Erasmus Mundus Joint Master - ChEMoinformatics+

Pedagogical activities

Courcelles Design — 2022-12-15T11:06:21Z

Chemoinformatics Summer School

The Chemoinformatics Summer School (CS3) is a central piece of the Erasmus Mundus master degree Chemoinformatics+, mandatory for first-year students of the programme, and optional for second-year students. Registration fees are therefore covered for first-year students, whereas second-year students have to fund their participation. It offers advanced lectures from the best worldwide specialists worldwide in the field of ChEMoinformatics.

A sample list of previously invited speakers includes Prof. J.-P. Sauvage, (Nobel chemistry in 2016), Prof. G. Schneider, Prof. J. Bajorath, Prof. A. Cherkasov, Prof. A. Tropsha.

The school proposes lectures in the morning and tutorials in the afternoon. It is a unique occasion to acquire new material and get familiar with cutting-edge technologies from internationally recognized experts of the field. It is an agora of a very diverse community. As observed from past events, attendees population is typically composed of 50% students, 30% academics and 20% industrials; participants come from Japan, Switzerland, Check Republic, Hungary, England, US, Austria, Italy, Norway, Israel, Russia, Brazil, Croatia, Equator, India, the Netherlands, Poland, China.

8th ChemoInformatics Strasbourg Summer School

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Chemoinformatics Summer School

The active participation of students in the Summer School will be validated via the attribution of additional 2 ECTS. Several specific events are satellites of the school: the molecular modelling project, a preparatory workshop dedicated to the industrial project and a hackathon dedicated to open science.

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Chemoinformatics Summer School

Remediation period

Since, the first year is performed on 7 sites, the level of training of the students on the various topics will be heterogeneous. The month of September of the second year will be dedicated to a personalized teaching activity to solve this issue.
All students will pass a test to verify the pre-requisites for the lectures of the second year. The remediation teaching unit consists of 24 hours of teaching during which each student discusses with the lecturer(s) of the topics identified as weaker in the student's profile. To help the students to find the relevant lecturers, all chemoinformatic-related courses of the participating universities will be organized in an ontology. The appreciations of this teaching unit count for 25% in the result of the final defence.

Language courses

In order to facilitate the integration of students from different cultural and social backgrounds into the Erasmus Mundus master degree ChEMinformatics+, part or all of the courses during the first year are proposed in one of the local languages, depending on the track followed (French, Italian, Slovenian, Russian, Ukrainian, Portuguese, Hebrew), and the others in English. Didactic materials and evaluations are provided both in local languages and in English.

The second year, whether in Paris or Strasbourg, will be in English.

Molecular Modelling Project

The teaching for Molecular Modelling using force field or quantum mechanics, starts in the first year at all sites. The evaluation of this competence will include an open science project on each site, performed by the students of first year under the supervision of second year students. These projects will run from January to February. The results of these projects will be presented in a dedicated session of the summer school.

Industrial Project

The consortium share a common Industrial Project, a pedagogical activity to promote entrepreneurship, innovation and open up to civil society. The activity starts at the semester 1 and is validated at the semester 2. The aim of the Industrial project is to help non-academic entities (associations, trusts, industry, department or laboratories of a company, etc.) to innovate by overcoming technical and technological obstacles in the field of chemoinformatics.

The Industrial Project is conducted by a team of 2-3 students from different sites that analyses the problem in detail, writes a letter of engagement, schedules the tasks to be carried out, establishes a functional specification, searches for solution concepts and selects the more appropriate to solve the problem. The activity favors a multidisciplinary approach in relation with the non-academic entity proposing the subject. This activity involves regular communications, meetings and interviews. The project will be conducted between September and May and it is worth 450 to 500 hours with 5 collective work sessions. The work is supervised by a teacher of the consortium and by a professional for management. It is worth 3 additional ECTS.

The assessment of the project is performed through an intermediate educational report, a technical report and an oral presentation. The evaluation is typically oriented towards the organization of work, the division of tasks between the students, data-sharing, productions and how they collectively evaluate their results. The goal is to build a common structure in which every student will contribute and build interpersonal skills.

Hackathon

An open science dedicated hackathon is organized before or after the summer school, typically Saturday and/or Sunday, with distinct registration procedures. At least three Chemoinformatics topics will be proposed to the participants. First, the software programming topic will aim at adding functionalities to an existing open source software projects. Second, documentation consisting to analyse an existing open source project and to improve or complement its documentation. Third, the dataset topic will create high quality datasets through expert data cleaning, involving from bibliographic search up to advanced machine learning and artificial intelligence techniques.

