Nighat Kokan Cardinal Stritch University

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First Time Implementation Spring 2009

GEP annotations projects were implemented in two courses namely Genetics (BL308) and Readings and Research (BL402) at Cardinal Stritch University during spring 2009.  My future plans are to implement annotations in the lab portion of the Genetics course.  

Lessons learned during implementation

Annotation projects were implemented in the genetics course, taught as directed study due to low enrollment, and continued as independent projects in another course. Implementation of GEP projects in the classroom was definitely challenging for the first time, but subsequent implementations should become easier for the instructor. Students should be “warned” of the challenging nature of the projects and also be reminded that in the end it would be an extremely rewarding experience.

If adjoining contigs are being annotated, the instructor and students should examine their data as a group to ascertain any overlapping regions and genes on different contigs. This would eliminate duplication of effort by different students in the class.

Emphasize to students the value of recording their data and programs used in collecting data from different databases. The students should keep a record of their work in a Word document and save multiple copies of their work /data.

Impact of GEP on students

Students were initially apprehensive and felt overwhelmed due to the extensive base of knowledge that they were required to know in order to complete the annotation research projects. Being a real research project gave the students a sense of excitement and also compelled them to learn more than they would in a standard lab project. Both of my students said annotation projects were a valuable learning experience where they gained insights into how real research was done. They had the realization that science research is often a collaborative effort, where they are contributing their data to a greater whole.

BL 308 Genetics Directed Study Syllabus Spring 2009

The BL308 Genetics,  a 4 credit course, was taught as directed study to two students in spring 2009 due to low enrollment.  These two students also took a Independent Readings and Research course (BL402) with me that same semester.  The GEP material and tutorials were introduced in BL308 genetics class, however, the work on contigs and annotations were completed in the BL402 class.  In future annotations will be implemented in the lab portion of BL308 course 

Professor:  Nighat P. Kokan, Ph.D., Office: RB 218
Contact: Office 414-410-4138 (Voice Mail); Mail Box # 371;e-mail

Office Hours: Mondays & Wednesdays 11:30-12:00; Tuesdays & Thursdays 10:00 – 11:00

Lecture/Lab Wednesday 1:10-4:00, Thursdays 11:00 – 12:20 SH 201
Textbook and website info: Genetics: From Genes to Genomes, Hartwell et al., 2008 3rd edition, William C. Brown Publishers as reference. Supplementary readings, original research papers published by nature journal can be obtained from
The online textbook of Molecular Biology from
Additional textbook readings will be assigned as we proceed in the semester.
Annotation Research Project information and supplementary materials from Genomic Education Partnership site at Washington University in St. Louis accessed at
Lab Manual & Materilas: Protocols provided by the Instructor on Educator and in class. Students should provide a 3-ring binder for filing lab protocols, a bound composition notebook for data collection and recording (lab log book) and a 2-4GB flash key for data collection and storage.
Course Website: for announcements, syllabus, course materials, assignments, problem sets and solutions, external links, grades, Internet resources and supplemental information.

Course Description:

BL 308 (4 Cr.) Overall Course Objectives: Considers the principles, theories and current concepts of heredity. Included are modern technologies, ethical issues, genetic manipulation and engineering that impact society. Three class hours, and three laboratory hours.
Note: Since this is a directed study, there are no formal lectures as such, you are to meet with me each week to work together, chart your progress, ask questions for topics that you are uncertain of and hand in the completed assignments.

