Course Content - Digital Sciences for Life Sciences and Healthcare

1. Cellular Biology

Teaching staff: Aurélien Serandour, Yannick Guillou, Xavier Saulquin, Sophie Limou
Lectures 16 hrs / Tutorials 10 hrs  / Labo 4 hrs / Evaluation 2 hrs

Cell / membranes and membrane transport / Protein synthesis / protein routing and degradation / cell adhesion / cytoskeleton and mitochondria / cell cycle / cell signalling / apoptosis and cancers.

Including the Nantes University MOOC “Ouvrez les portes du laboratoire: cellules et cellules souches” (Open the laboratory doors: cells and stem cells).

Following on from the work of Shinya Yamanaka, Nobel Prize winner in 2012, this course presents the main stages of stem cell culture and reprogramming, combined with the main concepts of cell biology.

Cell collection and extraction / Visualization of cells and microscope / Cell culture and freezing / Cell reprogramming / RT-PCR and cytometry / Cardiac stem cell differentiation / Immunohistochemistry / Electrophysiological analysis

2. Immunology

Teaching staff: Yannick Guillou, Laetitia Gautreau, Joelle Gaschet, Nadine Gervois, Xavier Saulquin
Lectures 18 hrs / Tutorials 8 hrs / Labo 4 hrs  / Evaluation 2 hrs

The immune system / components of innate and adaptive immunity / major histocompatibility complexes and immune response / T and B cell repertoires / lymphoid organs / immune deficiencies, immunization, transplant / immunotherapy / cancer.

3. Molecular biology, genetics, evolution

Teaching staff: Sophie Limou, Aurelien Serandour
Lectures 18 hrs / Tutorials 12 hrs  / Evaluation 2 hrs

Mendel, mutations and polymorphisms, molecular biology techniques, evolution,
phylogeny (epidemiology), introduction to epigenetics. Reading and interpreting scientific articles.

1. Bioinformatics and Genomics: biotechnological revolutions and “big data”

Teaching staff: Sophie Limou
Lectures 18 hrs / Tutorials 12 hrs  / Evaluation 2 hrs

Bioinformatics databases and algorithms (BLAST, PDB, etc.) / pattern discovery / Sequence alignment / Biotechnology revolution, booming of ‘’big data’’ and new challenges / Introduction to ‘’Omics’’.

2. Systems Biology: Discrete Modelling and Qualitative Analysis of Biological Networks

Teaching staff: Morgan Magnin, Loïc Paulevé
Lectures 18 hrs / Tutorials 10 hrs  / Labo 2 hrs / Evaluation 2 hrs

Boolean and multi-valued networks / Transition graph / Analysis of models and model-checking / Temporal representations

3. Systems Biology: Probabilistic Modeling and Quantitative Analysis of Biological Networks

Teaching staff: Jérémie Bourdon, Damien Eveillard, Halim Larhlimi
Lectures 18 hrs / Tutorials 12 hrs  / Labo 2 hrs / Evaluation 2 hrs

• Introduction to biological systems modelling / Laws and modelling based on differential equations
• Approximation of the dynamics based on probabilistic models (PBN and DBN) and asymptotic analysis of models: application to regulation models
• Approximation of quasi-stationary equilibrium dynamics and constraint analysis: application to metabolic models

1. Operating Systems and Databases

Teaching staff: Jean-Yves Martin
Lectures 11 hrs / Tutorials 5 hrs  / Labo 14 hrs / Evaluation 2 hrs

Elementary architecture, operating systems, processes and shells / Conceptual models of databases, relational model, physical models, SQL, programming for databases / NoSQL and BigData notions.

2. Statistics and stochastic modelling

Teaching staff: Eric Le Carpentier, Bertrand Michel
Lectures 15 hrs / Tutorials 13 hrs  / Labo 2 hrs / Evaluation 2 hrs

Probabilities / Parametric Estimation / Markov Representation and Bayesian Filtering
Inferential statistics / Statistical tests and duration models

3. Physics and Biomechanics

Teaching staff: Francisco Chinesta, Emmanuelle Abisset
Lectures 18 hrs / Tutorials 12 hrs  / Labo 2 hrs / Evaluation 2 hrs

Physics of polymers / DNA and RNA / Protein structure, folding and unfolding / Molecular motors and Nanomachines / Molecular network theory / Cellular mechanics / Statistical mechanics, complexity, emergence and theory of evolution.

4. Computational Surgery

Teaching staff: Domenico Borzacchiello
Lectures 18 hrs / Tutorials 12 hrs  / Labo 2 hrs / Evaluation 2 hrs

Behavioral laws of biological tissues: linear elasticity and hyperelasticity / Numerical solutions by finite element method / Model reduction for real-time applications: PGD / Modeling of contact and cutting / Dynamic regime.

5. Advanced Computer Science

Teaching staff: Olivier Roux, Richard Randritoamanana, Hugues Digonnet, Grégoire Guillaume
Lectures 10 hrs / Tutorials 4 hrs  / Labo 16 hrs / Evaluation 2 hrs

Object-oriented languages / Programming in JAVA / Multi-core architecture and parallelisation methods / OpenMP / MPI.

1. Conferences

Teaching staff: Olivier Roux, Sophie Limou, Aurélien Serandour, Pierre-Antoine Gourraud, Philippe Damier, Thierry Le Tourneau
Lectures 20 hrs / Tutorials 10 hrs  / Evaluation 2 hrs

Personalised medicine / Neurology / Physiology / Various conferences on pharmacology, plant biology, systemic and synthetic biology

2. Projects (80 hrs)

Minimum of 80hrs/student working in groups of 4 students.

Project performed in a research lab on a topic mixing biology / health and informatics
Examples: microbiome, dynamic modelling of a cell, biology system modelling, genomics, epigenomics, immunoradiotherapy