Research project and Organization of the Master thesis

Whatever their specialty, students do their internship in the institution of their choice, European or extra-European, academic or industrial. They can also choose one partner of the consortium that they did not visited before. If they did their first year in their country of residence, the internship must take place in a third country, not yet visited before. The defence of the research project will be organized in Strasbourg. Every consortium memver will send one member of his teaching staff to assist in the defence.

Field courses/Company visits

During the first year, every partner will organize locally a visit to a chemical or a pharmaceutical plant, a software company or any other industrial site, that might become relevant for students' job integration and to help them to find the right place to prepare their master thesis and contribute to the individual construction of the students' professional projects.

Communication

The communication skills are developed by a scientific blog activity. The blog will be published in English version to be accessible to all. Each student of the Erasmus Mundus master degree will be invited to contribute at least once each year. It can be a popularization work about a topic on Chemoinformatics, a report about a scientific event, an interview of recognized researcher, etc. The editorial board, managed by the students, is responsible for reviewing, rejecting or accepting the publications before they are released online. However, ultimately, the consortium is always responsible of the published contents and keep the final decision to edit or remove any publication. Technically, the blog will be published on LinkedIn using the existing group Master in Chemoinformatics. Occasionally, articles / abstracts of articles can be published also on the web portal of the Master.

Learning outcomes

Courcelles Design — 2022-12-15T10:23:19Z

The Erasmus Mundus master degree ChEMoinformatics+ covers all fundamental and applicative aspects of Chemoinformatics. The topics addressed below are considered as the common core present in all tracks:

Chemoinformatics

Computer coding of chemical structures (1D, 2D and 3D).
Molecules as objects of a chemical space.
Measures of structures similarity and diversity among molecules.
Chemical libraries, databases and data sources.
Chemical libraries analysis: diversity-based, focused on an application, comparison and novelty detection.
Molecular descriptors (molecular fragments, fingerprints, topological indices, physical-chemical properties, molecular surfaces and energies, pharmacophores).
Hansch and Free-Wilson approaches.
Data preprocessing (filtering, standardization of chemical structures, normalization, relevant descriptors selection).
Building and validating statistical models (multi-factorial analysis, classification and regression).
3D QSAR (comparative molecular field analysis).
Drug Design: chemical libraries of biological interests. Pharmacodynamics. Pharmacokinetics. ADME. Toxicity. Environmental fate.
Protein ligand docking and scoring functions.
Virtual screening.
Profiling of chemical libraries.
Structural determination and modelling of macromolecules.
Interactions of macromolecules with small molecular weight chemical entities. Biological environment.

Quantum Chemistry

Conventional quantum chemical methods (based either on the explicit calculation of the electronic wavefunction or on the electron density).
Physical motivations of quantum chemistry calculation methods.
Domain of applicability of quantum chemical models.
Introduction of main software packages for quantum calculations.

Molecular Modelling

Theoretical basics of molecular modelling.
Molecular mechanics and molecular dynamics.
Force fields and empirical potential energy functions.
Molecular modelling as a tool in chemical research.
Molecular recognition. Intra- and supra-molecular interactions.
Emerging properties at macroscopic scales.
Thermodynamics ensembles.
Solvation hydrophilic and hydrophobic.
Conformational analysis and empirical representations.
Practical use of modelling.
Rational choice of methods and evaluation of the reliability of results in molecular modelling
Comparison to experimental observations.

The EMJM will also cover additional topics that are essential for the technical implementation of Chemoinformatics solutions:

Software programming procedural languages (Fortran, C), object oriented (Java, Object Pascal) & functional programming (Maple, Matlab), scripting (bash, Perl, Python), workflow languages (Pipeline Pilot, KNIME)
Software engineering compilation & libraries, collaborative development (Git, Subversion), integrative development environment (Eclipse), debugging (GDB, GProf), multi-platform development, Parallel/GPU/cloud computing
Databases relational databases. Query languages (SQL). Non-relation databases (NoSQL). Main database management systems (MySQL/MariaDB, PostgreSQL)
Web services HTML/CSS (HTML 5), CMS (Spip, Typo3, WordPress), web server (Apache), CGI development, REST and JavaScript.
Data mining and artificial intelligence support vector machines, classification and regression trees, neural networks, generative and approaches, bootstrapping, cross-validation, clustering. Tuning method parameters. Ensemble modelling. Active learning. Multi-task learning. Semisupervised learning and transduction. Recommender systems. Generative models and adversarial learning. Autoencoders.

