Diplôme d’ingénieur « European Biotechnology for Sustainability » (en anglais)

Course Description / Aims

This module confers fundamental knowledge and practices in safety and emergency procedures in a biology, microbiology and chemistry laboratory, considering the different working environments.

Learning outcomes

Students will understand the potential hazards associated with working in a laboratory setting and how to mitigate these risks effectively. The course module aims to equip the students with the knowledge, skills, and attitudes necessary to work safely and responsibly in laboratory environments, ensuring their well-being and the integrity of their environment, the lab equipment and the results of their lab work.

Skills and competences

This module will confer the following skills:

• Apply appropriate procedures and good practices for chemical and biological safety of laboratory equipment.
• Apply appropriate procedures in case of emergency.

Course Description / Aims

Mathematical tools are essential to all scientific studies, for analyse experimental result, and improve the understanding of physical and chemical phenomena. The aim of this module is to consolidate and complete the mathematical knowledge, and to introduce new concepts required for process modelling and optimisation. The use of computer tools such as spreadsheets and text editing tools will also be covered. In particular, the statistical calculation tools available in spreadsheets.

Learning outcomes

• Master the mathematical and statistical tools needed to manage experimental data.
• Proficiency in the Office suite, especially Word and Excel.
• Master the study of mathematical functions and their derivation and integration.
• Understand and apply polynomial interpolation and simple linear regression methods
• Understand and apply methods for calculating differential equations.

Skills and competences

This module will provide the student with the skills required to perform calculations required for other teaching modules (fluid mechanics, reactors, …)

Course Description / Aims

The use of mathematical models to simulate chemical and/or biochemical processes requires knowledge of computational tools. The aim of the module is to introduce learners to the Python language and its use for data processing and modelling. Numerical methods for solving complex equations and optimization methods will be implemented in Python.

Learning outcomes

• Master a programming language (Python)
• Understand and apply numerical tools for integration and equation solving
• Understand and apply parametric optimization methods
• Use the R language for statistical calculations, multiple linear regression calculations and principal
• component analysis.
• Discover digital simulation of complex problems

Skills and competences

This module will provide the student with the skills required to properly analyze and evaluate any type of data used for calculations or sizing or understanding biotechnology and bioprocesses.

Course Description / Aims

This module aims at refreshing the knowledge in general and physical chemistry gained during the 2 preparatory years and to get into more in depth knowledge in general-physical chemistry for the students to follow the overall curriculum.

Learning outcomes

• To master the basis of physical chemistry including thermodynamics and kinetics.
• To master analytical chemical methods for solid analysis and water titration.
• To have some knowledge of industrial chemistry.

Skills and competences

This module will provide the student with the following skills:

To master the basics of chemistry and physical-chemistry for the optimal production, valorisation and transformation of products while minimizing the impact on the environment.

Course Description / Aims

This module aims at refreshing the knowledge in organic chemistry gained during the preparatory 2 years and to get into more in depth knowledge in organic chemistry for the students to follow the overall curriculum.

Learning outcomes

• To master basic knowledge in organic chemistry.
• To apply spectroscopic methods for identification of main chemical functional groups.
• To understand chromatography and how it can help to assess chemical purity.

Skills and competences

This module will provide the student with the following skills:

Understanding of the chemistry general principals of life for the optimal production, valorisation and transformation of products while minimizing the impact on the environment

Course Description / Aims

• Discovery of life sciences, biotechnology and bioprocesses
• Presentation of fundamental concepts in cell biology, microbiology, molecular biology, biochemistry

Learning outcomes

• Know the main characteristics of eukaryotic, prokaryotic, archaeal cells and viruses: their differences, their specificities
• Know the structure of cells
• Know the families of biomolecules, their characteristics and their synthesis routes
• Know the main pathways of metabolism and catabolism

Skills and competences

This module will provide the student with the following skill: Identify the biological agent and understand its specificities

Course Description / Aims

• Acquisition/recall of fundamental common knowledge in cell biology, microbiology, molecular biology, biochemistry for biotechnology and bioprocesses.
• Acquisition of basic notions in bioinformatics.

Learning outcomes

• Master the fundamental notions of cell biology, microbiology, molecular biology, biochemistry.
• Know the main pathways of cellular metabolism and catabolism.
• Know the basic techniques in cell culture, microbiology, molecular biology and biochemistry (theory and practicals).
• Know the main bioinformatics databases.
• Know how to use sequence and protein analysis software.
• Know the typical industrial applications of biotechnology.

Skills and competences

This module will provide the student with the following skills:

• Identify the biological agent and understand its specificities
• Manipulate microorganisms (bacteria, yeasts, filamentous fungi) in sterile laboratory conditions to isolate, identify and characterize microbial strains.
• Carry out manipulations of biological agents (cells, organisms, and biomolecules) in vitro.
• Analyse the specificities of the biological agent / biological model using IT tools (bioinformatics) for the implementation of a biotechnology project or a bioprocess.

Course Description / Aims

This highly academic and rigorous language course enables students to develop strong language skills while engaging with scientific fundamentals and intercultural topics. Through a structured curriculum encompassing independent study, group projects, and general language learning activities, students will immerse themselves in academic discourse, vocabulary acquisition, grammar, and intercultural understanding, with a focus on scientific contexts.

Learning outcomes

• English: Intensive instruction in English language skills including reading, writing, listening, and speaking, tailored to academic and professional contexts. Language Instruction: Developing and consolidating a C1 level; introduction to Cambridge tasks and exercises.
• European Language: Students will choose one European language to study alongside English, such as French, German, Spanish, or Italian. Language courses will cover grammar, vocabulary, conversation, and cultural nuances.

Skills and competences

• Listening and Speaking Skills: Practice in listening comprehension and oral communication through dialogues, role-plays, and interactive exercises.
• This course is designed for students at the C1 level who have a strong command of the English language and are interested in exploring ethical issues in science and biotechnology.

Course Description / Aims

This module aims to give an understanding of the typology of biotechnologies and give an overview of the contribution of biotechnologies in each sector of activity.

