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 is a cross-disciplinary L2 SV course designed to provide Biology students with a basic knowledge of how plants function, enabling them to understand current issues in plant agro-sciences.

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

essential experimental approaches: plant transgenesis, direct and reverse genetics

basics of autotrophy

mechanisms underlying the main stages in angiosperm development: meristem function, floral transition, fertilization.

auxin, a major hormone in plant development and response to the abiotic environment

Practical work sessions will enable students to manipulate the regulation of water nutrition in plants and analyze their mineral nutrition using various biochemical assays (flame photometry, spectrophotometry). 

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

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Linear Algebra Complements, Reduction Theory, and Applications 

# Complements of linear algebra, the notion of direct sum

# Determinants

# Reduction: diagonalization and applications to the study of discrete and continuous dynamical 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 (may be modified depending on the year and the time available):

# Matrix Numerical Analysis

# Digital Integration

# numerical solution of diffential equations

# Introduction to the qualitative study of nonlinear differential equations

.

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The 2nd year computer science course taught at the Lycée is focused on advanced concepts in algorithmics and programming:

# Tree data structures: binary trees, heaps, ABRs, priority queues

# Sort by heap, lower bound on sorting

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

# Basic algorithms (connectedness, depth and width paths, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

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

# Programming in Python

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

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

# Databases: creation, manipulation and querying of relational databases.

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This module will enable students to acquire :

Physiology basics : 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 systems.

Immunology basics :

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 teaching is focused on the written and oral practice of English, with a particular emphasis on oral expression.

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This course covers the theoretical concepts of plant biology, using the spermatophyte group as a model. It aims to define the notions and specific vocabulary of morphology, anatomy, reproduction and biological cycles.

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The EU aims to describe the morpho-anatomical characteristics of the major organizational plans of metazoans found in present and past faunas, and to explain their origin and the dynamics of their appearance. It thus develops a vision of organisms based on paleontology and zoology. It will focus on the origin of metazoans and the main divisions, diploblastic and triploblastic, as well as basic notions of phylogenetic positioning and relationships between taxa (mono- and paraphylly, evolutionary convergence, etc.). The course is classically divided into lectures, tutorials aimed primarily at illustrating and supporting aspects of taxon biodiversity, and practical work in sessions aimed at acquiring skills, particularly and necessarily in dissection.

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General culture (epistemology and philosophy):

# history of ideas

# Epistemology of science and digital technology

#argumentatition and communication

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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 is a cross-disciplinary L2 SV course designed to provide Biology students with a basic knowledge of how plants function, enabling them to understand current issues in plant agro-sciences.

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

essential experimental approaches: plant transgenesis, direct and reverse genetics

basics of autotrophy

mechanisms underlying the main stages in angiosperm development: meristem function, floral transition, fertilization.

auxin, a major hormone in plant development and response to the abiotic environment

Practical work sessions will enable students to manipulate the regulation of water nutrition in plants and analyze their mineral nutrition using various biochemical assays (flame photometry, spectrophotometry). 

See full page

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

See full page

Linear Algebra Complements, Reduction Theory, and Applications 

# Complements of linear algebra, the notion of direct sum

# Determinants

# Reduction: diagonalization and applications to the study of discrete and continuous dynamical 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 (may be modified depending on the year and the time available):

# Matrix Numerical Analysis

# Digital Integration

# numerical solution of diffential equations

# Introduction to the qualitative study of nonlinear differential equations

.

See full page

The 2nd year computer science course taught at the Lycée is focused on advanced concepts in algorithmics and programming:

# Tree data structures: binary trees, heaps, ABRs, priority queues

# Sort by heap, lower bound on sorting

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

# Basic algorithms (connectedness, depth and width paths, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

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

# Programming in Python

See full page

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

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

# Databases: creation, manipulation and querying of relational databases.

See full page

This module will enable students to acquire :

Physiology basics : 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 systems.

Immunology basics :

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

See full page

See full page

This modern language teaching is focused on the written and oral practice of English, with a particular emphasis on oral expression.

See full page

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General culture (epistemology and philosophy):

# history of ideas

# Epistemology of science and digital technology

#argumentatition and communication

See full page

See full page

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

General culture (epistemology and philosophy):

# history of ideas

# Epistemology of science and digital technology

#argumentatition and communication

See full page

Introduction to the use of data mining methods:

# Motivations, areas of application

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

# Processing on the data (pre/post-processing)

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

# Unsupervised learning (k-means)

# Evaluation of methods

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

# Notions of populations and random samples.

# Estimators.

#Erreur mean square and bias-variance decomposition.

# Empirical estimators of mean and variance. Construction of estimators by the method of moments. Maximum plausibility.
Interval estimation.

# Hypothesis tests: null hypothesis, alternative hypothesis. Errors of the first and second kinds. Power of a test. Test Statistic, Rejection Region. Examples of classic tests.

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The aim of this course is to understand evolutionary processes on both micro- and macro-evolutionary scales.

Using examples, manipulations and accessible modeling, the aim of the lessons is to present, in a concrete and quantitative way, the effects of the 4 evolutionary forces operating on the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes on 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 (tree reading and construction), making it possible to study macro-evolutionary events (diversification, extinction) and trace changes in character states, notably by integrating fossil data.

