2012

Masters M1: Sciences des Genomes et des Organismes

• Examen donné aux étudiants: phylogénie et métabolismes des microbes et leur influence environnemental.
• Revue et discussion
  • Discussion de l'article The evolution of life without oxygen by Fenchel and Finlay, American Scientist 1994
  • Revue des thèmes de nos Travaux Dirigés;.
• Les cycles biogeochimiques et les rôles des microbes dans l'environnement (avec réponses)
• Le métabolisme microbien: classification du métabolisme, glyolyse, le cycle TCA, la chaîne réspiratoire, la fermentation (avec réponses)
• Généralités. l'importance et characteristiques des microbes. La résistance aux antiobiotiques (avec réponses)

2011

Masters M2: Systems and Synthetic biology

• Exam given to students focusing on Marliere et al, 2011 along with the supplementary information
• Discussion of advances and challenges in microbial engineering by focusing on Bokinsky et al, 2011 Synthesis of three advanced biofuels from ionic liquid-pretreated switchgrass using engineered Escherichia coli. PMID 22123987.
• Lectures "New technologies in synthetic biology: manipulation of microbial genomes"
• Lectures "New technologies in systems biology"

Lectures from the MBL-TIGR Genome Technology Course

Programming fundamentals for the computational biologist

These lectures introduce the Perl programming language as a tool to investigate problems in biology. The goal is to demonstrate that basic programming skills turn the computer into a tool just like the PCR machine; they are both means to test biological hypotheses. So why does the course focus on the Perl programming language?

"Perl is the duct tape of the internet." -Randal Schwartz

"Perl is optimized for problems which are about 90% working with text and about 10% everything else." -Schwartz and Phoenix "Programming Perl"

Which is what makes Perl perfect for the computational biologist because the essence of bioinformatics is searching for patterns in two huge sets of text files: genome files and the internet.

Here are the handouts for the course:

• Class Handout 1
• Lab Handout 1
• Class Handout 2
• Lab Handout 2