Learning outcomes

• Foundational Knowledge: Students will gain a solid understanding of the fundamental principles and concepts underlying biotechnology, including molecular biology, genetics, and bioprocess engineering.
• Applications Understanding: Students will be able to identify and describe the diverse range of applications of biotechnology in various fields, including healthcare, agriculture, industry, and the environment.
• Ethical and Regulatory Awareness: Students will understand the ethical, legal, and social implications of biotechnology and be aware of the regulatory frameworks governing its practice in the EU.

Skills and competences

This module will confer the following skills:

• Carry out literature a research project in various fields of biotechnology
• Identify the sector of activity concerned by a given biotechnological process
• Indicate aspects that are subject to regulations
• Report and discuss the results of the literature research in oral form

Course Description / Aims

This module gives a solid foundation in ecosystem ecology and enables the students to develop the knowledge, skills, and perspectives necessary to address sustainability challenges in biotechnology engineering.

Learning outcomes

• Define and describe the biogeochemical cycles of C, N, P, O and water at the ecosystem scale.
• Describe and explain the flows that contribute to the energy balance of an ecosystem.
• Describe the flows of energy and matter within ecosystems and explain how abiotic factors impact them.
• Use the knowledge acquired in ecology to develop a holistic approach to problems and understand global issues.
• Develop critical thinking and problem-solving skills.

Skills and competences

This module will provide the student with the following skills:

• Identify environmental and societal issues at different scales (global/local);
  Identify the main potential environmental impacts
• Use collective intelligence to facilitate exchanges and co-construction.
  Transmit and present orally information relating to the results of an analysis;
  Exchange in a relevant way with different interlocutors

Course Description / Aims

• Use of artificial intelligence for biotechnology and bioprocesses.
• Use of databases & exploitation of big data (large data sets) for biotechnology and bioprocesses.
• Use of process/reaction simulation software and acquisition of knowledge on the use of digital twins for biotechnology and bioprocesses.

Learning outcomes

• Know how to code/program in Python
• Know how to create an “sdf” or “sql” database.

Skills and competences

This module will provide the student with the following skills:

• Identify the tools for creating, managing and analysing databases considering the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Develop scripts in Python and use process/reaction simulation tools considering the specificities of the biological agent to optimize a bioprocess or a biotechnology project.

Course Description / Aims

This module will provide the students with an understanding of European institutions, their roles, and functions in shaping biotechnology and sustainability policies.

Learning outcomes

• Develop linguistic competence, cultural awareness, critical thinking skills, and practical knowledge to navigate the complexities of Europe’s linguistic, cultural, and environmental landscapes.
• Cultural Awareness: Exploration of cultural aspects influencing scientific practices in Europe, including cultural norms, values, and attitudes toward science.
• Professional Communication: Development of professional communication skills relevant to scientific contexts, such as email writing, formal presentations, and academic discourse.

Skills and competences

This module will provide the student with the following skills:

• Intercultural Competence: Development of intercultural communication skills, cultural sensitivity, and awareness of cultural differences and similarities.
• Identify European institutions and policy frameworks which impact the biotechnology and sustainability sectors

Course Description / Aims

This teaching module aims to initiate students in project management within the context of sustainable biotechnology. Within this group project, students will:

• Interact with peers coming from different backgrounds and/or countries
• Adopt an active stance towards their engineering studies
• Learn and use essential project management principles, tools, and techniques while applying them to sustainable biotechnology projects.

Learning outcomes

• Understand the fundamentals of project management and its relevance to sustainable biotechnology projects.
• Develop skills in project planning, execution, monitoring, and control.
• Apply project management tools and techniques to effectively manage sustainable biotechnology projects.
• Enhance communication, teamwork and collaboration skills through group project work.
• Analyze and evaluate the sustainability aspects of biotechnology projects.

Skills and competences

This module will provide the student with the following skills:

• Conduct a literature review using IT tools and scientific and technical databases
• Use and implement management and collaborative project management tools and techniques;
• Position yourself in a project team considering your assigned role to guarantee the completion of a project within deadlines;
• Interact with team members in an efficient and productive manner by mobilizing soft skills (behavioral skills) to guarantee the completion of a project on time;
• Receive and integrate criticism and suggestions by mobilizing soft skills (“relational” behavioural skills) to guarantee the progress of the project;
• Transmit and present orally information relating to a project.

Course Description / Aims

This module provides on basic knowledge in applied cell and molecular biology. The students will learn the basic cell structure / organisation and the control of all living processes by genetic mechanisms. They will have an opportunity to handle and manipulate genetic material provided in the laboratory. This module will explore the impact of a wide range of model organisms, gene manipulation technologies through case studies and real-world examples

Learning outcomes

Applied Cell Biology

• Understanding the functioning of animal and plant cells: structure and physiology of eukaryotic cells, the different cellular systems, their divisions and their specificities.
• To master the techniques of animal cell culture in the laboratory: growth, contamination, nutritional needs, control of the speed of development
• Be able to differentiate cellular systems and compare different culture modes to choose the best cellular tool and appropriate culture conditions
• To master good laboratory practices to ensure the reliability of cell culture experiments in the laboratory

Applied molecular biology

• Know and understand the basics and the technics of molecular biology
• Apply modern molecular biology techniques for strain modification or strain analysis and characterization of biomolecules
• Generate strategies for new strain construction that will be useful for the development, innovation and improvement of bioprocesses

Skills and competences

This module will provide the student with the following skills:

• Integrate the principles of life at the cellular and molecular scale, upstream of an industrial project, to explore new approaches
• Analyse the biological specificities by integrating behaviours and cultivation principles in different environments and conditions for the selection of the biological agent to be produced.
• Develop strategies for new strains construction that will be useful for the development, innovation and improvement of bioprocesses

Course Description / Aims

The learning content of this module provides a comprehensive understanding of microorganisms structural and molecular diversity, physiologies, metabolisms and their applications in industrial productions. Concepts of microbial communities and consortia are introduced. Lectures are completed by practicals and projects revolving around the basics techniques and methodologies employed at laboratory scale to cultivate, isolate, and characterize microorganisms, notably bacteria, yeasts and filamentous fungi.

