Gerry McNeil York College/CUNY

From GEP Wiki
Jump to: navigation, search

Genomics at York College, The City University of New York
We initially ran GEP at York using the independent study platform (Bio 490-493). This was due a limited number of macintosh computers and also it allowed me to run through the curriculum with a small number of students. In the Spring of 2009, we plan to run GEP through our Bioinformatics course Btec 352 which can accommodate up to 20 students.

Comments about time: The independent study format worked very well allowing us to schedule two three-hour blocks per week for 14 weeks. This enabled us to use the first 6-7 weeks on finishing and the last 7-8 weeks for annotation and student presentations. The downside to this format is that the instructor recieves very little teaching credit, only 1/3 an hour per student. So instead of recieivng 6 contact hours, I recieved only 1 since I had three students. The other drawback is finding a time slot that everyone can attend. This would prevent having more than a few students per semester since our students schedules are quite compressed leaving little free time to work with. 

Projects versus Exercises: For each section (finishing and annotation) I started with lectures using materials provided through the GEP and other s materials. This was followed by practice excercises also provided by the GEP which we did together as a group. We then started with individual projects for the remaining part of the aloted time (see schedule). Students worked independently on their individual fosmids with help from our TA and myself. I did encourage them to discuss their successes and failures with their classmates throughout the semester. Interesting findings or p[roblems were presented to the class by the TA or instructor for learning purposes.

Outcomes: All the students prepared written reports for both finishing and annotation and were required to do an oral presentations on either of the two projects. Student were very excited about the idea of their own fosmids and posssibly making a real contribution to the scientific community. They were totoally engaged and each of the students was able to complete a fosmid for both finishing and annotation during the semester.

Grading: Grades were determined based on attendance, submitted reports, and oral presentations. This was handled in a similar way to students working in my lab for indepenedent study credit (Bio 490-93).

Future: I plan to incorporate finishing and annotation into our Btec 352 course (Bioinformatics). Although the course is designed for 2 hours lecture and 2 hours lab per week, I am going to require 6 hours lab. Some of the time will be used for recitation at the begining of the finishing and annotation sections. I am training a student this semster (Fall 2008) on how to do annotation in the context of independent study credit and he will be my TA for this course next Spring.


Biology 490-493 Syllabus

Independent Study-GEP
YORK COLLEGE/CUNY

BIOLOGY DEPARTMENT

Spring 2008

Tuesdays and Fridays from 2-5pm
--------------------------------------------------------------------------------

Dr. Gerard McNeil

Rm 4E03 Academic Core Building

718-262-2192 (office)

718-262-2700 (department)

email: mcneil@york.cuny.edu


--------------------------------------------------------------------------------

Office hours

MWF 10:00-10:50

TF 1:00-2:00pm

and by appointment


--------------------------------------------------------------------------------

Schedule

1/25:  A brief talk on goals and requirements for the class. Distribute articles on "Consed: a graphical tool for sequence finishing" and "Sequence analysis of genes and genomes" and a handout on "A guide to consed".

1/29: Introduction to the Drosophila dot chromosome project. Watch video on sequencing pipeline at WU Genome Sequencing Center. Discussion of articles distibuted last week.

2/1: Lecture: Introduction to finishing and consed/phred/phrap. Lab: Go over as a group, "Introduction to consed" and "Using consed graphicaly" handouts.

2/5: Lab exercise on "A simple Drosophila fosmid" developed by Andrew Nylander

2/8: Distribute and start working on individual fosmids for D. mojavensis finishing project. Think aboiut new reads to solve problems.

2/12: College closed

2/15: Analysis and editing of fosmids.

2/19: Get first round reads, add new reads, analyze new problems, and order new reads if necessary.

2/22: Continue working on own fosmids. AS a group, go through lab exercise "A complex Drosophila fosmid" developed by Andrew Nylander.

2/26: Finsih the complex fosmid exercise. Work on own fosmids. Ordered second round of sequencing reactions.

2/29: Continue working on fosmids.

3/4: Waiting for new reads. Begin working on finishing reports. Give students handouts on restriction digests.

3/7: Added seconds reads; further analysis of fosmids. Lecture on resctriction digests. Work on finishing list.

3/11: Conform finished fosmid assembly by in-silico digest. Finish checklist. Create files for submission and submit projects. Give handouts on "Genes and homology" by C. Weber and CP Ponting, "BAsics of Blast" and "A simple introduction to NCBI Blast".

