Alfonso Jaramillo's Group

Summary of teaching activities

Click here for my course materials

1  Teaching Philosophy and Goals

2  Teaching Responsibilities

3  Teaching Methods

4  BIO552 Practical Course Syllabi

5  Supervision of Trainees

6  Teaching Improvement and Future Plans

7  International cooperation programs

1 Teaching Philosophy and Goals

I believe that one of the most important tasks of an instructor is to provide motivation through the appropriate selection of topics and the interaction instructor-student. A motivated student may want to go beyond the course materials. By preparing stimulating material, with important technological and social relevance, I also get ideas for my own future research. In addition, a student could be motivated to do a research internship with me. But motivation is not enough, it is most important that the courses be very interactive, so the student could interact with the instructor and with other students. This exchange of ideas not only multiplies the student's knowledge but it also provides self-confidence in proposing new ideas stimulating their creativity. In this way the students will get used to propose new ways to solve the problems, preparing them to make innovations in whatever career path they choose. My goals in teaching are to provide the spark that could direct the student's future career.

2 Teaching Responsibilities

Bioinformatics "TP" (BIO552)

I was responsible for designing the course syllabus of the practical sessions that consisted in directed exercises, the associated "polycopies" (available upon request in French and in English) and the necessary software and experimental data. There are 8 sessions of 2 hours each. For the 3 computer sessions (of one hour each), I had the help of two teaching assistants (Ms. Lopes and Mr. Noirel), which helped students to resolve computer-related questions. I had 20-25 students regularly. Together with Prof. Simonson we will evaluate the students by the reading and defense of an appropriate research article.

Master SFIP. Bioinformatics. (year 2 SFIP master)

Together with Prof. Bontems and Ms. Lopes, we coordinated the practical session on molecular modeling simulations (5 students). Together with Prof. Simonson, we evaluated the students by the reading and defense of a selected research article.

Master SFIP. Molecular modeling practical. (year 2 SFIP master)

(within the course BIO534 directed by Prof. Mechulam). Together with Ms. Lopes, we coordinated the practical session on molecular modeling simulations (15 students).

3 Teaching Methods

One of the best ways to learn a technical subject is through exercises that simplify a real exciting problem. I believe that it is as important to understand the mathematical algorithms behind most Bioinformatics methodologies as to know how you could apply it to a given biological problem. Therefore in my practical courses I use two types of exercises. For the BIO552 course I have used:

Analytical exercises:

To enforce this type of teaching methodology the practical sessions contain an important part of pencil-and-paper exercises (80% ).

Computing exercises:

3 practicals contained a one hour computer session, which consisted on using provided software to analyze a biological problem.

Participation to iGEM competition:

iGEM is the acronym for " international Genetically Engineered Machine competition ". iGEM has a double intention: stimulate the research on synthetic biology and form future investigators on this new emerging discipline. For this purpose, the university teams participating on iGEM had to develop a project based on: i) designing a genetic circuit with an interesting function, ii) model and simulate the design before the construction and iii) construct and characterise the designed circuit using either the plasmid library provided by the organisation or by constructing new plasmids that would be added to the libary. All teams have to physically submit the plasmids before the final meeting (the " iGEM Jamboree "), which took place at MIT (USA) on November 2006. I created and supervised the iGEM-Valencia team which consisted on 12 undergraduate and master students from various disciplines (http://www.intertech.upv.es/wiki/index.php). The team obtained an award at the final meeting. Two of its students are now conducting a PhD thesis under my supervision.

4 BIO552 Practical Course Syllabi

Genome Assembly

Introduction to shot-gun assembly.

Assembly of a toy genome exercise.

With computer: Real case assembly of Brugia Malayi mitochondrial genome.

Assembly guided by the Onchocerca Volvulus mitochondrial genome.

Outline of SARS virus assembly using TIGR.

Sequence comparisons

Introduction to dynamic programming algorithms.

Global and local alignment exercises.

Heuristic alignment exercise.

Blosum matrix and random sequences exercise.

Multiples alignments

Introduction to phylogenetics.

Simple phylogenetic tree exercise.

HIV background.

With computer: Multiple alignment of HIV gp120 protein using clustalx.