Learning outcomes

• Knowledge of the different classes of microorganisms, their composition, structures, specificities, applications in research or industry
• Strong understanding of microbial metabolisms (primary, secondary), and metabolites of interest in the industry
• Master the basics methods in microbiology: isolation, identification, culturing, biochemical characterization, counting and biomass evaluation
• Ability to design, test and improve a culture method at laboratory scale

Skills and competences

This module will contribute to get the student with the following skills:

• Design a microbial bioproduction by mobilizing the bibliography and performing laboratory tests in order to substitute a petro-based chemical process by a bio-based bioprocess.
• Analyse the biological specificities of microorganisms in the context of the development or conduct of a bioprocess in order to select the biological agent to produce.
• Handle microorganisms under sterile conditions in the laboratory to isolate, identify and characterize microbial strains.

Course Description / Aims

This module provides basic knowledge of the chemical constitution, utilization and modification of biomass and biopolymers. Students will explore the diversity of biopolymers and biomass in both their sourcing, compositions and structures at different scales, as well as their chemical modification/functionalization for, notably, industrial or medical applications. Furthermore, through case studies and real-world examples, the module highlights the societal and environmental stakes of biopolymers & biomass utilization in the global context of sustainability.

Learning outcomes

• Master the fundamentals concepts related to the principal biosourced and natural polymers: structures, physico-chemical properties, extraction & preparation methods, applications
• Understand the stakes of natural and biosourced polymers in the global context of sustainability
• Explain and evaluate biopolymer properties based on their structure (at atomic, nano-, micro- and macro-level) and give their chemical structure;
• Relate a specific biopolymer to biological structures in nature;
• Reflect on the polymeric material choices for different applications taking in account its properties;
• Identify and discuss current environmental issues with a focus on the material’s impact in relation to the sustainable development objectives set by the community;
• Suggest and discuss the choice of biopolymers synthetic polymers suitable for common applications with respect to raw materials, energy aspects, material properties, function, environmental impact, waste management, ethical aspects and economy.

Skills and competences

This module will provide the student with the following skills:

• Integrate living principles to produce, valorise, and transform a product optimally with minimal environmental impact.
• Develop innovative biotechnology projects by incorporating European and French frameworks for biotechnology and sustainable development.
• Undertake scientific and technical projects, whether industrial or research-oriented, in complex and multidisciplinary environments.

Course Description / Aims

This module will provide the bases in chemical engineering to the students in order to understand the behaviour of bioreactors.

Learning outcomes

• Understand the behaviour of fluids within a system.
• Understand agitation phenomena and the characteristics of an agitator impeller.
• Know the applications of agitation in bioprocesses.

Skills and competences

This module will provide the student with the following skills:

• Calculate the pressure losses experienced by a fluid flowing through a pipe.
• Select the most suitable type of pump for conveying a fluid.
• Size an entire pumping installation.

Course Description / Aims

This module will provide the bases in chemical engineering to the students in order to understand the behaviour of bioreactors.

Learning outcomes

• Understand the constraints imposed by the thermodynamics of chemical and biological processes.
• Know the physical laws governing the processes of mass and heat transfer.
• Understand the terms involved in a mass and heat balance.
• Master the criteria for selecting equipment and materials used in bioproduction.

Skills and competences

This module will provide the student with the following skills:

• Calculate thermodynamic properties to establish balances and define equilibrium conditions.
• Be able to establish heat and mass balances at the boundaries of equipment in both steady-state and transient conditions.
• Calculate, simulate, and predict the operation of installations that optimize material and energy consumption, product quality, and consistency.
• Design the dimensions of a bioproduction facility.
• Know how to draft a specifications document for design offices or equipment manufacturers.

Course Description / Aims

This module will provide the bases in chemical engineering to the students in order to understand the behaviour of bioreactors.

Learning outcomes

• Understand the behaviour of chemical / Biochemical reactors.
• Evaluate the impact of the coupling between mass transfer and the chemical/biochemical reactions

Skills and competences

This module will provide the student with the following skills:

• Choosing the necessary reactor for developing a process at the pre-industrial scale (laboratory and pilot).
• Be able to establish heat and mass balances at the boundaries of equipment in both steady-state and transient conditions.
• Calculate, simulate, and predict the operation of installations that optimize material and energy consumption, product quality, and consistency.
• Design the dimensions of a reactor.
• Know how to draft a specifications document for design offices or equipment manufacturers.

Course Description / Aims

This module will introduce the concepts of sustainable development, sustainability and the bioeconomy. Serious games will enable the students to interact with their peers and develop ideas and sustainability strategies based on crowd intelligence.

Learning outcomes

• Understand the major environmental issues and the societal transitions underway;
• Understand the concepts of sustainable development, sustainability and the bioeconomy;
• Analyse the benefits of an integrated approach to biotechnology in a context of change

Skills and competences

This module will provide the student with the following skills:

• Analyse case studies/best practice/feedback to improve sustainability/CSR practices;
• Integrate the principles of sustainability and environmental responsibility into projects;
• Develop critical thinking and problem-solving skills.

Course Description / Aims

Establishing social and environmental responsibility as a common objective while solidifying a B1 (minimum) level in a European language other than English: Social and environmental responsibility will be studied in the student’s third language, with the objective of fostering ethical, sustainable, and socially conscious practices among future engineers. Develop effective communication skills in a third language for engaging with diverse stakeholders, including policymakers, community members, and industry partners as well as the ability to understand the issues in « layman’s » terms.

Learning outcomes

• Solidify a B1 level in a European language
• Reading and speaking about environmental issues
• Interdisciplinary thinking
• Integration of diverse perspectives in problem-solving.