Grade Weights Percent
Exams 30%
Problem Sets & Assignments 30%
Research & Lab Reports 20%
Final Exam 20%
Total 100%

BL 308 Genetics Tentative Lecture/Lab Schedule Spring 2009

Week Dates Topics, Chapters & Readings Assignments, Notes, Tests
1. January 21:  Study of Biological Information. Mendelian Genetics (1-2) Use of Model Organisms in Genetics Model organism for Huntington disease example
2. January 26:Transmission Genetics: Monohybrid & Dihybrid Crosses Introduction to FlyLab, Determining Patterns of Inheritance, Probability
3. February 4 Extensions and Exceptions to Mendelian Genetics (3) Chromosome Theory of Inheritance (4) FlyLab continued…Sex Chromosomes Chi Square Test
4. February 11 Linkage, Recombination & Mapping (5) FlyLab continued…. Two Point Crosses
5. February 18 DNA Structure, Replication (6) Gene Anatomy and Function (7) FlyLab Report 1 Due Exam 1
6. February 25 Gene Expression (8) Deconstructing the Genome (9) FlyLab Report 2 Due
7. March 4 Reconstructing the Genome through Genetic and Molecular Analysis (10); HGP Primer; BLAST Family of Programs. Bioinformatics Exercise 1
8. March 11 Overview of Databases NCBI, Entrez, and Data Mining Tools Predicting Genes Bioinformatics Exercise 2
9. March 18 **********Spring Break***********
10. March 25 Eukaryotic Chromosome (12) Exercise 1 & 2 due; Bioinformatics Exercise 3&4
11. April 1 Genetic Analysis in Bacteria (14) Exam 2
12. April 8 Gene Features and Regulation in Prokaryotes versus Eukaryotes (16, 17)
13. April15 Genome Annotation Project Exercise 3 due

14. April 22 Genome Annotation Project, Research Report Draft Due
15. April 29 Genome Annotation Project, Exercise 4 due
16. May 4 Genome Annotation Project Final Report Due
17. May 12 Final Comprehensive Exam @ 10:30 am

BL 402 Readings and Research  Syllabus Spring 2009
Professor: Nighat P. Kokan, Ph.D.
Office: RB 218
Contact: Office 414-410-4138 (Voice Mail); Mail Box # 371; e-mail Best way to contact me is via e-mail!
Office Hours: Mondays, Wednesdays 11:30-12:00, Tuesdays, Thursdays10:00-11:00; Walk-ins are always welcome without appointment for quick clarifications. You can also meet with me at times other than the office hour by consultation and/or appointment.
Class Time: By arrangement with the instructor
Textbook: There is no textbook, scientific journals, library and Internet resources for review of literature and experimental methods.
Lab material: A three ring binder for filing literature and experimental protocols, a bound notebook for recording data and project log. A 2-4 GB flash key for storing data files.

Annotation Research Project information and supplementary materials from Genomic Education Partnership site at Washington University in St. Louis accessed at

BL 402 (2 Cr.) Overall Course Objectives: This is an introduction to current biological literature as a basis for and result of investigation. Students will design and conduct an independent research project under the direction of the instructor. Prerequisites: Consent of department. Two class hours.
Course Outcome: Demonstrate and apply the process of science to a “unique problem” in the biological sciences in an independent research project and present these findings in the form of a research paper and an oral presentation to the faculty and peer group.
Measurable Course Objectives:
1. Survey scientific literature to investigate the relevancy of a project topic using scientific journals and Internet research tools.
2. Be able to design, conduct and test hypotheses in experiments related to the chosen independent project.
3. Be able to collect, analyze, interpret and draw conclusions from data collected from experiments.
4. Demonstrate competency in the use of various techniques, instruments and data bases related to the independent project.
5. Communicate research findings to the faculty and classmates.
Assessment: The course outcomes # 1- 5 above, will be evaluated by the following criteria
1. Literature Reading and Research Proposal
2. Regular Progress Report to Advisor
3. Laboratory Work/ Laboratory Notebook
4. Written Research Paper
5. Oral Report to the Department

Grade Weights
Research Proposal 10%
Lab Work/ Progress Reports/Notebook 30%
Research Paper 30%
Oral Report 30%
Total 100%

Implementation in BL308 Genetics Lab Spring 2010

BL308 Genetics Spring 2010 Syllabus

See Alumni Workshop June 2010 PPT for implemenation strategies, challenges, and lessons learned. for Spring 2010