Licence 2 CPES Modeling and Numerics in Life Sciences

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Second year mathematics program, part taught at Lycée Joffre :

# Reminders of linear algebra and complements of Euclidean geometry

# Advanced probability

# Analysis of functions of one variable

# Functions of several variables

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This UE is a transversal UE of L2 SV aiming at giving to the students in Biology a basic knowledge on the functioning of plants allowing to understand the current stakes of the plant Agro-sciences.

The following basic Plant Physiology/Functional Biology will be studied: 

essential experimental approaches: plant transgenesis, direct and reverse genetics

basics of autotrophy

mechanisms underlying the major stages of angiosperm development: meristem function, floral transition, fertilization.

auxin, a major hormone for the development of plants and their response to the abiotic environment

The practical sessions will allow students to manipulate the regulation of water nutrition in plants and to analyze their mineral nutrition using different biochemical assays (flame photometry, spectrophotometry). 

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This course is an introduction to the general concepts of scientific ecology: levels of organization, measurement and conservation of biodiversity, biogeography, biotic and abiotic factors of distribution and dynamics of biodiversity. It also provides an understanding of the methods used in scientific ecology: the importance of experimentation, reflection on the construction of a protocol, data analysis, oral and written reports of an experiment

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Complements to linear algebra, reduction theory and applications 

# Complements to linear algebra, notion of direct sum

# Determinants

# Reduction: diagonalization and applications to the study of discrete and continuous dynamic systems in physics, chemistry, biology or economics.

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This course continues the training of students in applied mathematics, with a focus on numerical methods.

Program (subject to change depending on the year and time available) :

# numerical matrix analysis

# digital integration

# numerical resolution of diferential equations

# introduction to the qualitative study of nonlinear differential equations

.

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The 2nd year computer science course at the Lycée focuses on advanced concepts in algorithms and programming:

# Tree-like data structures: binary trees, heaps, ABR, priority queues

# Heap sorting, lower limit on sorting

# Graph structure: representations (adjacency matrices, edge lists, neighbor lists)

# Basic algorithms (connectivity, depth and width traversal, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

# Introduction to object programming (encapsulation, late linking, classes, methods, etc.)

# Programming in Python

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This UE completes the computer science training by opening up to the study of information systems and databases (design of processing in an information system and management of relational databases):

# Information systems: introduction of the entity/association model, relational model, processing modeling (conceptual processing model, organizational processing model).

# Databases: create, manipulate and query relational databases.

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This module should enable students to acquire:

Basic notions in Physiology : Concept of homeostasis; levels of organization of the human body; compartments of the Internal Environment; study of the endocrine system; acid-base and hydro-mineral balance; anatomical and functional studies of the central and peripheral nervous system.

Basic concepts in Immunology:

General presentation of the immune system; study of T and B lymphocytes, antigen presenting cells; study of antimicrobial immunity and complement.

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This modern language course focuses on written and spoken English, with particular emphasis on oral expression.

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This course deals with the theoretical notions of plant biology, using the Spermatophytes as a model. It aims at defining the notions and the specific vocabulary of morphology, anatomy, reproduction and biological cycles.

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The EU is interested in describing the morpho-anatomical characteristics of the major organizational plans of metazoans found in present and past faunas, as well as in explaining their origin and their dynamics of appearance. It thus develops a vision of organisms based on paleontology and zoology. It will mainly deal with the origin of metazoans and the main divisions that are diploblastic and triploblastic as well as basic notions related to the positioning and phylogenetic relationships between taxa (mono- and paraphylly, evolutionary convergence...). It is classically divided into lectures, tutorials that will mainly aim at illustrating and supporting aspects related to the biodiversity of taxa and practical work in sessions aiming at the acquisition of skills, especially and necessarily in dissection.

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General culture (epistemology and philosophy) :

# history of ideas

# epistemology of science and digital technology

#argumentatition et communicatition

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Second year mathematics program, part taught at Lycée Joffre :

# Reminders of linear algebra and complements of Euclidean geometry

# Advanced probability

# Analysis of functions of one variable

# Functions of several variables

See full page

This UE is a transversal UE of L2 SV aiming at giving to the students in Biology a basic knowledge on the functioning of plants allowing to understand the current stakes of the plant Agro-sciences.