Skills and competences

• Examine the environmental impact of engineering activities across different sectors.
• Introduce strategies for designing and implementing environmentally sustainable engineering solutions.
• Understand the importance of considering diverse perspectives and addressing social inequalities in engineering practice.
• Encourage students to identify opportunities for leveraging engineering skills to address social and environmental challenges.
• Foster a commitment to lifelong learning and continuous improvement in ethical and sustainable engineering practice.
• Strengthen language skills:

– Understand the main points of clear standard speech on current affairs or topics of personal or professional interest when the delivery is relatively slow and clear.

– Enter unprepared into conversation on topics that are familiar

– Briefly give reasons and explanations for opinions and plan; narrate a story or and describe reactions.

– Understand texts that consist mainly of high frequency language

Course Description / Aims

The student will be working full-time in a company in biotechnologies related to Bioprocesses & Biotechnologies, for a period of 2 months. The student is guided by a CPE LYON tutor and a supervisor in the company. The evaluation of the internship will be conducted by the tutor and the supervisor. The final mark is based on the evaluation of the student behavioural & social skills demonstrated during the internship (tutor evaluation report), and of an individual report produced by the student (tutor & supervisor).

Learning outcomes

• Write a technical report based on results obtained from physico-chemical measures (production, research, or development), commented & discussed based on the main objectives of the internship
• Collaborate with a team in the context of a short-term project
• Understand & apply internal rules, good practices of manufacturing or laboratory
• Apply a protocol or guidelines to operate equipment or conduct an experiment
• Gather & analyse written technical resources, reach relevant experts, from the team or from other departments, to provide expertise on specific project tasks
• Communicate through written reports, oral presentations in meetings or seminars, and interpersonal discussions
• Manage working time & plan tasks
• Develop a critical thinking toward results obtained & take initiatives

Skills and competences

This module will provide the student with the following skills:

• Develop deliverables associated with the context / work situations considering the purpose of the document to support production and/or technology transfer.
• Transmit and present orally information relating to a project, in context / work situations, considering the specificities of the various interlocutors (internal and external partners, experts or professionals who are not experts in the field), to inform the various actors and stakeholders.
• Work in multidisciplinary and inclusive teams and interact with the various specialists or engineers from another discipline by mobilizing soft skills (« relational » behavioural skills) to solve a problem related to bioproduction.
• Consider the specificities of the various interlocutors and collaborators (e.g. situations of disability) in a professional context by mobilizing soft skills (« relational » behavioural skills) to optimize collaboration.
• Receive and integrate criticism and suggestions by mobilizing soft skills (« relational » behavioural skills) to guarantee the progress of the project.

Course Description / Aims

Cells are commonly used as biocatalysts to transform various materials into products of interest for industry or end-consumers. Rational approaches to engineering cells to better make molecules/products are of crucial technical, economic and scientific interest, particularly in the context of industrial mutations toward sustainable production means. This module provides an advanced knowledge of the cell as a biocatalyst for productions, and the approaches to modify, adapt and study the biocatalysts.

Learning outcomes

• Understand the specificities of biocatalysts and cell factories as technological tools
• Ability to choose the type of cell and adapt it to a production
• Ability to design a protein expression or biomass production strategy
• Understand advantages and disadvantages of whole-cell catalysis versus enzymatic catalysis
• Ability to apply methods for cell modification, culture and protein expression for production in microbial or in animal cells

Skills and competences

This module provides the student with the following skills:

• Define the experimental procedures and resources necessary to carry out the experiments based on the analysis of the bibliography carried out from relevant documentary databases to design an improved production strain;
• Modify a biomanufacturing strain using the principles of genetic, metabolic and biochemical engineering to design an improved strain as part of a bioprocess development
• Execute experimental protocols for the isolation, identification and culture of bioproduction strains, for the sterilization of materials and equipment, the characterization of cell growth and the main metabolisms involved

Course Description / Aims

This module provides basic knowledge of operation for biomanufacturing upstream processing production area. The student will explore the difference between mammalian, plant and microbial upstream processing. Through examples and exercises, they will understand areas process design and bioreactor technology.

Learning outcomes

Knowledge and understanding the theory of metabolism and microbial or animal cell growth in bioreactors.

To implement and optimize culture processes with bacteria, yeasts, fungi or animal cell culture processes in respect of BPL

Skills and competences

This module will provide the student with the following skills:

Design, implement and optimize the production process (USP/DSP) of a biological agent, biological or biosourced product on an industrial scale

• Operate a bioreactor by ensuring offline and online analytical monitoring to validate the pilot design.
• Identify the process indicators and characterize a monitoring strategy by selecting the relevant parameters for control the culture and the bioreactor to ensure the compliance of the indicators and the appearance of possible drifts and failures
• Analyse critical process parameters and their impact on bioprocess outcomes.
• Analyse the collected data by using representation tools and mobilizing private or public documentation resources, patents, scientific & technical publications, to propose corrective actions

Course Description / Aims

This module will explore fundamental knowledge on the purification of biotechnological products using different technologies and various purification procedures.  Students will also gain understanding of the processes involved in downstream production of biomolecule or biomass

Learning outcomes

• Acquisition of Knowledge of the theories and concepts of different techniques for the purification of products of interest or biomass harvesting
• Understand the strategy of the different chromatography techniques in a purification process.
• Know how to implement the different unit operations of separation and purification of products of interest
• Be able to identify the critical parameters of these processes for controlling of their implementation.

Skills and competences

This module will provide the student with the following skills:

• Design, implement and optimize the production process (USP/DSP) of a biological agent, biological or biosourced product on an industrial scale.
• Implement and manage unit separation and purification operations by ensuring offline and online analytical monitoring.
• Define the process indicators and define a monitoring strategy by selecting the relevant parameters for conducting the separation and purification step.
• Ensure the compliance of the indicators and the possible deviations and failures

Course Description / Aims

This module will equip students with the knowledge and skills necessary to assess the environmental impacts of chemical and biotechnological processes and products, and to make informed decisions aimed at improving sustainability of the biotechnological products throughout their life cycles.