Learning Outcomes	Lecture
create, manage and use databases on chemistry subjects.	Methodology (S1, Strasbourg), Banche dati ed elementi di chemoinformatica (S2, Milan), Numerical methods in chemistry (S1, Ljubljana), Databases (S2, Lisbon), Управління базами даних (S2, Kiyv), Databases (S2, Bar-Ilan)
know and use the most important databases in Chemistry for knowledge or for commercial use.
be able to extract, interpret and analyse chemical information.	Chemoinformatics 1 (S3, Strasbourg), Cheminformatics 2 (S3, Strasbourg), Chemoinformatics 3 (S3 Strasbourg), Chemoinformatics (S1, Strasbourg), Data Mining (S3, Strasbourg), Data analysis in drug design (S3, Paris)
understand, build and validate qualitative and quantitative chemical structure-activity relationships (QSAR/QSPR).
understand and use machine learning algorithms.
implement technical solutions to manage and exploit big data sources in chemistry.
implement and use artificial intelligence technologies for solving chemical problems.
understand, use and analyse quantum chemistry models.	Molecular Modeling (S1, Strasbourg), Simulation, modeling and biomolecules (S2, Milan), Chim Fis A (S1, Milan), Chim Fis B (S2, Milan), Metodi matematici applicati alla chimica (S1, Milan), Modelling of Chemical Systems (S1, Ljubljana), Applied Computational Chemistry (S2, Lisbon), Комп'ютерне моделювання в природничих науках (S2, Kiyv), Computational Chemistry (S2, Bar-Ilan), Molecular Modeling (S2, Bar-Ilan), Molecular dynamics analysis and drug design (S3, Paris), Structural Biology and molecular modeling (S3, Strasbourg), Molecular dynamics simulation (S3, Strasbourg), Advanced Quantum Chemistry (S3, Strasbourg)
understand, use and analyse molecular mechanics models.
understand, use and analyse heuristics to model inter-molecular recognition, such as docking or pharmacophores.	Virtual screening application : Structure and ligand -based (S3, Paris), Structure-based drug design (S3, Strasbourg), Супрамолекулярна хімія (S1, Kiyv), Біоінформатика (S2, Kiyv), Комбінаторна хімія та технологія пошуку біологічно активних речовин (S2, Kiyv), Medicinal Chemistry (S2, Milan), Medicinal Chemistry (S1, Lisbon), Комбінаторна хімія та технологія пошуку біологічно активних речовин (S2, Kiyv)
perform a virtual screening of chemical libraries.
understand the basics of medicinal chemistry
understand and solve medicinal chemistry problems
implement chemical design strategies.	Methodology (S1, Strasbourg), Metodi fisici avanzati in chimica organica (S1, Milan), Catalysis and Modern Organic Chemistry (S1, Ljubljana), Modern Methods in Organic Synthesis (S1, Ljubljana), Organic Chemistry (S2, Ljubljana), Modern inorganic materials and catalyst (S2, Ljubljana), Asymmetric Organic Chemistry I (S1, Lisbon), Physical Organic Chemistry (S1, Lisbon), Asymmetric Organic Chemistry II (S2, Lisbon), Applied Organic Synthesis (S2, Lisbon), Вибрані розділи неорганічної та органічної хімії (S2, Kiyv), Комбінаторна хімія та технологія пошуку біологічно активних речовин (S2, Kiyv), Organic Synthesis (S1 or S2, Bar-Ilan), Industrial Organic Chemistry (S1, Bar-Ilan)
understand and write computer software using procedural, object and programming workflow paradigms.	C Programming (S2, Milan), Numerical methods in chemistry (S1, Ljubljana), Mathematics II (S1, Ljubljana), Introduction to Programming (S1, Lisbon), Вибрані розділи вищої математики та інформаційних технологій (S1, Kiyv), Програмування на мовах C, C++, Java (S1, Kiyv), Веб-технології в хімії (S2, Kiyv), Цифрові технології в науковому експерименті (S2, Kiyv), Internet Technology (S3, Strasbourg), Programming (S2, Bar-Ilan)
develop and publish internet services for chemistry.
present clearly and unambiguously research results, conclusions and rationale underpinning these; orally or by poster presentation to specialist and non-specialist audiences.	Communication (S1, Strasbourg), English proficiency (S2, Milan), Water as Hydrogeological, Ecological and Analytical System (S1, Ljubljana), Entrepreneurship (S1, Lisbon), Laboratory Quality Control (S2, Lisbon), Іноземна мова (S1 / S2, Kiyv), Спеціальний семінар науковий (S2, Kiyv), Research project (S2, Bar-Ilan), Internship (S4, Strasbourg)
independently read and critically interpret the scientific literature, including the patent literature.
continue to learn about their field on their own in a largely self-directed manner.
integrate into a new and unfamiliar research environment, be confronted with a new research problem and to independently develop an experimental plan to tackle the problem.
handle complexity and formulate judgements with incomplete or limited information, including reflecting on social and ethical responsibilities linked to the application of their knowledge and judgements.
Innovate and transfer innovation into public and private domain in the European market
Innovate in line with the European regulation on chemicals

Specialization.

