BINF 4445/5445  Bioinformatics Theory and Applications

Here is general information about the course. A tentative schedule of topics and assignments follows the general information.

 

Fall 2009

Location: Ross Hall 404

Lectures (taught by D. Berleant): Mondays starting at 6:00 p.m., continuing for approximately 150 minutes plus breaks but no later than 9 p.m. 

Labs (taught by R. Nagarajan): Wednesdays starting at 6:00 p.m., continuing for approximately 100 minutes plus breaks until about 8:00 p.m.

Web site for lectures: http://ifsc.ualr.edu/jdberleant/courses/BINF4445+5445/. (For information on the labs, refer to Dr. Nagarajan.)

Office hours:

Dan Berleant is available:

·    Mondays 3:30-5:30 p.m. in ETAS 259D, after class, and by appointment. Please avoid times between 5:30 and class time at 6:00 if possible.

·    24/7 by email at berleant@gmail.com. My UALR email address works slower, so I don't recommend it, however UALR is currently transitioning to gmail as a service provider, at which time my UALR address may become faster.

 

Instructor:
Daniel Berleant
Office: ETAS 259D
Phone: 569-3488 (if no answer, email may get a faster response than leaving a voice mail message)
Email (primary): berleant@gmail.com (primary; note the @gmail.com, not @ualr.edu)

Email (secondary): jdberleant@ualr.edu (slower, and forwards to berleant@gmail.com anyway)

Web site: http://ifsc.ualr.edu/jdberleant

Course Description
An overview of concepts central to the science and use of bioinformatics. Draws upon the fields of biostatistics, computer and information science, and the life sciences. Course is offered for both graduate and undergraduate credit. The graduate version of the course is an integral part of the UALR/UAMS Joint Graduate Program in Bioinformatics. The undergraduate version of the course is the final course in the UALR undergraduate minor in bioinformatics.

Course Objectives

·     Students will be able to apply important ideas in bioinformatics to solve representative problems and exercises in the field.

·     Students will be able to work with a team to complete a technical project and present their findings in a professional manner.

·     Students will be able to research the Web for information needed to understand and state in their own words ideas presented in passages in the field written at an advanced level for professionals.

·     Students will be well prepared for advanced specialized study of narrower topics in bioinformatics.

·     Students will complete a research oriented task that is modest in size and scope, but must be done to a high degree of quality (when writing for publication in a major journal, for example, quality must be equivalent to an A+, or it will be rejected). This semester the research component will be to write a small section, and eventually be one of the authors, of a group-authored paper on the genetic code. In the past, related tasks have led to two student posters at a conference (one winning a student poster award), and a student being a coauthor of a published journal paper. This time, I am ambitiously hoping all students will become coauthors of a published paper. (This paper will not be published until after the course is over, due to long lead times on such things, so patience is needed!.)

Textbook and Other Information Sources

  • Required for lectures: M. Zvelebil and J. Baum Understanding Bioinformatics, Garland Science, 2007. ISBN 0815340249.
  • Required for labs: Last time the required book was Stekel, D., Microarray Bioinformatics, Cambridge University Press, 2003. ISBN 052152587X. This year, it may be different.
  • Free textbooks may be obtained from: http://www.textbookrevolution.org/.
  • Videos:

·         Journal of Visualised Experiments (JoVE) : http://www.jove.com/

·         Bioscreencast: http://www.bioscreencast.com/

·         SciVee: http://www.scivee.tv/taxonomy/term/4

·         http://openhelix.com/sponsored.shtml

  • http://wikipedia.org has a surprisingly extensive collection of relevant articles
  • On-line glossaries (please inform me if you find any other useful ones) include:
  • Assistance and advice regarding presentations can be useful. The Communication Skill Center (CSC) is a campus resource devoted to helping students in the various stages of preparing a presentation. Services include, but are not limited to, anxiety management, brainstorming, research, organization, outlining, PowerPoint presentations, and providing presenters with ethical feedback. The CSC is located in room 201 of the Speech Communication building, which is located across from the tennis courts. Appointments are available and walk-ins are welcome; please feel free to stop by or call at 569-8208.