Learning outcomes

• Know and understand the main principles of eco-design;
• Understand the value of LCA methodology in a bioindustrial context;
• Acquire the methodology applied to bioproducts (ISO standard);
• Understand the potential and limitations of this environmental impact assessment method.

Skills and competences

This module will provide the student with the following skills:

• Carry out an assessment and analysis of the impact of a bioproduct using a standardized methodology.
• Write the LCA study report and communicate the results of the study.

Course Description / Aims

In this module, students will deepen their understanding of the complex interplay between EU policies, and ethical considerations in the field of biotechnology, while developing critical thinking, research, and communication skills essential for informed citizenship and professional engagement in the European context and continuing to develop English language skills that will allow them to successfully pass a Cambridge exam.

Learning outcomes

• Develop advanced English language skills in reading, writing, listening, and speaking within the context of science and biotechnology ethics.
• Explore and analyse ethical principles, theories, and frameworks relevant to scientific research, experimentation, and technological innovation.
• Engage in critical discussions and debates on contemporary ethical issues in science and biotechnology.
• Collaborate on project-based assignments that require research, analysis, and reflection on ethical implications in scientific practice.
• Enhance cross-cultural awareness and communication skills through interaction with diverse perspectives and viewpoints.

Skills and competences

This module will:

• Develop linguistic competence, cultural awareness, critical thinking skills, and practical knowledge to navigate the complexities of Europe’s linguistic, cultural, and environmental landscapes.
• Professional Communication: Development of professional communication skills relevant to scientific contexts, such as email writing, formal presentations, and academic discourse

Course Description / Aims

Within this group project, students will apply their knowledge to develop a new bioprocess or to improve an existing one. The bioprocess may be based on biomass feedstocks (e.g. hemp, straws, hardwoods, sugarcane bagasse etc.), biomass-derived wastes and residues (e.g. waste papers, composts, municipal waste etc.), or compounds/chemicals obtained or derived from biomass (e.g. lignin, glucose, ethanol etc.). Size and constitution of groups: 3 to 5 students of diverse and complementary skills and backgrounds.

Roles and Responsibilities:  the roles will be assigned at the beginning and generally maintained throughout the duration of the project. Switching roles is possible but should be explained to the tutor.

Learning outcomes

• Students who complete the module will be able to identify the characteristics of biomass from different resources
• describe suitable microbial processes for processing different types of biomass to produce biofuels or biochemicals
• account for the metabolic interactions in microbial cells
• explain the principles for the concept of renewable bioenergy and sustainability
• explain the bottlenecks and/or inhibition effects of the different biomass conversion processes
• account for calculation and simulation tools to determine metabolic fluxes
• explain techniques to measure cellular metabolic fluxes

Skills and competences

This module will provide the student with the following skills:

• assess and select relevant original scientific literature and current scientific methods, models and other tools used in the project and asses the problem of the project and results in relevant scientific and social contexts
• select appropriate modelling strategies
• model carbon fluxes in microorganisms
• manipulate the direction of metabolite fluxes
• propose strategies to genetically optimize production strains
• use software for process design
• perform techno-economic analysis for microbial bioprocesses
• write an electronic project report following the standards of the field of study, include relevant original scientific literature, use the correct terminology, and communicate the research-based foundation and problem and results in writing, graphically and orally in a professionally reasoned and coherent way
• use relevant software to present, analyse and visualize theories, hypotheses and data in writing as well as orally

Course Description / Aims

Cells are commonly used as biocatalysts to transform various materials into products of interest for industry or end-consumers. Rational approaches to engineering cells to better make molecules/products are of crucial technical, economic and scientific interest, in particular in the context of industrial mutations toward sustainable production means. This module provides an advanced knowledge of the cell as a biocatalyst for productions, and the approaches to modify, adapt and study the biocatalysts.

Learning outcomes

• Ability to apply methods of enzymology, protein characterization and analysis
• Ability to design an expression system to produce a specific protein, enzyme
• Understand the composition, advantages, disadvantages, case applications of enzymatic reactors
• Integrate biocatalytic properties of an enzyme for bioprocess design and biotechnological development

Skills and competences

This module will provide the student with the following skills:

• Use innovative biological tools (enzymes, microorganisms, microbial consortia) in processes developed at the laboratory scale
• Integrate the constraints specific to reactor production, at the laboratory reactor scale, in the development of biocatalytic solutions for bioprocesses in order to comply with production specifications
• Modify a bioproduction strain using the principles of genetic, metabolic and biochemical engineering to design or adapt protein production as part of a bioprocess development
• Implement an experimental protocol to modify a protein or enzyme as part of the improvement, adaptation or creation of a biocatalytic process

Course Description / Aims

• Understanding of the challenges of industrial analysis of biomolecules
• Mobilization of analytical techniques for the implementation of analytical strategies in biotechnology or bioproduction
• Mobilization of analytical techniques for the implementation of online analyses in biotechnology or bioproduction

Learning outcomes

• Understanding the challenges of industrial analysis of biomolecule
• Analysis strategy
• Understanding the challenges of industrial analysis strategies for biomolecules from the laboratory to the foot of the production process
• Know the main analytical techniques of biomolecules used in biotechnology and bioprocesses
• Be able to coordinate and evaluate an analysis strategy approach, integrate data from several techniques
• Choosing and implementing the right techniques
• Online analysis & PAT
• Understand the challenges of online analysis for improving the safety and quality of products and manufacturing processes
• Knowledge of the methodology and main on-line analysis techniques for designing, analysing and controlling manufacturing processes in biotechnology and bioprocesses
• Be able to coordinate and evaluate an online analysis process

Skills and competences

This module will provide the student with the following skills:

Analysis strategy

Propose and implement analysis tools by establishing technological and bibliographic monitoring to optimize production conditions;

Define the process indicators and define a monitoring strategy by selecting the relevant parameters for monitoring the culture and the bioreactor to ensure the compliance of the indicators and the appearance of possible drifts and failures within the framework of permanent monitoring of the process;

Propose and implement a strategy for analysing biomolecules or cells to optimize production conditions.