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

- Cell 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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The 2nd year computer science course taught at the Lycée is focused on advanced concepts in algorithmics and programming:

# Tree data structures: binary trees, heaps, ABRs, priority queues

# Sort by heap, lower bound on sorting

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

# Basic algorithms (connectedness, depth and width paths, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

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

# Programming in Python

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This modern language teaching is focused on the written and oral practice of English, with a particular emphasis on oral expression.

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

-understanding bioenergetics to study the processes by which living cells transport, transmit, use, accumulate and release energy;
-studying the catabolism and anabolism of carbohydrates, lipids, nucleotides and 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 about the terms, principles, concepts and methods used in formal genetics, as well as their fields of application, particularly in human and medical genetics. The 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 genetics and molecular genetics.

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The aim of this course is to broaden previously acquired knowledge in various areas of microbiology, in particular microbial ecology.

She will focus on pathogenic relationships, but will also present examples of symbiotic associations. Applications of microorganisms in biotechnology will be discussed. It will describe the mode of action of antibiotics and associated resistance phenomena, as well as their impact.

This course will introduce the notion of viral ecology, presenting the place and role of viruses in ecosystems. The case of bacteriophages will be dealt with more specifically, and the mechanisms of bacterial resistance to phagic infection will be detailed. The different types of viral infection in animals will be presented (acute and persistent infections) and illustrated by studying the pathogenesis of selected viral infections.

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

Practical work will focus on carrying out an antibiogram and its interpretation, and on bacteriophage titration.

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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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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

General culture (epistemology and philosophy):

# history of ideas

# Epistemology of science and digital technology

#argumentatition and communication

See full page

Introduction to the use of data mining methods:

# Motivations, areas of application

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

# Processing on the data (pre/post-processing)

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

# Unsupervised learning (k-means)

# Evaluation of methods

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

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This course is a continuation of the L2 S3 course, which focuses on describing the morpho-anatomical characteristics of the major organizational plans of metazoans found in present and past faunas, and on explaining their origin and the dynamics of their appearance, through the acquisition of skills in paleontology and zoology. In S4, the main focus will be on the major subdivisions within protostomian organisms such as lophotrochozoa (annelids, mollusks, brachiopods, etc.) and ecdysozoa (arthropods, nematodes, etc.), with emphasis on their phylogenetic relationships and their socio-economic importance and impact. The course is classically divided into lectures and tutorials, mainly aimed at illustrating and supporting aspects of taxon biodiversity, and practical work in sessions aimed at acquiring skills, in particular and necessarily through the performance of certain dissections.

See full page

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

# Notions of populations and random samples.

# Estimators.

#Erreur mean square and bias-variance decomposition.

# Empirical estimators of mean and variance. Construction of estimators by the method of moments. Maximum plausibility.
Interval estimation.

# Hypothesis tests: null hypothesis, alternative hypothesis. Errors of the first and second kinds. Power of a test. Test Statistic, Rejection Region. Examples of classic tests.

See full page

The aim of this course is to understand evolutionary processes on both micro- and macro-evolutionary scales.

Using examples, manipulations and accessible modeling, the aim of the lessons is to present, in a concrete and quantitative way, the effects of the 4 evolutionary forces operating on the scale of individuals and populations (mutation, migration, selection and drift). The integration of these micro-evolutionary processes on 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 (tree reading and construction), making it possible to study macro-evolutionary events (diversification, extinction) and trace changes in character states, notably by integrating fossil data.

See full page

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

- Cell 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.

See full page

The 2nd year computer science course taught at the Lycée is focused on advanced concepts in algorithmics and programming:

# Tree data structures: binary trees, heaps, ABRs, priority queues

# Sort by heap, lower bound on sorting

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

# Basic algorithms (connectedness, depth and width paths, topological sorting)

# Distance calculation (Dijkstra, heap implementation)

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

# Programming in Python

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The EU covers the different groups of plants ("algae", "cryptogams", spermatophytes), specifying for each of them their position and phylogenetic nature (mono- or paraphyletic group), their origin and their morpho-anatomical, reproductive and ecological specificities.

4 CM present different plant groups: CM1, diversity of "algae"; CM2, life cycles of "algae"; CM3, "cryptogams"; CM4, Spermatophytes.

6 TDs cover cross-disciplinary concepts based on oral or written exercises: TD1, Biological cycles; TD2, Endosymbiosis; TD3, Interactions; TD4, Adaptation; TD5, Polyploidy; TD6, Phylogeny.

6 practical sessions illustrate the concepts covered in the lectures and practical sessions using living material: TP1, "algae "1 ; TP2, "algae "2 ; TP3, "bryophytes" ; TP4, "pteridophytes" ; TP5, Gymnosperms, vegetative apparatus ; TP6, Gymnosperms, reproduction.

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The Functional Ecology UE aims to provide a solid grounding in the functioning of terrestrial ecosystems, and in particular the role played by living organisms in the flow of matter within them. The main processes covered are primary production, consumption and, in particular, herbivory, and the decomposition and transformation of soil organic matter. For each of these processes, particular attention is paid to (1) the link between organisms' strategies and their function in the ecosystem, and (2) basing the presentation of concepts on field findings, highlighting characteristics of organisms or the ecosystem that students may encounter on field trips.

This course fits in with the broader presentation of ecology in S1 (HLBE304) and provides the concepts required for the L3 course on community ecology.

Emphasis is placed on practical aspects, in particular through a series of group assignments, where a simple but scientifically relevant hypothesis is experimentally tested using an appropriate protocol.

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This modern language teaching is focused on the written and oral practice of English, with a particular emphasis on oral expression.

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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.

See full page