The following basic Plant Physiology/Functional Biology will be studied: 

essential experimental approaches: plant transgenesis, direct and reverse genetics

basics of autotrophy

mechanisms underlying the major stages of angiosperm development: meristem function, floral transition, fertilization.

auxin, a major hormone for the development of plants and their response to the abiotic environment

The practical sessions will allow students to manipulate the regulation of water nutrition in plants and to analyze their mineral nutrition using different biochemical assays (flame photometry, spectrophotometry). 

See full page

This course is an introduction to the general concepts of scientific ecology: levels of organization, measurement and conservation of biodiversity, biogeography, biotic and abiotic factors of distribution and dynamics of biodiversity. It also provides an understanding of the methods used in scientific ecology: the importance of experimentation, reflection on the construction of a protocol, data analysis, oral and written reports of an experiment

See full page

Complements to linear algebra, reduction theory and applications 

# Complements to linear algebra, notion of direct sum

# Determinants

# Reduction: diagonalization and applications to the study of discrete and continuous dynamic systems in physics, chemistry, biology or economics.

See full page

This course continues the training of students in applied mathematics, with a focus on numerical methods.

Program (subject to change depending on the year and time available) :

# numerical matrix analysis

# digital integration

# numerical resolution of diferential equations

# introduction to the qualitative study of nonlinear differential equations

.

See full page

The 2nd year computer science course at the Lycée focuses on advanced concepts in algorithms and programming:

# Tree-like data structures: binary trees, heaps, ABR, priority queues

# Heap sorting, lower limit on sorting

# Graph structure: representations (adjacency matrices, edge lists, neighbor lists)

# Basic algorithms (connectivity, depth and width traversal, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

# Introduction to object programming (encapsulation, late linking, classes, methods, etc.)

# Programming in Python

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This UE completes the computer science training by opening up to the study of information systems and databases (design of processing in an information system and management of relational databases):

# Information systems: introduction of the entity/association model, relational model, processing modeling (conceptual processing model, organizational processing model).

# Databases: create, manipulate and query relational databases.

See full page

This module should enable students to acquire:

Basic notions in Physiology : Concept of homeostasis; levels of organization of the human body; compartments of the Internal Environment; study of the endocrine system; acid-base and hydro-mineral balance; anatomical and functional studies of the central and peripheral nervous system.

Basic concepts in Immunology:

General presentation of the immune system; study of T and B lymphocytes, antigen presenting cells; study of antimicrobial immunity and complement.

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This modern language course focuses on written and spoken English, with particular emphasis on oral expression.

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General culture (epistemology and philosophy) :

# history of ideas

# epistemology of science and digital technology

#argumentatition et communicatition

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- Physiology of major functions: anatomy and functions of the cardiovascular, respiratory, renal and digestive systems.

- Cellular and molecular biology 3: cytoskeleton function, cell adhesion, protein trafficking and study methods, cell cycle regulation, immunoprecipitation, fluorescence videomicroscopy, RNA interference, overexpression, regulation of gene expression: transcriptional regulation (repressor, activator) and attenuation in prokaryotes, mechanisms of expression regulation in eukaryotes.

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General culture (epistemology and philosophy) :

# history of ideas

# epistemology of science and digital technology

#argumentatition et communicatition

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Introduction to the use of data mining methods :

# Motivations, fields of application

# Data mining tasks (classification, estimation, prediction, etc.)

# Data processing (pre/post-processing)

# Supervised learning (Bayes method, k nearest neighbors, neural networks, etc.)

# Unsupervised learning (k-means)

# Method evaluation

# Data mining software (R, Scikit, Weka, etc.)

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The Physiology of major functions course in semester 4 of the CPES is designed to complement the course devoted to the study of the role and interactions of the various systems of the organism that contribute to keeping the internal environment constant. This course is taught through practical work and tutorials.