3/14: Lecture on comparative annotation and Blast. Discussion of "Genes and Homology" article. Lab on "A simple introduction to Blast". Give "Detecting and interpreting genetic homology" handout.

3/18: Lab exercise 1 on "Detecting and interpreting genetic homology" (done together as a group).Give handout on "Using mRNA and EST evidence in annotation".

3/21: No classes

3/25: Lab exercise 2 "Using mRNA and EST evidence in annotation" (done as a group).

3/28: Briefly discuss various browsers, databases, and gene predictors available for anotation. Practice annotation with D. virilis March 25, chr 10 assembly at the UCSC genome browser.

4/1: Assign students claimed D . erecta annotation projects. Access and analyze assigned fosmids at the UCSC genome browser.

4/8-4/18: Continue analysis and annotation of assigned fosmid

4/22, 4/25: Spring break

4/29: Validate annotated gene models using gene model checker; create <projectname>.gff, .pep, and .fasta plain text files and start working on project reports.

5/2: Continue working on project reports

5/6: Submit annotation projects, complete course evlauations

5/9: Preparation for oral presentations

5/13: Oral presentations on finishing and annotation projects

 Finishing reports were due the first week of annotation (4/18) and annotation reports were due the firdt day of final exam week (5/19).


Bio 490 Independent Study (Fall semesters)

I have also had students working in my research lab do an annotation projerct during fall semesters. We work in between wet experiments and during free time during the semester. Students can easily finish a fosmid project suring this time and it provides the student added exposure to genomics and enhances their research experience.




BTEC 352 Bioinformatics
SPRING 2009

In the spring of 2009, the GEP curriculum (finishing and annotation) was offered to students in our existing Bioinformatics course, Btec 352. Here this curriculum was w the sole source of instruction in this stand alone course. Again, we ofered the course in two three hour blocks on Monday and Friday afternoons. The first 30-60 minutes was used as a recitiation period for lectures and student progress reports. I did not change much from how the material was presented in the Independent Study format since it worked well. However, in this course setting I was more rigorous with grading assignments and when things were due to present a more objective grading criteria. The one thing I did add was weekly written and oral progress reports. This allowed me to keep up with the progress of students and allowed students to see problems that arose in other student projects which might help them in their own. We solved many common problems as a group this way. I think it was a very successfult reaching tool for them. I also instituted paper summaries inot the requirements. This forced students to read pertinent research papers related to the topic and allowed me to work on both their abilities to read these types of papers and wrtie about them.

SYLLABUS

Description: Bioinformatics encompasses both the evolving conceptual basis, as well as the expanding methodology, for the organization and analysis of sequence data. It involves the application of computational and analytical methods to problems in biotechnology, biology and biochemistry. This course is designed to develop a structures approach to biological data as well as to build the tools required to analyze the data. Students need access to a computer and the internet to complete the course assignments.

Course Objectives: This course is designed to provide students with a hands on opportunity to learn bioinformatics by analyzing real sequence data and contributing new information to the growing sequence database as part of a nationwide research community.. By the end of the course students should:
- Understand the structure of genomes and genes and how they are analyzed using
bioinformatic tools
- Demonstrate when a sequence of DNA is finished to a high level of accuracy.
- Understand how to annotate a sequence of DNA including identifying genes and
repetitive DNA sequences.
- Design experimental approaches to solve genomic problems using a variety of
approaches.
- Illustrate and translate finishing and annotation of a genome to its peers.
- Compose a written and verbal description of their data including a prediction of what it
means at both the gene and genomic levels.

Prerequisites: Btec 203, Bio 344, Chem 233, and Math 121 or permission of instructor.

Required Textbook: There are no required textbooks for this course. All required course materials will be either provided as handouts or through the internet.

Course Details (When, Where, Who…)
Section: GHJ
Class Times: MF 2-4:50pm
Room: AC-4E07
Instructor: Dr. Gerard P. McNeil
Office: AC-4E03f
Phone: 718-262-2192
E-mail: mcneil@york.cuny.edu
Office Hours: MF12:30-1:50pm