Grading (current grades here)

  • There will be a homework assigned in lecture approximately every week. Most will be worth from 50 points for an assignment not handed in, to 100 points for a perfect job. The homeworks will not always be identical for students in the undergraduate section of the course and students in the graduate section.
  • There will be lab assignments. See the lab instructor for full details. The lecture (3 contact hours, equivalent to 3 credits) will count for 75% of the grade, and the lab (2 lab contact hours is equivalent to 1 credit) will count for 25% of the grade. Recall this is a 4-credit course.
  • There will be one test and one final, each worth from 50 for one not taken to 100 points for all correct.
  • No quizzes are currently scheduled, but we reserve the right to give both scheduled and unscheduled (“pop”) quizzes worth 0-25 pts. if in our judgment it leads to more learning. By more learning, we include things like doing reading assignments, attendance, more studying, etc..
  • In-class exercises may be assigned point values. 
  • Letter grades will be assigned as follows:

A+ (96.67-100%)

A (93.33-96.67%)

A- (90-93.33%)

B+ (86.67-90%)

B (83.33-86.67%)

B- (80-83.33%)

C+ (76.67-80%)

C (73.33-76.67%)

C- (70-73.33%)

D+ (66.67-70%)

D (60-66.67) 

F (0-60)

(+’s and –’s will not appear in the grades submitted to the registrar.)

Lateness: homework assignments are due at the beginning of class unless otherwise announced. Do not attempt to finish your assignments during class (15% off penalty)! Late hand-ins will be penalized at 15% if handed in after (or during) class, 10% if handed in by 9:00 the following evening, plus 10% for each additional 24-hour day or fraction thereof.

If you get sick or have some other hardship with some particular assignment let the instructor know and a reasonable solution will be arranged.

About last year's lab portion of the course (for this year, contact the lab instructor): The lab sessions focus on material helpful to students with their class project analyzing microarray datasets (each two-person team will be given a different dataset).  The deliverables of this project constitute a significant part of the course.  Graduate students will be held to a higher standard in the grading of their class projects.  Some laboratory sessions will draw upon the insight of outside experts who will participate in class discussions and who can consult on problems students are encountering. 

Students with disabilities:  It is the policy and practice of the University of Arkansas at Little Rock to create inclusive learning environments.  If there are aspects of the instruction or design of this course that result in barriers to your inclusion or to accurate assessment of achievement--such as time-limited exams, inaccessible web content, or the use of non-captioned videos--please notify the instructor as soon as possible.  Students are also welcome to contact the Disability Resource Center, telephone 501-569-3143 (v/tty). For more information, visit the DRC website at www.ualr.edu/disability.  

Schedule of Activities, Fall 2009

..

  • Note: bold text in the table below is accurate.  Non-bold text is provided for historical & informational purposes only.

 

 

Comment: our advancing-the-field themes in past years have been new visualizations of the codon table, and glossary/study guide for the old textbook (we have a much newer one this year). For this year, we will do the codon table again, but this time be specifically focused on two successor papers to the one we recently published. Another possibility, if there are enough people in the class or people want to do two researchy activities, is new metrics for advances in biotechnology.

 

Day & date

Notes

Assignments

(instructor & historical use)

 

 Wednesdays

Mondays

 

Fall 2007 changes

M Aug. 24, 2009

Intro to course; what is bioinformatics? How is DNA sequenced?

HW #1 (due M Aug. 31)

Ser. #1, lecture1

old lab

Motivation for microarrays; Introduction to Microarrays (Tao Han, PhD, NCTR);

Project Assignments

Read before class: Stekel chapters 1 & 2, www.gene-chips.com.

Ser. #2, lab1B (2006: Steve Jennings lectured)

M Aug. 31, 2009

Gel electrophoresis (e.g. PAGE), applied to analyzing proteomic data, and student contributions; protein chips; protein sequencing; possible demo and lab exercise

HW #2 (due M Sept. 14)

Ser. # 28, lecture 14, chap. K in Westhead

old lab

Image Analysis;

ScanAlyze tutorial & hw (Michael Bauer)

Read before class: Stekel chap. 4 and rana.lbl.gov/manuals/ScanAlyzeDoc.pdf (ScanAlyze manual)

ScanAlyze HW and tutorial lab, due W. Sept. 10

Ser. #3. lab2B

M Sept. 7, 2009

Labor Day – vacation

 

Ser. #4, lecture2 

old lab

Seminar report instead of Nidhal Bouaynaya guest lecture

 

 

 

ArrayTrack Workshop will be on 12/3/08

Read to prepare: www.fda.gov/nctr/science/centers/

toxicoinformatics/ArrayTrack

(If no workshop, instead find public domain tool and demonstrate its use, or demonstrate ArrayTrack anyway, due 11/7.)

