Teaching Assistant

TBD, email: TBD
Office Hours: TBD

Course Description

Molecular data analysis Systems biology Analysis of heterogenous information sources Human Computer Interaction in Information Mining Computational proteomics Integrative data analysis Statistical data analysis Data mining Molecular simulation Biological networks / Metabolism Molecular informatics Data pipelining Data visualization Large scale chemical computation Data integration/semantics Grid/web services Computer architectures in life sciences. The traditional graduate student load is 3 courses. Be prepared to commit 15 to 20 hours per week to this course!

Course Goals

 

The primary goal of this course is to write a paper that is published in a peer-reviewed journal, conference, or workshop. A secondary goal is to provide the student with the necessary knowledge and skills to be very competitive in the Bioinformatics marketplace.

Prerequisites

The prerequisites for this course is the Data Mining Course (CSCI5833). If you do not meet the prerequisites, then you need to drop this course!  

Methodology

Highly interactive.

Appraisal:

  Paper 100%
  Presentations/Participation 30%
  Final Exam 70%

Grading:

    93+ = A; 90 = A-; 87+ = B+; 83+ = B; 80+ = B-;

      77+ = C+; 73+ = C; 70 = C-; 67+ = D+; 63+ = D; 60+ = D-; 0+= F

My motto:

Seek the Truth.

Show altruistic love.

Appreciate beauty.

Required Textbook  

NONE

Journals, Conferences, Workshops, and Organizations

Data Bases

 

Computational Bioinformatics Data Resources

Computational Bioinformatics Software

 

Schedule

 

Jan 14  Course Overview, Introduction to Bioinformatics

FOR NEXT WEEK (IF NOT SOONER)

   Read: Lorentz CP, Wieben ED, Tefferi A, Whiteman DA, Dewald GW. Primer on Medical Genomics, Part I: History of Genetics and Sequencing of the Human Genome. Mayo Clin Proceedings 2002;77:773-782.

   Read: Tefferi A, Wieben ED, Dewald GW, Whiteman DA, Bernard ME, Spelsberg TC. Primer on Medical Genomics, Part II: Background Principles and Methods in Molecular Genetics. Mayo Clin Proceedings 2002;77:785-808.

   Read: Online notes from this semester’s CSCI5833 Course

   Read: Description of the research paper

 

Jan 28  Data Mining Review (What was taught in CSCI5833)

FOR NEXT WEEK (IF NOT SOONER)

  Read: Tefferi A, Bolander ME, Ansell SM, Wieben ED, Spelsberg TC.  Primer on Medical Genomics, Part III: Microarray Experiments and Data Analysis. Mayo Clin Proceedings 2002;77:927-940.

  Microarray tutorial links:

http://www.bio.davidson.edu/courses/genomics/chip/chip.html

http://www.affymetrix.com/corporate/outreach/lesson_plan/educator_resources.affx

 

Feb 04 –  Microarray Data Analysis

FOR NEXT WEEK (IF NOT SOONER)

  Read: Pardanani A, Wieben ED, Spelsberg TC, Tefferi A. Primer on Medical Genomics, Part IV: Expression Proteomics. Mayo Clin Proceedings 2002;77:1185-1196.

   Read: W. Yu, B. Wu, T. Huang, X. Li, K. Williams, H. Zhao, Statistical Methods in Proteomics, Springer Handbook of Enginerring Statistics, 2005, Pp. 1-37.

 

Feb 11 – Expression Proteomics

FOR NEXT WEEK (IF NOT SOONER)

  Read: Elkin PL. Primer on Medical Genomics, Part V: Bioinformatics. Mayo Clin Proceedings 2003;78:57-64.

 

Feb 18 – Bioinformatics

FOR NEXT WEEK (IF NOT SOONER)

  Read: Ansell SM, Ackerman MJ, Black JL, Roberts LR, Tefferi A. Primer on Medical Genomics, Part VI: Genomics and Molecular Genetics in Clinical Practice. Mayo Clin Proceedings 2003;78:307-317.

 

Feb 25 – Genomics and Molecular Genetics in Clinical Practice

FOR NEXT WEEK (IF NOT SOONER)

  Read: Wieben ED.  Primer on Medical Genomics: Part VII: The Evolving Concept of the Gene. Mayo Clin Proceedings 2003;78:580-587.

 

Mar 03 – The Evolving Concept of the Gene

FOR NEXT WEEK (IF NOT SOONER)

  Read: Shaughnessy J Jr. Primer on Medical Genomics, Part IX: Scientific and Clinical Applications of DNA Microarrays — Multiple Myeloma as a Disease Model. Mayo Clin Proceedings 2003;78:1098-1109.

 

Mar 10 –  Scientific & Clinical Applications of DNA Microarrays

FOR NEXT WEEK (IF NOT SOONER)

  Read: Russell SJ, Peng K-W. Primer on Medical Genomics, Part X: Gene Therapy. Mayo Clin Proceedings 2003;78:1370-1383.

 

Mar 17 No class - Spring Break

 

* Last day to drop a class/withdraw for the semester is Mar 24th *

   

Mar 24 –  Gene Therapy

FOR NEXT WEEK (IF NOT SOONER)

  Read: Goetz MP, Ames MM, Weinshilboum RM. Primer on Medical Genomics, Part XII: Pharmacogenomics — General Principles with Cancer as a Model. Mayo Clin Proceedings 2004;79:376-384.

