I've taught some courses as part of an ATER contract at Bordeaux 2 University (Victor Segalen) during the university year 2008-2009. The courses are described in more details below.

A few years ago, the French Ministry for Education and Research has launched a program which aims at providing high-school and university students with a certificate which proves that the holder has mastered certain IT and network tool skills. In particular, the C2i Level 1 vouches for the student's proficiency in a full range of skills needed for carrying out the activities that higher education programmes now require:

• Researching, creating, using and managing information,
• Gathering and processing data,
• Managing data,
• Saving, archiving and researching data
• Presenting the results of a project both in class and at distance
• Exchanging dialogue and communicating at distance
• Producing work as part of a group
• Adopting a standpoint with regard to the problems and issues related to the use of ICT: rights and obligations, legal aspects, deontological and ethical concerns, etc.

More information regarding this certificate can be obtained on the Ministry Web site.

In order to prepare students for the exam corresponding to this certificate, practical courses are proposed in all under graduate curriculums. In this context, I've been teaching 6 groups of around 20 students in order to introduce them to the use of a common Office suite. The courses were dispatched as follows:

• Microsoft Word 2007: 3 practical courses, 2h each,
• Microsoft Excel 2007: 2 practical courses, 2h each,
• Microsoft Power Point 2007: 1 practical course, 2h.

Another teacher was responsible for a third 2h Excel course and a second 2h Power Point course.

Most 1st year master degrees in fields linked with biology and healthcare include this module. Its objective is to provide students with the required information to understand and use bioinformatics resources such as molecular biology databases or biological data analysis software (comparing and analysing biological sequences, predicting molecular structure and function, etc.)

In this context, I have taught a 2h course introducing biomedical ontologies so that these students have a basic idea of:

• The problem which lead to the introduction of the ontology concept if computer sciences,
• The ontology concept in itself,
• The various knowledge organisations which can be considered as ontologies,
• The various formats and languages used to represent ontologies,
• The use which can be made of ontologies, from vocabulary standardisation to reasoning.

The PDF version of the course presentation (in French) can be downloaded below.

Download:

This course is intended for Bioinformatics Master 2 students. It aims at providing them a knowledge of industrial bioinformatics: the domain, the products and the careers. The objective is to help them devise their career project.

The theoretical part of the course includes lectures regarding project management in an industrial setting and conferences where professionals from the private sector introduce their companies and jobs and answer students' questions regarding possible career opportunities. Practical activities consist in projects run individually or in groups. Personal projects include:

• Collecting information regarding a bioinformatics company and presenting the results through a written report and an oral presentation,
• Searching for a job offer conducting to the simulation of a recruitment process (writing a CV and an application letter, job interview simulation).

Collective projects consist in the evaluation of a bioinformatics software. These projects also lead to a written report and an oral presentation.

I am responsible for the collective projects part of this course. It consist in about ten hours with the students for about fifteen students. Softwares which evaluation is planned for the university year 2008-2009 are:

• BioMAJ
• Mobyle
• MRS

The PDF version of the presentation which introduces the software analysis project (in French) can be downloaded below.

Download:

All biology curriculums include a basic statistics course in third year. The objective of this course is to provide the students with basic notions regarding statistical tests used in biology. It includes courses regarding the following topics::

• probability notions,
• descriptive statistics (distribution, mean, variance, etc.),
• probability laws (binomial law, Poisson's law, normal law, exponential law),
• frequency comparison,
• two means comparison notions.

In this context I'm teaching the 6 exercises sessions associated with this course, for 5 groups of around 30 students and a total of 60h

The written material for the exercises sessions and exams which I have conceived can be downloaded below (in French). Solutions for the exercises will be provided after the courses or exams took place.

Download:
Session	Wording	Solution
TD1 - Probability notions
TD2 - Observed distributions
Mid-term exam - February 2009 - Exam 1
Mid-term exam - February 2009 - Exam 2
TD3 - Probability laws
TD4 - Frequency comparison
TD5 - Chi2 tests

This course is optional for third year students in biology. The objective is to provide complements to the notions learnt as part of the "basic statistics" course. It includes:

• Reminders regarding the test notion,
• Sampling deviation, estimation,
• Means comparison,
• Variance analysis,
• Correlation, regression, non parametric tests.

In this context I'm teaching the 3 4h practical courses associated with this course, for two groups of around 30 students and 24h total.

This course regarding mathematics tools used by biologists is optional for second year biology students. Its objective is to provide students with basic notions regarding matrix calculus (with an application to metabolic networks structure) and basic notions regarding dynamic systems. The following topics are introduced:

• Linear algebra
  • Matrix : definition, product
  • Matrix inversion
  • Linear system resolution
  • Geometric transformations associated with a matrix
  • vector space notion
  • Matrix diagonalisation: eigenvectors, eigenvalues
  • Applications : metabolic network representation through its stoicheiometry matrix, introduction to metabolism control theory.
• Differential equations
  • First order differential equations,
  • Linear systems of differential equations,
  • Analytic resolution of differential equations,
  • Application : population evolution models.

In this context I'm teaching the 6 exercises sessions of 2h associated to this course, for a group of around 30 students and a total of 12h.

The written material for the exercises sessions which I have conceived can be downloaded below (in French). Solutions for the exercises will be provided after the courses took place.

Download:
Session	Wording	Solution
TD1 - Operations on matrices, matrix inversion
TD2 - Vectorial space, geometry, rank
TD3 - Stoicheiometry matrices, diagonalisation
TD4 - Differential equations
TD5 - Systems of differential equations
TD6 - Applications with Excel