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BINF 4445/5445 Bioinformatics Theory and Applications

 

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

 

Fall 2013

·         Location: EIT 220

·         Lectures (taught by D. Berleant): Tuesdays   9:25–12:05

·         Labs      (taught by M. Yang):     Thursdays 9:25–12:05

·         Web site: http://ualr.edu/jdberleant/courses/BINF4445+5445/syllabus.html.

Lecture instructor: Daniel Berleant, PhD

·         Office: EIT 562

·         Phone: 569-3488 (email will most likely get a faster response than leaving a voice mail message)

·         Email: jdberleant@ualr.edu

Lab instructor: Mary Yang, PhD

·         Office: EIT 303

·         Phone: 683-2035

·         Email: mqyang@ualr.edu


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 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 prepared for advanced specialized study of narrower topics in bioinformatics.

· Graduate students will complete and write up 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).

 

Textbook and Other Information Sources

·         Buy 2 relevant textbooks of your choice. They should be from amazon.com, half.com, bestwebbuys.com/books, or some other place where you can get inexpensive or even free books. Students might be asked to review their books and we might make the reviews available for students in future years.

·         Free textbooks may be obtained from:  

·         http://www.freebookcentre.net/Biology/Biology-Books-Online.html,

·         http://www.textbookrevolution.org/, &

·         http://www.e-booksdirectory.com/.

·         http://openhelix.com

·         http://wikipedia.org has a surprisingly extensive collection of relevant articles

Videos:

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

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

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

On-line glossaries (please inform me if you find any other useful ones) include:

·         http://www.biochemistry.org/groups/ppsg/glossary.htm

·         http://chevreux.org/thesis/node9.html

Lecture slides from other places:

·         http://gcat.davidson.edu/Pirelli/index.htm. Cool interactive video site about biotechnologies.

·         http://bioinformatics.ca/workshops/

·         http://ocw.mit.edu/OcwWeb/Biology/index.htm

·         http://ocw.mit.edu/OcwWeb/Biological-Engineering/index.htm

Tutorials, movies, slides, documentation on assorted (noncommercial) tools:

·    http://openhelix.com/cgi/freeTutorials.cgi

 

Assistance and advice regarding presentations:

·         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.

 

Assignments & grading

·         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 necessarily be identical for students in the undergraduate section of the course and students in the graduate section.

·         Lab assignments, when graded, will count the same as homework assignments.

·         Final exam: 2013 will not have a final exam. Instead, the project report will be due at the scheduled time of the exam.

·         The graduate student projects (2-3 students per project team) will count equivalently to 4 HWs, 2 for the presentation and 2 for the report. The undergraduate student demo (2-3 students per team) will count as 2 HWs, 1 for the presentation and 1 for the report.

·         No quizzes are currently scheduled except for an in-class exercise on the biologically major amino acids, 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 in general may be given and may be assigned point values from 0-25 pts.

·         Letter grades are equivalent to number ranges 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.)

 

·         When letter marks are used to score assignments, they are equivalent to numbers as follows:

A+   (100%)

A   (95%)

A-   (91.166%)

A-/B+   (90.5%)

B+/A-  (89.5%)

B+   (88.833%)

B   (85%)

B-   (81.166%)

B-/C+   (80.5%)

C+/B-  (79.5%)

C+   (78.833%)

C   (75%)

C-   (71.166%)

C-/D+   (70.5%)

D+/C-  (69.5%)

D+   (68.833%)

D   (63.33%)

D/F   (60%)

F/D   (55%)

F   (50%)

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 right after (or during) class, or 10% if handed in by 9:00 p.m. 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.

 

Students with disabilities: It is the policy 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 http://ualr.edu/disability/.

 

Schedule of Activities, Fall 2013

 

·         Bold text in the table below is updated (partly or fully) for this semester.

·         Non-bold text is *not* yet updated, but is from last year (or before) and is provided for informational purposes.

 

Days & dates

Notes

Assignments

(Instructor use)

Tu Aug. 20, 2013

·       Intro to course: syllabus & course info, icebreaker (name card scramble), login check

·      History & background: What is bioinformatics? DNA sequencing background

HW #1 (due M&Tu Aug. 26-7, 2013)

Ser. #1, lecture1,

check lecture1/queue

Th Aug. 22, 2013

Introduction to R for bioinformatics

Lab #1 (due Th Sept. 5, 2013)

Ser. #5, Ser. #5a, lab1c

Tu Aug. 27, 2013

·         Student slides

·         Microarrays

·         Next generation genome sequencing (read & discuss); Exponential change; Nanopore approach; When Genomes get Cheap (no longer online)

HW #2b (due Tu Sept. 3, 2013)

Ser. #31, lecture 3a, Supplementary: Motivation for microarrays, www.gene-chips.com

Th Aug. 29, 2013

Guest speakers:

·         Weida Tong, PhD (NCTR) on "Bioinformatics for biomarker development and personalized medicine," and

·         Hong Fang, PhD (NCTR) on the ArrayTrack tool

Sample microarray data (for lab HW)

Lab3B, Ser. #6; old: www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack. Find public domain tool and demonstrate its use. There was once an Array/Track workshop (Drs. Weida Tong and Fang)

Tu Sept. 3, 2013

HW #3b (due Tu Sept. 10, 2013): see form

Ser. #32, lecture 4a

Th Sept. 5, 2013

P. Williams: Codon bias, microarrays, R for processing microarray data, exercise

 