 

Mar 31 –  Pharmacogenomics - Gen. Principles with Cancer as a Model

FOR NEXT WEEK (IF NOT SOONER)

  Read: Morel NM, Holland JM, van der Greef J, et al. Primer on Medical Genomics, Part XIV: Introduction to Systems Biology — A  New Approach to Understanding Disease and Treatment. Mayo Clin Proceedings 2004;79:651-658.

   Read: Tefferi A, Thomas C., Spelberg TC.  Primer on Medical Genomics: The End of the Beginning, Mayo Clin Proceedings, 2004; 79:659-660.

 

Apr 07 –  Introduction to Systems Biology, BioGrids  

FOR NEXT WEEK (IF NOT SOONER)

 

Apr 14 – Paper Presentations

FOR NEXT WEEK (IF NOT SOONER)  

 

Apr 21 – Review for final

FOR NEXT WEEK (IF NOT SOONER)  

 

Apr 28 – Final Exam

 

 

Other Policies

Homework, Projects, Research Paper

  • Homework and projects are due exactly at the prescribed time (usually the beginning of class). As soon as a homework or project is collected, then all others are considered 1 day late (even if it only 3 minutes). In the event you might be running late, you might want to email the assignment. Also, when preparing your assignment, be mindful of possible backlogs at the printer, jammed printer, printer out of toner, etc.

  • Late homework/projects are accepted with a penalty of 10% deduction per 24-hour period after the due date. No late project will be accepted one week after the due date. The last homework/project cannot be late.

  • There will be no extra-credit homework or projects in this course.

  • All homework and projects must be typed not hand-written.

  • A cover page is expected for all homework and projects.

  • VERY IMPORTANT! In certain classes students are encouraged to work in groups. For this class you are expected to work on all homework and projects individually. Students may not discuss, use, email, show, give, buy, sell, borrow, trade, steal, etc. in whole or part, any of the homework or projects in any manner not prescribed by the instructor. Penalty for cheating will be extremely severe and may result in an F for this course. This condition applies even after you complete this course!

  • VERY IMPORTANT! Failing to report to the instructor any incident in which a student witnesses an alleged violation of the Academic Honesty Code is considered a violation of the academic honesty code. Please see me to discuss any incidents.

  • VERY IMPORTANT! Purchasing, or otherwise acquiring and submitting as one's own work any research paper or any other writing assignment prepared by others constitutes cheating. Penalty for cheating will be extremely severe and may result in an F for this course.

  • VERY IMPORTANT! Plagiarism on either an abstract, draft of a paper, or final paper will result in a 0 for all three parts (abstract, draft version, final paper). Please review the following links regarding plagiarism very carefully: http://www.indiana.edu/%7Ewts/wts/plagiarism.html              http://www.hamilton.edu/writing/style/plagiarism/plagiarism.html                 http://ollie.dcccd.edu/library/Module4/M4-VII/plagar.htm                                                 http://www.realisticdiplomas.com/A-Guide-To-Plagiarism.aspx

  • Standard academic honesty procedure will be followed. See the following link for additional information: http://b3308-adm.cl.uh.edu/PolicyProcedures/Policy.html

Tests and Quizzes

  • There are no make-up tests except in verified medical emergencies and with immediate notification. Rescheduling a final exam in order to catch a plane flight is unacceptable. Make up exams are harder, and different, than original exams.

  • There are no make-up quizzes. Allow plenty of additional time in the event that webCT crashes.

  • You are responsible for all required readings assigned throughout the semester.

  • Students are to work on test and quizzes individually.  Students may not discuss, show, give, sell, borrow, trade, share, etc. their tests or quizzes. Penalty on cheating will be extremely severe. Standard academic honesty procedure will be followed.

  • VERY IMPORTANT! Providing answers for any assigned work or examination when not specifically authorized by the instructor to do so. Or, informing any person or persons of the contents of any examination prior to the time the examination is given is considered cheating. Penalty for cheating will be extremely severe and may result in an F for this course.

  • VERY IMPORTANT! Failing to report to the instructor any incident in which a student witnesses an alleged violation of the Academic Honesty Code is considered a violation of the academic honesty code. Please see me to discuss any incidents.

Miscellaneous

  • Any person with a disability who requires a special accommodation should inform me and contact the Disability services office or call 281 283 2627 as soon as possible.

  • You are expected to come fully prepared to every class!

  • Incomplete grades or administrative withdrawals occur only under extremely rare situations.

  • The ringing, beeping, buzzing of cell phones, watches, and/or pagers during class time is extremely rude and disruptive to your fellow students and to the class flow. Please turn off all cell phones, watches, and pagers prior to the start of class.

  • There is no formal attendance policy. However, it is my experience that those students who do attend class on a regular basis do better on tests than those that don't.

  • I am willing to provide letters of recommendation/references only if you have attained an 'A' in one of my classes, or two 'A-' in two of my classes.

  • I highly recommend that you seek out your advisor and complete you Candidate Plan of Study (CPS) as soon as possible. I am normally not available for advising during the summer months.

  • Pay very careful attention to your email correspondence. It reflects on your communication skills. Below is a compilation of email errors I have received during the past year.

    dear sir.

    wen r u gonna grad the homework, bcoz i have a doubt about the third problem

    Some student

    Common problems:

       *   wen instead of when

       *   bcoz instead of because

       *   r instead of are

       *   u instead of you

       *   lowecase i instead of I

       *   starting a sentence with a lowercase letter

       *   doubt instead of question

  • I immediately discard anonymous emails.

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2700 Bay Area Boulevard
Delta Building. Office 171
Houston, Texas 77058
Voice: 281-283-3805
Fax: 281-283-3869
boetticher@cl.uh.edu


2002-2009 Boetticher: Computational Bioinformatics course, All Rights Reserved.

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