Construction of unrooted trees using NJ algorithm and bootstrap.

Tree rooting.

Creation the corresponding DNA alignment and detect positively selected sites.

Genetic networks

Introduction to boolean genetic networks.

Temperate phage exercise.

Hematopoiesis regulation background.

Exercise of identification the pathways of hematopoietic differentiation using a 3-gene model.

Hidden Markov Models

Introduction to HMM. Splice-site recognition exercise.

Immunology background.

With computer: Identify MHC-I binding motif.

Train a peptide-MHC binding prediction method.

Find potential HLA-A*0201 epitopes in the SARS virus.

RNA Structure

Introduction to RNA secondary prediction methods.

RNA folding exercise with a toy RNA sequence.

Exercise with the s2m SARS sequence using multiple alignments. Exercise of calculation of the thermodynamics of RNA.

Protein structure

Introduction to protein structure with exact models.

Lattice folding exercise.

Calculation of the aggregation modes of a toy protein and their applications to amyloid fiber formation.

5 Supervision of Trainees

As I am working at the interface between several disciplines (biology, mathematics, engineering, physics, chemistry, and computer science, among others) and I had the chance to attract trainees from several disciplines (mathematics, engineering and physics) to do research with me.

Supervised research internships:

April-July 2004, Ëvolution des proteines in-silico". Ms. Belotserkovets. She was a mathematician who wanted to do some work in biology. Although her biological background was very small, she could learn very qiuckly the basics of protein folding and design to succeed with her protein design project.

April-July 2006, "Simulation et modélisation des circuits biologiques". Mr. Rodrigo. He is a physics/engineering student from X2003 eager to work in interdisciplinary bioinformatics. He has started in early April 2006 working in a project that deals with systems biology, where he models and simulates genetic circuits. This is a very suitable project for his formal background and it allows him to get introduced to the corresponding state-of-the-art research.

Doctoral: I am supervising the PhD thesis of Mr. Rodrigo (since Spetember 2006) and Mr. Carrera (since January 2007). Mr. Rodrigo has received his B.Sc. in Industrial Engineering from the Universidad Politecnica de Valencia (UPV) in 2006, following the last year at Ecole Polytechnique (France). His research interests involve several aspects of synthetic biology, including networks design, metabolic engineering and systems biology. Mr. Javier Carrera has received his B.Sc. in Industrial Engineering from the Universidad Politecnica de Valencia (UPV) in 2007, following the last year at Royal Technology Institute (KTH, Sweden) where he did his master thesis. His research interests also involve several aspects of synthetic biology, including inference of transcriptional networks from microarray data, metabolic engineering and systems biology.

Postdoctoral: Dr. Tortosa had done his Ph.D. in particle physics before deciding to move to biology last October 2005. I have trained him to quickly learn the necessary biology and bioinformatics algorithms. Recently, he has obtained very promising results that our experimental collaborators in Granada U. (Spain) have successfully validated. Dr. Suarez has also done her PhD in particle physics and has joined my group in October 2006.

6 Teaching Improvement and Future Plans

The BIO552 students where quite involved in the theoretical practicals, but the computer sessions attracted 30% fewer students. I am thinking to require them in the future to handle me a report on each computer practical. In this way they will be more motivated and they will learn more. As each computer practical has been designed so it requires several hours if one wants to assimilate all the different concepts, the take-home part would force them to deepen on the details (in the classroom they would learn the necessary steps to be able to do the exercise but a full understanding requires some thought).

I have been using a web page to give the teaching material (slides, but also some video-conferences on related subjects) to the BIO552 students:

http://www.enseignement.polytechnique.fr/profs/biochimie/Alfonso.Jaramillo/teaching2.html

There I have put a server where the students are able to post anonymously their comments and evaluations, so I could get an appropriate feedback to improve my teaching.

7 International cooperation programs

In 2006, thanks to my network of scientific collaborators, the Ecole Polytechnique has signed a new student cooperation program with the ETSII Universidad Politecnica de Valencia (one of the top engineering schools in Spain) that will provide the means to bring here undergraduate students interested in bioinformatics. In fact, already a student has enrolled the International program in the promotion X2003 and he conducted a research internship during 2006 in bioinformatics under my supervision.