Old: Supplement: 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, Ser. #9, Lab 4B)

Tu Sept. 10, 2013

Gel electrophoresis (e.g. PAGE) & analyzing proteomic data (instr. note: mass spec needs more on after cleaving); protein sequencing; demo; and lab-like exercise

HW #4b (due Tu Sept. 17, 2013)

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

Th Sept. 12, 2013

Next generation data analysis — short reads and alignment 

lab7

Tu Sept. 17, 2013

Amino acid substitutionsbackground:

·         www.icp.ucl.ac.be/~opperd/private/pam1.html (not a PAM matrix, a precursor to it) and

·         www.lmb.uni-muenchen.de/Groups/Bioinformatics/04/ch_04_3.html

HW #5a (due Tu Sept. 24, 2013)

Ser. #10, lecture 5a

Th Sept. 19, 2013

RNA-Seq data analysis

lab5c

Tu Sept. 24, 2013

HW6a

HW9

Th Sept. 26, 2013

ChIP-Seq data analysis

lab14

Tu Oct. 1, 2013

HW7c

old HW 11

Th Oct. 3, 2013

Machine Learning (decision trees, regression)

lab6

Tu Oct. 8, 2013

More protein structure prediction (ser. #26, I7-);
News: computing flu structure

News: ancient protein structures
News: DNA and some proteins act like machines

HW8b (due Tu, Oct. 22, in 2 weeks)

 

Th Oct. 10, 2013

Machine learning (Bioconductor packages)

lab15

Tu Oct. 15, 2013

Fall Break, no class

 

Th Oct. 17, 2013

Perl workshop

lab16

Tu Oct. 22, 2013

HW #9a

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

Th Oct. 24, 2013

UCSC Genome Browser

 lab17

Tu Oct. 29, 2013

  • Possible supplements:

·         PhenX

·         Pig genome; (ser. #36)

·         Cladogenesis isn't the only way...

·         Gene pollution; (ser. #35)

·         Do we have our own genome? (Ser. #15)

·         Discussion: pigs, gene pollution and the simplification called "divergent evolution "

HW #10a (due Tu, Nov. 5, 2013)

 

Th Oct. 31, 2013

Ensembl genome browser

 lab18 

Tu Nov. 5, 2013

  • Possible supplements:

·         PhenX

·         Pig genome; (ser. #36)

·         Cladogenesis isn't the only way...

·         Gene pollution; (ser. #35)

·         Do we have our own genome? (Ser. #15)

·         Discussion: pigs, gene pollution and the simplification called "divergent evolution "

HW #11b (due Tu, Nov. 12, 2013); old HW, another old HW (test-like part and plagiarism part, ser.#10)

Too much material here to cover it all!

Th Nov. 7, 2013

Software tools: sequence alignment and phylogenetic trees

 

lab19

Tu Nov. 12, 2013

HW #12 (due Tu, Nov. 19, 2013)

 

Th Nov. 14, 2013

Biological databases

 

lab20

Tu Nov. 19, 2013

HW #13 (due Tu, Nov. 26, 2013)

lecture 6; 2006: test HW #6 ; hw13, 14 (like a final)

Th Nov. 21, 2013

DeepView

lab21

Tu Nov. 26, 2013

  • Supplements:

·         PhenX

·         Gene pollution (ser. #35)

(No HW over Thanksgiving vacation)

test; HW #6

....

Th Nov. 28, 2013

Thanksgiving Vacation

 

Tu Dec. 3, 2013

  • Possible supplements:

·    Pig genome; (ser. #36)

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

·        Interpreting your genome (find updated news)

·    Cladogenesis isn't the only way...

·    Do we have our own genome? (Ser. #15)

·         Discussion: pigs, gene pollution and the simplification called "divergent evolution "

 HW #14a

 

Th Dec. 5, 2013

Project presentations (15 min. per student)

HW: Finish project reports. Due at time of scheduled final (Tu Dec. 17, 2013, 8:00 a.m. – 10:00 a.m.)

 

Tu Dec. 10, 2013

Consultation day (no classes, exams, or assignments due)

 

 

Tu Dec. 17, 2013, 8:00 a.m. – 10:00 a.m.

Final exam F’13 (which is the due date to hand in your project report; no actual test)

 

 

Extra lecture

 Global local sequence alignment

 

 lecture17 (from web)

old lecture

 

 

old lab

OU Supercomputing Conference, no class (but what in that conference is bioinformatics related?)

 

lab 7B

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

old lab

2008: student demos of lab assignments; Statistics guest speaker;

Final project report and presentation due Dec. 10, 2009

lab12B, ser #25a

old lab

Experimental design: Stekel chap. 10; 2008: seminar report

Reading before class: Stekel chap. 10

Ser. #24, lab11B

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

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

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

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

old lab

DNA extraction demo

ArrayTrack HW emailed out Nov 16, due Nov. 28

Ser. #26b

old lab

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

old lecture

Automatic processing of biological texts (Ser. # 29, lecture 15); Chapter C in Westhead et al. (biological formats and databases) Ser. #4, lecture2; student contributions; transcription codon poster talks; Tools (by 4445 students); Annotation (by students); 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"); review for final

HW 13; HW14 (like a final)

 

old lab

Array/Track workshop (Drs. Weida Tong and Fang) Lab3B, Ser. #6

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

 

old lecture

Chapter D and section E1 in Westhead et al. (searching for sequences; alignment); more alignment (Ser. #7, lecture 3)

HW3