Lab3B, Ser. #6

earlier year: Array/Track workshop (Drs. Weida Tong and Fang)

M Sept. 14, 2009

Microarrays; Exponential change. Application: next generation genome sequencing. Implications of cheap sequencing.

HW #3a (due M Sept. 21)

Ser. #31, lecture 3a

 

old lab

Guest lecture: Data Preprocessing Using Perl (Roger Hall); Data Management (Vinay Ravindrakumar); bioinformatics faculty research (a faculty member, e.g. RN, wishing to make one or more rotation, master's, or Ph.D. projects available to bioinformatics students)

Read before class: www.cpan.org, www.perl.com/pub/q/documentation;

Data Preprocessing Using Perl HW

Invite all BINF faculty to give talks to inform or recruit students to projects available in their labsSer. #9, Lab 4B;

M Sept. 21, 2009

HW slides that you emailed me; back to basics: DNA, RNA, & protein

HW #4a (due M Sept. 28)

Ser.  #32, lecture 4a

old lab

Data normalization; data normalization using S-Plus (Phil Williams)

Read before class: Stekel chaps. 5, 6;

elms03.e-academy.com/splus; statwww.epfl.Ch/splus/doc/juonen-fourth.pdf;

Assignment: data normalization using S-Plus, due 10/15/08

Ser. #10b, Lab 5B

M Sept. 28, 2009

Amino acid substitutions;

background: www.lmb.uni-muenchen.de/Groups/

Bioinformatics/04/ch_04_3.html and www.icp.ucl.ac.be/~opperd/private/pam1.html

HW #5 and supplementary note (due M Oct. 5)

 

Ser.  #10, lecture 5a

Old workshop

9/23/06: R and S+ workshop (Dr. John Thaden and Roger Hall)

 

 

old lab

Analysis of Differential Gene Expression (Eric Siegel)

2008: Go to a seminar instead.

Reading: Stekel chap. 7, www.weizmann.ac.il/home

/ligivol/publications/ Oncogene%202001a.pdf (1) Assignment: Sig Testing/Gene ID (diff. gene expr. analysis), due Oct. 29; also  (2) Assignment: provide a 1-page summary of a seminar

Ser. #8, lab 6B

 

Sa Sept. 30, 2006: bioPerl programming workshop (Roger Hall)

 

Ser. #12

M Oct. 5, 2009

Go over HW5 Q4; finish PAM from last time starting with slide 32; Baltimore essay (cached and on the Web); steps missing from the codon table (document); the codon table hardly even scratches the surface of the 68 molecules of life (credit: http://ucsdnews.ucsd.edu/graphics/images/2008/09-08MolecularBuildingBlocksBIG.jpg); folder “translation” has some videos & stuff; translation visualizations;  “The genetic code–more than just a table”

HW #6

Ser. #23, lecture 6

2006: test

 

 

 

 

M Oct. 12, 2009

Get grade posting codes; student slides; fractal globules update to earlier lecture; tRNA from the steps missing from the codon table (document); toxoplasmosis notes and paper lec. 10, ser. #33

HW #7 (dir hw7a)

 

old lab

OU Supercomputing Conference, no class

 

lab 7B

M Oct. 19, 2009

Multiple sequence alignment

HW #8a

lecture16, HW8a, Ser. #13

 

 

 

 

M Oct. 26, 2009

Phylogenetics, cladistics, ontologies; (Ser. #15)
background on varied speeds of evolution: the tuatara;
background on the background: the tuatara

HW #9a

(originally based on chapter G in Westhead et al.)

old lab

Analysis of rel. of genes, tissues/treatment (X. Xu)[about 1 hr.]; significance analysis of MA (SAM) and cluster analysis (Vinay); 2008: report on seminar instead

Read before class: Stekel chap. 8,

www-stat.stanford.edu/~tibs/SAM/,

Rana.lbl.gov/EisenSoftware.htm;

Cluster analysis and sig. testing/gene identification using SAM, due 11/5/08

Ser. # 16,

lab 8B

M Nov. 2, 2009

Newly sequenced pig genome; (ser. #36)

Generating cladograms & tuataras (finish from last time);

Floating prairies of the sea; (ser. #34)

Gene pollution; (ser. #35)

Discussions

HW #10a

 

M Nov. 9, 2009

Future human evolution (by students from HW) (Ser. # 19);

Annotation of the genome (from chapter H in Westhead et al.); ORFs (Ser. #19)

HW11a

HW8, HW10: test-like part and plagiarism part (ser.#10)

old lab

Classification analysis (Vinay);