Tentative Schedule
Date Topic Paper
Jan. 26 Introduction, student registration, study precourse survey and quiz. N/A
Jan. 30 Lecture: Introduction to the Drosophila dot chromosome project
Watch video on the sequencing pipline at WUGP
Paper discussion Sequencing of genes and genomes
Feb. 2 Lecture: Introduce finishing (phred/phrap/consed)
Lab: Introduction to consed and using consed graphically exercises Hardinson et al., 2003
Gordon et al., 1998
Feb. 6 Lab: A Simple Drosophila Fosmid by Andrew Nylander Webber and Ponting, 2004
Feb. 9 Start working on D. grimshawi finishing projects
Order first round of sequencing reactions for low consensus quality regions TBA
Feb. 13 Analysis and editing of fosmids TBA
Feb. 16 No classes, President’s Day
Feb. 20 Get first round reads
Add new reads
Analyze new problems, order new reads, if necessary TBA
Feb. 23 Continue working on fosmids
Lab exercise: A Complex Drosophila Fosmid by Andrew Nylander TBA
Feb. 27 Finish exercise on the complex Drosophila fosmid
Continue working on fosmids
Order new reads, if necessary TBA
March 2 Continue work on fosmids TBA
March 6 Lecture: Restriction Digests
Continue finishing
Add new reads TBA
March 9 Work on finishing checklists TBA
March 13 Confirm finished fosmid assembly by in silico digest
Finish checklist
Create files and submit projects to GEP TBA
March 16 Lecture: Comparative annotation and BLAST
Lab: A simple introduction to NCBI BLAST Ashburner and Bergman, 2005
March 20 Lab exercise #1: Detecting and interpreting genetic homology Kondrashov, 2005
March 23 Lab exercise #2: Using mRNA and EST evidence in annotation Eddy, 2004
March 27 Discussion of browsers, databases, and gene predictors
Practice annotation: D. virilis March 2005, chr10 assembly at the UCSC genome browser
Finishing reports due today TBA
March 30 Assign students claimed D. erecta annotation projects
Access and analyze assigned fosmids at the UCSC browser TBA
April 3 Continue working on annotation projects TBA
April 6 Continue working on annotation projects Slawson et al., 2006
April 10, 13, 17 No classes, Spring Break
April 20 Continue working on annotation projects TBA
April 24 Continue working on annotation projects TBA
April 27 Validate annotated gene model using gene model checker
Create <project name >.giff, .pep, and .fasta plain text files and start working on project reports TBA
May 1 Continue working on project reports
May 4 Submit annotation projects
May 8 Preparation of oral presentations
May 11 Oral presentations
Annotation reports due today
May 15 Oral presentations

Class preparation and attendance: Success in this course greatly depends on your attendance and teamwork during the class period. Most of the grade will depend on work done inside the classroom, therefore attendance is critical. Most of the outside work will be reading papers assigned each week and preparing summaries for some of these papers.

Grading: The final grade for this course will be the culmination of the following:

Finishing report 25%
Annotation report 25%
Progress reports 10%
Problem sets 10%
Paper summaries (5) 15%
Participation 15%

Progress reports will be due every third class while working on finishing and annotation projects. They will summarize what has been accomplished during the past two sessions and what problems have arisen. These will be used to follow progress, deal with problems in a timely fashion, and as learning tools for the other groups.

Several problems sets will be distributed at various points during the semester. Completion of these will be done mainly during class time and submitted to the instructor for grading.

We will be reading and discussing many original publications related to genomics and bioinformatics during this course. Each student must pick five of these and prepare summaries of the work.

The participation grade will be determined based on participation in during lectures, lab and paper discussions throughout the semester.



References

F Sterky F, Lundeberg J. (2003) Sequence analysis of genes and genomes. J
Biotechnology 76: 1-31.

M Warren RL, Varabei D, Platt D, Huang X, Messina D, Yang SP, Kronstad JW,
Krzywinski M, Warren WC, Wallis JW, Hillier LW, Chinwalla AT, Schein JE,
Siddiqui AS, Marra MA, Wilson RK, Jones SJ. (2006) Physical map-assisted wholegenome
shotgun sequence assemblies. Genome Res. 16: 768-75.

Hardison RC. (2003) Primer: Comparative Genomics. PloS Biology 1: 156-160.

Webber C, Ponting CP. (2004) Genes and homology. Curr Biol 14: R332-R333.
1/26 F Gordon D, Abajian C, Green P. (1998) Consed: A Graphical Tool for Sequence
Finishing. Genome Res. 8: 195-202.

M Gordon D, Desmarais C, Green P. (2001) Automated Finishing with Autofinish.
Genome Res. 11: 614-625.

M Felsenfeld G, Groudine M (2003) Controlling the double helix, Nature 421:
448-453.