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Second year mathematics program, part taught at Lycée Joffre :

# Reminders of linear algebra and complements of Euclidean geometry

# Advanced probability

# Analysis of functions of one variable

# Functions of several variables

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This course is designed to deepen in small groups the fundamental molecular and cellular processes seen in the BMC2 and BMC3 courses by approaching them through more concrete notions. The lessons will be based on real data (experimental results, scientific articles) to simply explain the main scientific approaches and to learn how to analyze and interpret the results (Example 1: show an interaction in cellulo by expression of tagged proteins in cell lines followed by immunoprecipitation and western-blot. Example 2: principle of immunofluorescence, intracellular distribution of an antigen. Example 3: transcription and translation in vitro and study of interaction by GST-pull down). The practical exercises will illustrate some of these basic approaches: cell culture, construction of expression vectors, transfection, immunolabeling, fluorescence microscopy.   

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This course aims to broaden the knowledge acquired previously in different areas of microbiology, particularly in microbial ecology.

It will deal with pathogenic relationships, but will also present examples of symbiotic associations. It will address the applications of microorganisms in biotechnology. It will describe the mode of action of antibiotics and the associated resistance phenomena and their impact.

The EU will approach the notion of viral ecology by presenting the place and role of viruses in ecosystems. The case of bacteriophages will be treated more specifically and the mechanisms of resistance of bacteria to phagic infection will be detailed. The different types of viral infections in animals will be presented (acute and persistent infections) and illustrated through the study of the pathogenesis of selected viral infections.

The knowledge on microorganisms will be extended by the study of Archaea and a model eukaryotic organism, the yeast.

The practical work will focus on the realization of an antibiogram and its interpretation, and on the titration of bacteriophages.

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This course continues the training of students in applied mathematics, in particular the use of statistical tools:

# Notions of populations and random samples.

# Estimators.

#Mean square error and bias-variance decomposition.

# Empirical estimators of mean and variance. Construction of estimators using the method of moments. Maximum likelihood.
Interval estimation.

# Hypothesis testing: null hypothesis, alternative hypothesis. First and second errors. Power of a test. Test statistics, rejection region. Examples of classical tests.

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The objective of this course is to understand evolutionary processes, both at the micro- and macro-evolutionary scales.

Based on examples, manipulations and accessible modeling, the lessons will aim at presenting in a concrete and quantitative way the effects of the 4 evolutionary forces operating at the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes at larger time scales (e.g. differentiation between lineages, speciation) will then be addressed. Finally, the course will include an introduction to the tools of phylogeny (reading and construction of trees) allowing the study of macro-evolutionary events (diversification, extinction) and the tracing of changes in character states, notably by integrating fossil data.

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The 2nd year computer science course at the Lycée focuses on advanced concepts in algorithms and programming:

# Tree-like data structures: binary trees, heaps, ABR, priority queues

# Heap sorting, lower limit on sorting

# Graph structure: representations (adjacency matrices, edge lists, neighbor lists)

# Basic algorithms (connectivity, depth and width traversal, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

# Introduction to object programming (encapsulation, late linking, classes, methods, etc.)

# Programming in Python

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This modern language course focuses on written and spoken English, with particular emphasis on oral expression.

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This compulsory course will allow students to deepen their skills acquired in "S3 biochemistry". It will allow them to understand cellular metabolism through:

-The understanding of bioenergetics in order to study the processes by which living cells carry, transmit, use, store and release energy;
-the study of catabolism and anabolism of carbohydrates, lipids, nucleotides, amino acids and the metabolic interactions between these pathways.

- description of metabolic pathologies.

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In this introductory course to genetic analysis, the objectives are to learn the terms, principles, concepts and methods used in formal genetics, as well as their application in human and medical genetics. This course covers the genetics of transmission (Mendelian or non-Mendelian), quantitative genetics and notions of population genetics. Throughout the course, close links are established between classical and molecular genetics.

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This course, similar in spirit to the first-year project, is an introduction to the research approach, more advanced than in the first year: it includes immersion in a research laboratory, a bibliographical study, and the realization of a project involving the study of a biological context, the acquisition of experimental or observational data, and the implementation of a modeling and/or digital simulation approach.

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