CBS >> CBS Courses >> Comparative Microbial Genomics >> Course Programme

The course meets on Wednesday mornings (kl. 8.30-12) and Thursday afternoons, (kl. 13-17), and will start on Wednesday, 31 August, 2011 at 08:30. Lectures, journal clubs and exercises will take place in lecture hall 060 (downstairs) in building 208, at the Technical University of Denmark, Lyngby.

Performance will be evaluated as described on the course overview page. Briefly, the grade is determined by a journal club report (25%), a poster (25%), and a final written manuscript (50%). The aims and learning objectives for this course are as described on the course webpage and also in the DTU course catalog.

8.30-9.15

Chapter 1 from textbook - "Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics"
Link to pdf file of lecture notes

9.15-9.30

Break

9.30-10.15

Chapter 2 from textbook - "Introduction to Bioinformatics"
Link to pdf file of lecture notes

10.15-10.30

Break

10.30-11.30

Journal Clubs and Posters - a brief overview
Link to pdf file of genomes list

Initial sign-up for teams of four students for computer exercises and papers

13.00-13.30

Discussion of projects and groups of genomes for computer exercises and reports
Link to pdf file of genomes list
Link to pdf file of Tammi's talk

13.30-13.45

Break

13.45-14.30

Chapter 3 from textbook - "Comparative Microbial Genomics: A Brief Overview"
Link to pdf file of lecture notes

14.30-14.45

Break

14.45-15.30

Chapter 4 from textbook - "Genomic Databases"
Link to pdf file of lecture notes

15.30-15.45

Break

15.45-16.30

Discussion about what is expected

8.30-9.15

Lecture by Matloob Qureshi - Chapter 5 from textbook - "The Challenges of Programming"

9.15-9.30

Break

9.30-10.00

"Unix How-to lecture" by Matloob Qureshi

10.00-12.00

Introduction to groups for the course:

Assignment of groups, projects, journal club articles (Dave)

Preperation of computer environments (Tammi Vesth)
    Instructions for Apple computers
    Instructions for PC computers

    biotools-xubuntu operating system in .iso format (disc image)     notes: this is a rather large file (600 Mbytes!), so you might want to use an ethernet connection, rather than wireless, to download this.     Tammi and Shinny have some memory sticks with the ISO files already loaded - might be quicker to use these to copy the files to your computer...

13.00-13.45

Chapter 6 from textbook - "Comparing Genomes - Bacterial Genomics"
Link to pdf file of lecture notes (final version)

13.45-14.00

Break

14.00-14.30

Example Journal Club - "Defining the Pseudomonas Genus"
Link to pdf file of presentation slides

14.30-16.30

Computer exercises - Week 1. Link to pdf file of lecture notes

8.30-9.15

Chapters 7, 8 from textbook - "Genomic Properties"
Link to pdf file of lecture notes (final version)

9.15-9.30

Break

9.30-10.00

Journal Club # 1 - Acinetobacter - Linda, Monica, Malene, Isa
Link to pdf file of journal club

10.00-10.15

Break

10.15-10.45

Journal Club # 2 - Lactobacillus - Linda, Dilek, Catharina
Link to pdf file of journal club

10.45-12.00

Computer exercises - Week 2, day 1.

other files - updated 14 September, 2011... GeneWiz executable      GenomeAtlas configuration file generator script      NEW genomeatlas shell script (to replace the old one!)     

13.00-13.45

Chapter 9 from textbook - "Transcriptomics"
Link to pdf file of lecture notes

13.45-14.00

Break

14.00-14.30

Journal Club # 3 - Salmonella - Martin, Tanni, Sandra, Sebastian, Julie
Link to pdf file of journal club

14.30-14.45

Break

14.45-15.15

Journal Club # 4 - Bifidobacterium - Stine, Dan, Lene, Sufia
Link to pdf file of journal club

15.15-17.00

Computer exercises - Week 2, day 2.

8.30-9:30

Computer exercises - Week 3, day 1.
PDF of presentation (overview of computer exercises for Week 3)

9.30-10.15

Chapter 13 from textbook - "Metagenomics" - special guest lecture by Professor Francisco Rodriguez-Valera, Universidad Miguel Hernandez, San Juan de Alicante, Spain
Link to pdf file of lecture notes

10.15-10.30

Break

10.30-11.00

Journal Club # 5 - Brucella - Ola, Una, Michael, Maja
Link to pdf file of journal club

11.00-11.15

Break

11.15-11.45

Journal Club # 6 - Escherichia - Yongguang, Katarzyna, Jing, Boryana
Link to pdf file of journal club

13.00-13.45

Chapter 10 from textbook - "Expression of Genes and Proteins"
Link to pdf file of lecture notes

13.45-14.00

Break

14.00-14.30

Chapter 11 from textbook - "Of Proteins, Genomes, and Proteomes"
Link to pdf file of lecture notes

14.30-14.45

Break

14.45-15.15

Journal Club # 7 - Vibrio - Iliana, Susan, Kasper, Dominika
Link to pdf file of journal club

15.15-15.30

Break

15.30-16.00

Journal Club # 8 - Staphylococcus - Henrik, Marc, Athansios, Rasmus, Marwa
Link to pdf file of journal club

16.00-17.00

Computer exercises - Week 3, day 2.

8.00-8.45

Chapter 12 from textbook - "Microbial Communities"
Link to pdf file of lecture notes

8.45-9.00

Break

9.00-9.45

Chapter 14 from textbook
Link to pdf file of lecture notes

9.45-10.00

Break

10.00-10.30

Journal Club # 9 - Bacillus - Tine, Martin, Niels, Sabine
Link to pdf file of journal club

10.30-12.00

Computer exercises.

13.00-17.00

Computer exercises.

10.00-10:30

Lecture on posters - some tips of what to include, and what makes a good poster
Link to page for zoomable atlases         Link to PDF of zoomable atlas paper describing method

13.00-14.00

Lecture on What is Expected for the final paper
link to pdf of lecture notes.