Elgin SCR, Grewal, SIS. (2003) Primer: Heterochromatin: silence is golden, Curr. Biol.13: R895-R898.

Grewal SIS, Elgin, SCR. (2002) Heterochromatin: new possibilities for the inheritance
of structure, Curr. Opin. Genetics & Develop. 12: 178-187.

Haynes KA, Caudy AA, Collins L, Elgin SC. (2006) Element 1360 and RNAi
Components Contribute to HP1-Dependent Silencing of a Pericentric Reporter.
Curr Biol. 16: 2222-7.

Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, CohenBA, Johnston M. (2003) Finding functional features in Saccharomyces genomes byphylogenetic footprinting, Science 301: 71-76.

Dermitzakis ET, Reymond A, Scamuffa N, Ucla C, Kirkness E, Rossier C, Antonarakis
SE. (2003) Evolutionary discrimination of mammalian Conserved Non-Genic sequences
(CNGs), Science 302:1033-1035.

Ashburner M, Bergman CM. (2005) Drosophila melanogaster: a case study of a
model genomic sequence and its consequences. Genome Res. 15:1661-1667.
Kondrashov AS. (2005) Evolutionary biology: fruitfly genome is not
junk. Nature 437:1106.

Eddy, S. (2004) What is a hidden Markov model? Nature Biotech. 22: 1315-16.

Slawson EE….Elgin SCR. (2006) Comparison of dot chromosome sequences
from D. melanogaster and D. virilis reveals an enrichment of DNA transposon
sequences in heterochromatic domains. Genome Biology 7: R15

Mardis ER (2006) Anticipating the $1,000 genome. Genome Biol. 7: 112.


The following papers may be helpful during the second half of the course:

Cooper GM, Sidow A. (2003) Genomic regulatory regions: insights from comparative sequence
analysis, Curr. Opin. Genet. Develop. 13: 604-610.
Thomas JW…..Green ED (2003) Comparative analyses of multi-species sequences from targeted
genomic regions, Nature 424: 788-793.
Celniker SE, Rubin GM. (2003) The Drosophila melanogaster genome. Annu Rev Genomics
Hum Genet. 4:89-117.
Celniker SE, …Gibbs RA, Rubin GM. (2002) Finishing a whole-genome shotgun: release 3 of the
Drosophila melanogaster euchromatic genome sequence. Genome Biol. 3(12):RESEARCH0079. Epub
2002 Dec 23. PMID: 12537568 [PubMed - indexed for MEDLINE]
Kaminker JS, Bergman CM, Kronmiller B, Carlson J, Svirskas R, Patel S, Frise E, Wheeler DA, Lewis
SE, Rubin GM, Ashburner M, Celniker SE. (2002) The transposable elements of the Drosophila
melanogaster euchromatin: a genomics perspective, Genome Biol. 2002;3(12):RESEARCH0084. Epub
2002 Dec 23. PMID: 12537573 [PubMed - indexed for MEDLINE]
Bartolome C, Maside X, Charlesworth B. (2002) On the abundance and distribution of
transposable elements in the genome of Drosophila melanogaster. Mol Biol Evol. 19:926-37.
Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D.
(2005) Combined evidence annotation of transposable elements in genome sequences. PLoS
Comput Biol. 1:166-75.
Yang H-P, Hung T-L, You T-L, Yang T-H. (2006) Genome-wide comparative analysis of the highly
abundant transposable element DINE-1 suggests a recent transpositional burst in Drosophila yakuba.
Genetics, 173: 189-96.
Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ,
Sullivan BA, Sutton GG, Yasuhara JC, Wakimoto BT, Myers EW, Celniker SE, Rubin GM, Karpen
GH, (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly, Genome
Biol. 2002;3(12):RESEARCH0085. Epub 2002 Dec 31. PMID: 12537574
Bergman CM, Pfeiffer BD, Rincon-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM,
Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM,
Celniker SE. (2002) Assessing the impact of comparative genomic sequence data on the functional
annotation of the Drosophila genome. Genome Biol. 2002;3(12):RESEARCH0086. Epub 2002 Dec 30.
PMID: 12537575
7
Ohler U, Liao GC, Niemann H, Rubin GM. (2002) Computational analysis of core promoters in the
Drosophila genome, Genome Biol. 2002;3(12):RESEARCH0087. Epub 2002 Dec 20. PMID: 12537576

--------------------------------------------------------------------------------


--------------------------------------------------------------------------------