Classification (Dr. Mariofanna Milanova)

2008: seminar report

Read before class: Stekel chap. 9;

www.cs.waikato.ac.nz/~ml/weka/;

Classification HW, due 11/12/08

Ser. #18, Lab 9B

M Nov. 16, 2009

Tools (by 4445 students)

Annotation (by students)

Dino-chickens (ser. #37); evo-devo video clip

Protein structure (Ser. #21, I1-I3)

HW12a

HW9

old lab

Mechanisms, Function & Pathway Analysis (Dr. Wong)

Pathway analysis (Vinay)

2008: seminar report

Reading before class: genenet2.utmem.edu/geneinfoviz/search.php,

Vortex.cs.wayne.edu/research.htm;

HW on Mechanisms, Function/Path. Analysis, due W Nov. 19

Ser. #22, lab10B

old lab

Experimental design: Stekel chap. 10

2008: seminar report

Reading before class: Stekel chap. 10

 

Ser. #24, lab11B Dr. James Chen from NCTR wasn’t available Last year: Data Standards {Ted Bearden?}

M Nov. 23, 2009

Attend two bioscience seminars by the end of the course, and submit your notes. We will meet today only to answer any questions you might have about the course, if you have any.

No HW over Thanksgiving

 

old lab

2008: student demos of lab assignments

(Statistics guest speaker)

Final project report and presentation due

W Dec. 10, 2009

lab12B, ser #25a

M Nov. 30, 2009

Discuss 6-D codon representation paper and dodecahedron lab; (ser. #21)

Sections I4-I6 in Westhead et al. (amino acid substitution & protein structure) (ser. #25); movie clip; http://molvis.sdsc.edu/visres/index.html could be good for demoing or accompanying lab

Finish chapter I in Westhead et al. (protein structure prediction); Ser. #26

Illustrative demo; original Drexler paper (1, 2) Ser. #26

Jed: Also someone needs to code the gull wing table in java or c++

Take-home test to be handed out Wednesday, due next Monday

HW 11

HW 12

old lab

DNA extraction demo

ArrayTrack HW emailed out Nov 16, due Nov. 28

Ser. #26b

M Dec. 7, 2009

Chapter J in Westhead et al.(gene expression data) Ser. # 27, lecture 13

The various –omics. Genomics. Methylomics / epigenomics (see methylomics.doc file). (Next lecture does proteomics, followed by literaturomics.)

 

 

old lab

No class if Thanksgiving; otherwise bioinformatics career survey introduction, results (http://github.com/michaelbarton/bioinformatics-career-survey/tree/master%2Fdata%2Fsurvey.csv?raw=true), and analysis (http://openwetware.org/wiki/Biogang:Projects/

Bioinformatics_Career_Survey_2008_Results)

Assignment: in this lab session, analyze the data and present your results

lab13B

 

Chapter C in Westhead et al. (biological formats and databases); student contributions; transcription codon poster talks

 HW 13; HW14 distributed on Wednesday

 

old lab

ArrayTrack Workshop

Read to prepare: www.fda.gov/nctr/science/centers/

toxicoinformatics/ArrayTrack

Lab3B, Ser. #6

earlier year: Array/Track workshop (Drs. Weida Tong and Fang)

 

Chapter D and section E1 in Westhead et al. (searching for sequences; alignment); more alignment

 

HW3

Ser. #7, lecture 3

 

old lab

Student project presentations

Student project presentations

2008: Final project write-ups are due by 6pm on Monday, Dec. 2 (both emailed to Dr. Jennings and a hard-copy delivered)

Ser. # 29, lab 15B

 

 

 

 

M Dec. 14, 2009

Student project presentations

Student project presentations

Hand out take-home HW/Final

Ser. # 29, lab 15B

Supplement

Chapter L in Westhead et al.(biomolecular interactions and pathways); transcription codon poster talks; review for final

biotech futures (e.g. http://www.edge.org/3rd_culture/church_venter09/church_venter09_index.html. Includes but not limited to: "Edge hosted an amazing session that described the looming future of biology — this is for the real futurists. It featured George Church and Craig Venter talking about synthetic genomics — how we're building new organisms right now and with presentiments for radical prospects in the future... There are six hours of video there")

 

Ser. # 29, lecture 15

2008: Tu Dec. 16, 6 p.m.

The actual final exam session will be for making up late HWs. Attend only if you have HWs to make up. (last year: Take-home HW/Final due.)

 

Ser. # 30

2006 Final exam