Course Description / Aims

This module will explore the basic of omics approaches for studying biological systems (cells or microorganisms) in interaction with other biological systems. The student will understand the consequences of these interactions or be able to propose models of synthetic biological systems possessing new functions or allowing the bioproduction of molecules of interest.

Learning outcomes

Understand the concepts of omics approaches and multi-scale analyses for the study of biological systems and metabolic networks

Know the different multi-scale analysis tools allowing the study of the biological system / metabolic networks

Be able to use bioinformatics tools for the analysis of data from omics approaches

Simple omics data analyser

Understand the concepts of integrated and simultaneous analysis of different omics data in order to study cellular mechanisms and their deregulations or to reconstruct biological networks.

Skills and competences

This module will provide the student with the following skills:

Integrate the principles of life at the cellular and molecular scale, upstream of an industrial project, to explore new approaches

Use digital technologies to create biological models or industrial processes to optimize biotechnological applications, biotransformation/bioproduction strategies

Course Description / Aims

Using artificial intelligence for biotechnology and bioprocesses

Use of databases and exploitation of big data for biotechnology and bioprocesses

Use of process/reaction simulation software and knowledge of the use of digital twins for biotechnology and bioprocesses

Learning outcomes

• Know the principles of AI and the main uses for biotechnology
• Discover the tools for digital simulation and the creation/use of digital twins
• Discover the main tools for processing « big data » in biotechnology and bioprocesses

Skills and competences

This module will provide the student with the following skills:

• Identify artificial intelligence tools considering the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Use artificial intelligence tools considering the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Identify the tools for creating, managing and analysing databases considering the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Identify the tools for creating, managing and analysing databases considering the specificities of the biological agent to optimize a bioprocess or a biotechnology project

Course Description / Aims

This module provides an introduction to frameworks for ethical decision-making in scientific research and professional practice. Concerning the professional Development, this module enables the students to develop professional skills such as communication, project management, and leadership, essential for success in the biotech industry and regulatory agencies.

Learning outcomes

• Regulatory Compliance: Understanding the regulatory frameworks governing biotechnology in the European Union, including laws, directives, and guidelines.
• Communication Skills: Effectively communicating regulatory requirements, compliance strategies, and scientific concepts to diverse audiences in English, French and possibly a third language.
• Comprehensive Understanding: Develop a deep understanding of the EU regulatory landscape governing biotechnology.
• Critical Analysis: Enable students to critically analyse and interpret EU biotech regulations in the context of technological advancements, market dynamics, and societal concerns.
  • Innovation and Compliance: Equip students with the skills to navigate regulatory requirements while fostering innovation in biotechnology, balancing the need for safety and compliance with the drive for technological progress.
  • Global Perspective: Explore the harmonization of EU regulations with international standards and the implications for global biotech markets, preparing students for careers in multinational companies or consulting firms. 

    Skills and competences

    This module will provide the student with the following skills:

    -Comprehensive Understanding: Develop a deep understanding of the EU regulatory landscape governing biotechnology, including key directives such as GMO regulations, medical device regulations, and clinical trial directives.

    – Critical Analysis: Enable students to critically analyse and interpret EU biotech regulations in the context of technological advancements, market dynamics, and societal concerns.

    – Applied Knowledge: Provide opportunities for students to apply regulatory knowledge to practical scenarios through case studies, simulations, and internships in biotech companies or regulatory agencies.

    – Hands-on projects focusing on sustainability challenges and solutions, allowing students to apply language skills, critical thinking, and interdisciplinary knowledge to real-world issues.

    – Develop recommendations for policymakers, industry stakeholders, and civil society organizations to address ethical concerns and enhance the governance of biotechnology within the European Union.

    – Comparative Analysis of European and International Biotechnology Regulations

    – Propose strategies for promoting transparency, accountability, and public participation in decision-making processes related to biotechnology.

   

Course Description / Aims

The student will be working full-time in a company in biotechnologies related to Bioprocesses & Biotechnologies, for a period of 4 months.  It aims to provide students with their first significant experience in a professional environment, exposing them to the relevant technical, managerial, and safety aspects and requirements. The student is guided by a CPE Lyon tutor and a supervisor in the company. The evaluation of the internship will be conducted by the tutor and the supervisor. The final mark is based on the evaluation of the student behavioural & social skills demonstrated during the internship (tutor evaluation report), and of an individual report produced by the student (tutor & supervisor).

Learning outcomes

• Write technical reports based on results obtained from physico-chemical measures (production, research, or development), with associated discussions based on the main objectives of the internship.
• Write a project report including project context, description of the methods, & detailed results.
• Analyse & propose additional conclusions based on the study of several results together.
• Collaborate with the team, other departments, and experts on the field.
• Understand & apply internal rules of procedure, good practices of manufacturing or laboratory.
• Apply protocol or guidelines to operate equipment or conduct an experiment.
• Conduct a short bibliographical study.
• Reach relevant experts, from the team or from other departments, to provide expertise on specific project tasks.
• Communicate through written reports, oral presentations in meetings or seminars, and interpersonal discussions.
• Design & follow a planning for the project execution.
• Demonstrate critical thinking on the methods applied, the results obtained.
• Take initiatives & propose improvements on technical operations.

Skills and competences

This module will contribute to get the student with the following skills:

• Complete a mission by solving complex technical problems (with objectives, timelines, cost and quality).
• Behave with creative and independent thinking.
• Present findings and proposals; provide technical expertise and support of decisions made; convey a message with strength and conviction.
• Write a report feting both academic and industrial expectations.

Course Description / Aims

This course module provides the students with a comprehensive understanding of Quality by Design (QbD), Design of Experiments (DoE), and Process Analytical Technology (PAT) and their integrated application to enhance the efficiency and robustness of the bioproduction processes and to enhance product quality.

Learning outcomes

Students will:

Understand the principles and importance of QbD, DoE, and PAT in bioproduction engineering.

Learn how to systematically design experiments using DoE to optimize bioproduction processes.

