When the new master program Molecular Life
Sciences was launched in 2010 in the University of Lausanne, it contained a
very unusual course. One made possible by the progress of technology, the
concentration of competences in Lausanne, and the daring of a small team of
instructors: the "Sequence a genome" class.
The principle is simple: a few bacterial
species whose genome is unknown, and which are studied in Lausanne
laboratories, are provided to the students. The class isolates and prepares the
DNA, and sends it to the sequencing facility. A few weeks later (which are used
to learn about modern computing systems), the class recovers the raw DNA read
files, and spends the autumn semester assembling them into an actual genome
sequence. There are always some gaps, so the spring semester starts with a few
extra PCR experiments to close them. Then the students divide the genome into
sets of interest, according to the known biology of the species (e.g., heavy
metal resistance) or to unexpected features of the genome (e.g., a very large
plasmid). They annotate these sets, which means that they identify the relevant
genes and provide the best guess of their function. Finally, the full
information is gathered into a paper, which is submitted for publication,
co-authored by all the class!
A unique feature of this course is the work
on an actual research project, for which the results are totally unknown at the
start of every year, and for which the methods are continuously evolving: the
teachers and the students must stay at the forefront of the latest experimental
and computational expertise. In the end, the students have produced new
knowledge, and have learned to work with cutting-edge sequencing and
bioinformatics technologies.
As far as the Lausanne team knows, they
were the first in the world to propose such a course. The course received a
collective Excellence in teaching award from the Faculty of Biology and
Medicine in 2012.
We are now going to add a new feature to this class: blogging the progress of the sequencing, assembly and annotation of the genomes, with the students. Stay tuned!