Gain knowledge of PAT tools and techniques for real-time monitoring and control of bioprocesses.

Understand the integration of QbD, DoE, and PAT for process optimization and quality assurance in bioproduction.

Skills and competences

Students will develop practical skills through case studies and practical exercises in applying QbD, DoE, and PAT to bioproduction processes: Calculate, simulate, and predict the operation of an installation using a digital bioprocess simulation tool in order to transfer from the pilot scale to the industrial scale.

Course Description / Aims

« Peace engineering strives to establish and emphasize the roles and contributions of engineers and scientists in diplomacy and policymaking. This includes promoting science, technology and engineering literacy in policy makers, and increasing diplomacy and policy literacy in scientists, technologists and engineers. »

These tools can assist diplomats, policy makers and the business community in designing and implementing strategies to anticipate and address problems with sustainable solutions that promote human security and wellbeing.

The ultimate vision is to foster a self-sustaining peace industrial complex, where economic impact and return on investments in peace-tech can be measured consistently and predictably for global sustainability.

Learning outcomes

• Interdisciplinary Approach: Encourage interdisciplinary collaboration between students from diverse backgrounds such as law, science, ethics, and policy, reflecting the multifaceted nature of biotech regulation.
• Innovation and Compliance: Equip students with the skills to navigate regulatory requirements while fostering innovation in biotechnology, balancing the need for safety and compliance with the drive for technological progress.
• Global Perspective: Explore the harmonization of EU regulations with international standards and the implications for global biotech markets, preparing students for careers in multinational companies or consulting firms.

Skills and competences

This module will provide the student with the following skills:

Geopolitical Analysis: Examine the geopolitical factors influencing biotechnology policies and regulations within the European Union, including EU integration, international trade agreements, and geopolitical rivalries.

Ethical Awareness: Foster ethical awareness and responsibility in biotech professionals by exploring the ethical implications of regulatory decisions and industry practices.

Examination of issues of social justice, equity, and access in scientific research and technological innovation.

Discussion of ethical responsibilities of scientists, policymakers, and industry stakeholders in addressing disparities in scientific advancement.

Course Description / Aims

This module aims to deepen the understanding of bioproduction engineering students in assessing and mitigating the environmental impact of bioproduction processes, with a specific focus on carbon footprint and environmental impact analysis.

Building upon the knowledge acquired in the previous Life Cycle Assessment (LCA), this module will focus on carbon accounting methodologies, emissions quantification, and strategies for reducing the environmental footprint of bioproduction processes.

Learning outcomes

Consolidate the understanding of carbon footprint and environmental impact analysis concepts in the context of bioproduction engineering.

Develop skills in quantifying carbon emissions and conducting carbon accounting for bioproduction systems.

Explore advanced strategies for reducing carbon footprint and mitigating environmental impacts in bioproduction engineering.

Analyse real-world case studies and best practices in environmental sustainability within the bioproduction industry.

Foster critical thinking and problem-solving skills for optimizing bioproduction processes while minimizing environmental impact

Skills and competences

This module will provide the student with the following skills:

Develop a mitigation plan integrating LCA results and carbon footprint reduction strategies;

Present project results and recommendations for environmental improvement and optimisation of bioproduction processes.

Course Description / Aims

In this Track students will acquire advanced knowledge of cells modifications principles, enzyme improvement, and development of the first step of the scale-up process, at laboratory scale. A broad assessment of scientific and technical methods and technologies for research and development will be taught and aims to provide the student with technical skills usable for research and development in laboratories, in the industry or academia, in a varied array of fields: biopharmaceutical, biotechnologies, chemical (bio)productions, food technologies, etc. The Track is composed of five modules providing both theoretical and practical knowledge, with an emphasis on projects and tutorials:

1. i) Biocatalysis and Chemical Biology for bioprocessing, takes interest in using enzymes for biochemical transformation of materials,
2. ii) System Biology and Synthetic Biology, provides deep knowledge in the use of computational tools to develop and improve bioprocesses

iii) Bioprocess Design and Engineering, provides a good understanding of how to scale-up a production from flask to laboratory scale reactor

1. iv) de novo Enzyme Design is a shared module with Track 3, and emphasizes computational methods to study and develop enzymes from scratch
2. v) Sustainable Design and Development, providing key understanding elements for future engineers to integrate sustainability considerations immediately at the laboratory stage

Learning outcomes

• Master the methods and principles to design and experimental procedure to improve cells, enzymes, or products for a production process
• Ability to use advanced computational tools to analyse data on biologic materials, from pure biomolecules to complex consortia of organisms
• Integrate the European sustainability principles into the research and development procedures to improve processes sustainability
• Deep understanding of enzyme functioning, utilization and characterization for chemical biology, biocatalysis and enzymatic bioprocesses
• Design a development strategy including cutting edge methods in wet biology, computational biology, biochemistry and process engineering
• Ability to apply the intensification to experimental research by the use of high-throughput technologies

Skills and competences

This module will contribute to get the student with the following skills:

• Design a bioprocess improvement strategy to reduce its environmental impact
• Integrating circular bioeconomy concepts into the development and/or optimization of bioprocesses
• Design an experimental strategy to create or improve a bioproduction
• Integrating new digital approaches into the development of new biocatalysis
• Design an in-vitro and in-silico experimental strategy to create or improve enzymes

Course Description / Aims

In This Track, Students will acquire advanced knowledge of in bioprocess engineering for applications in the biopharmaceutical, industrial biotech, chemical industries or food tech industries. It composes of 5 different modules that provides to the student solid skills in bioprocess design, dimensioning, scale-up and optimisation and transition from lab to industrial production. Students will explore the conventional unit operations in bioprocesses engineering as well as innovative technology and bioprocess intensification (continuous bioprocessing, High Cell Density Cultures processes, waste limitation, improvement of energy yields, miniaturisation, etc.). A substantial part will be dedicated to a case study or industrial example, executed in teams of 4-6 participants, on the design of a bioprocess.

Learning outcomes

Master the specificities of equipment associated with the culture of animal or microbial cell for biomass or biomolecule production

Design, implement and optimize an upstream process and downstream process in response to specifications for producing a biomolecule or bio sourced product in in the global context of sustainability.

Be able to implement or optimize a process for cultivating microalgae or plants in a bioreactor in response to specifications.

Know the methodology and intensification technologies, at the laboratory and production scale.

Skills and competences

This module will contribute to get the student with the following skills:

Design, implement and optimize the production process (USP/DSP) of a biological agent, biological or biosourced product on an industrial scale allowing the improvement of the efficiency, productivity and sustainability of Bioprocesses

Course Description / Aims

In This Track, Students will acquire advanced knowledge of in computation biology for applications in the biopharmaceutical, industrial biotech, chemical industries or food tech industries. It composes of 5 different modules that provides to the student solid skills with in-silico tools: Artificial Intelligence, Big Data, Data management, Machine Learning, Bioinformatics, Python programming, Process Simulation, Protein design.

A substantial part will be dedicated to projects, executed in teams of 4-6 participants, on bioprocess applications.

Learning outcomes

• Develop a digital twin of a bioprocess
• Use and adapt AI & machine learning tools for biotechnology and bioprocesses.
• Through simulation, design, implement and optimize an upstream process and downstream process in response to specifications for producing a biomolecule or bio sourced product in in the global context of sustainability.

Skills and competences

This module will contribute to get the student with the following skills:

• Implement scale up methods by sizing the bioprocess to reach a given production volume with a view to developing the bioprocess on an industrial scale.
• Implement scale transfer methods (scale down) using simulation tools and mobilizing bibliographic resources for bioprocesses in order to test the effectiveness of the process
• Identify the causes of possible anomalies using analytical methodologies/tools in order to guarantee product quality and maintain production stability
• Select avenues for correcting deviations and/or malfunctions and propose technological and strategic tools for improving and optimizing processes.
• Analyse and take into account the specificities of the biological or biosourced product to be concentrated/purified by integrating the principles of separative approaches in order to design the DSP phase of a bioprocess
• Design the isolation, purification and concentration process to be implemented by choosing the equipment necessary to develop the process on a pre-industrial scale (laboratory and pilot).
• Implement mathematical, statistical and probability tools to exploit and represent experimental data
• Apply numerical methods of integration and equation resolution
• Implement tools: calculation platform, spreadsheet, simulation software (Matlab, xppaut, Excel) for data analysis
• Implement IT tools for data representation and modelling
• Formulate the numerical simulation of a complex problem
• Arguing the choice of specific algorithms
• Formulate mathematical models based on differential equations for xxx biological reaction pathways
• Use bioinformatics tools for the integrative and simultaneous analysis of data from different omics approaches
• Perform multivariate and multi-scale analyses using digital technologies to study biological systems and metabolic networks
• Develop mathematical models using specific software and numerical tools to simulate and analyse biochemical reaction pathway models
• Identify the tools for creating, managing and analysing databases taking into account the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Create and operate databases
• Simulate bioprocesses using digital twins
• Develop scripts in Python and use process/reaction simulation tools taking into account the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Identify artificial intelligence tools taking into account the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Use artificial intelligence tools taking into account the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Create scripts in Python and use process/reaction simulation tools taking into account the specificities of the biological agent to optimize a bioprocess or a biotechnology project
• Use Machine Learning to automate and improve the analysis of omics technique results
• Use digital technologies and data analysis for the development of new optimized cell strains in order to improve bioproduction/biotransformation processes
• Exploiting the results of omics sciences to improve bioproduction/biotransformation processes
• Design, activate and characterize an improved enzyme
• Design an enzyme de novo
• Modify, adapt and study biocatalysts using different screening methods
• Select the appropriate enzymes to produce a given molecule of interest by biocatalysis based on bibliographic and database searches
• Selecting the Right Combination of Design and Screening Methods
• Propose and design an expression system for enzyme production
• Size the biocatalytic reactor (enzymatic or cellular)

Course Description / Aims

This Six-month internship takes place from February to July at the end of the fifth year of the engineering curriculum and is currently named “End-of-Study-Project » or “ESP”. It involves applying the teachings of the school to an industrial or applied fundamental research subject, taking into account the scientific, technological, economic, international and industrial property aspects specific to the subject. The internship requires a level of autonomy and responsibility equivalent to what is expected of a junior engineer.

Learning outcomes

To apply the teachings to the study of a concrete problem by carrying out a mission at the level of a junior engineer. The intern must consider the bibliographic, scientific, technological, and economic aspects related to the subject. A school tutor supervises the intern.

Skills and competences

This module will contribute to get the student with the following skills:

• Mobilize resources from a broad field of fundamental sciences.
• Know and understand a specialized scientific and technical field.
• Identify and clarify the problem(s).
• Select resolution methods or propose innovative solutions.
• Design, select, or appropriate techniques, resources, and tools.
• Implement technical solutions (installation, processes, methods, etc.).
• Analyse a subject in its entirety.
• Synthesize and take into account intermediate and final results.
• Write a report
• Communicate results, present a report

Contents – contact hours and Teaching methods

The intern is supervised by an engineer from an industrial company or by a researcher from a university or industrial laboratory. A school tutor, appointed during the establishment of the internship agreement, is responsible for monitoring the internship. The End-of-Studies Project (PFE) results in a report and a presentation.

The PFE internship is supported by a 4 hours meeting on internship preparation. The objectives and expectations of the internship will be presented. An introduction to job search techniques will also be addressed. Students will advance their reflection on their professional project using the competency portfolio methodology.

The intern must have fulfilled all examinations as required by the school regulations before getting to the internship.

Assessment

The End-of-Studies Project (ESP) results in a report and a presentation. The internship supervisor at the company is required to evaluate the work and behaviour of the student using a detailed evaluation form.

The evaluation of the intern by the company, as well as the writing of the internship report, allow for the assessment of professional behaviour and skills, the scientific and technical quality of the project, and the ability to write a report.