Each track of the master complete the curriculum with specialization topics and skills

Specialization	Learning outcome	Lecture
In Silico Design of Bioactive Molecules (Strasbourg - Milan - Paris)	Model sites of interaction and biotransformations in proteins	Structural biology and enzymology (S2); Target modelling (S3)
	Understand the basics of medicinal and biophysical chemistry for the design of bioactive molecules	Medicinal Chemistry (S2); Structural Biology and enzymology (S2); Simulation, modeling and biomolecules (S2)
	Rationalize biomolecular event with therapeutic effects	Medicinal Chemistry (S2); Data analysis in drug design (S3)
Chemoinformatics and Physical Chemistry (Milan - Strasbourg)	Understand, build and analyze quantum chemistry and molecular mechanics models	Chimica Fisica A (S1/S2); Metodi matematici applicati alla chimica (S1/S2); Simulation, modeling and biomolecules (S1/S2)
	Use of databases in Chemistry, Implementation of programming workflows and computer simulation of biomolecules; Modelling physico-chemical processes	Banche dati ed elementi di chemoinformatica (S1/S2); Programming C (S1/S2); Simulation, modeling and biomolecules (S1/S2)
	Theoretical and practical knowledge of methods for the structural characterization of compounds; Critically assess the experimental results of physical chemistry experiments	Chimica Fisica B (S1/S2); Metodi fisici avanzati in chimica organica (S1/S2)
Chemoinformatics for Biophysical & Computational Chemistry (Ljubljana - Strasbourg)	Optimize biophysical processes	Biophysical chemistry (S1); Physical Chemistry II (Statistical Thermodynamics) (S2)
	Model biophysical processes	Numerical methods in chemistry (S1); Modelling of Chemical Systems(S1)
Chemoinformatics for Organic Chemistry (Lisbon - Strasbourg)	Design innovative organic chemical structures	Physical Organic Chemistry (S1); Applied Organic Synthesis (S2)
	Design of asymetric chemical libraries	Asymmetric Organic Chemistry I (S1); Asymmetric Organic Chemistry II (S2)
Chemoinformatics of chemical reactions (Strasbourg)	Rationalize the reactivity of chemical species	Механизмы химических реакций (S1); Биоорганическая химия (S1); Современные проблемы органической химии (S1)
Chemoinformatics of chemical reactions (Strasbourg)	Model the reactivity of chemical species	Основы компьютерного программирования в приложении к химическим задачам (S1)
Ultra Large Chemical Library Design and Virtual Screening (Kiyv - Strasbourg)	Design target oriented chemical libraries	Біохімія (S1); Супрамолекулярна хімія (S2); Біоінформатика (S2)
	Design ultra-large chemical libraries	Комбінаторна хімія та технологія пошуку біологічно активних речовин (S2)
Chemoinformatics and materials informatics (Bar Ilan - Strasbourg)	Design innovative new nanomaterials	Nanotechnology (S1/S2); Material Sciences (S1/S2); Organometallic Chemistry (S1/S2)
	Design innovative new materials for energy production and storage	Advanced Analytical Chemistry (S1/S2); Material Sciences (S1/S2); Organometallic Chemistry (S1/S2)

General view

Courcelles Design — 2022-12-14T17:18:13Z

Chemoinformatics is a sub-discipline of Theoretical Chemistry. It is engaged with the development, creation, organization, storage, sharing, analysis, visualization and use of chemical information. As such, it requires strong experimental background in chemistry and physical chemistry, but also numerous skills in data science and software programming. Besides, modelling of chemical entities (for instance as graphs, as molecular descriptors, as interacting atoms, as electron distribution) are the corner stone of chemoinformatic methods, as they are the fundamental abstractions of chemical information; it is therefore a main element of the curriculum.

The pedagogical content of each track is characterized by the presence of teaching elements linked to Chemoinformatics during the first year, that are completed by the lectures offered in the University of Strasbourg during the second year. On this base, the first year's lectures have been assembled in order to transfer to the students skills and knowledge specific to chemoinformatics, modelling and experimental chemistry, while providing the necessary pre-requisites to continue in Strasbourg or Paris in the second year.

The Speciality Tracks

Chemoinformatics provides applications in various fields of study. That is why, students start in a specialty track during their first year, taking advantage of the specific local expertise, with some of the finest experts in their respective field.

The fundamentals and advanced topics in Chemoinformatics are provided during the third semester either in Strasbourg or in Paris. During the fourth semester, students do their internship in the institution of their choice, European or extra-European, academic or industrial. They can also choose one partner of the consortium, that they did not visite before.

1. In Silico Design of Bioactive Molecules (In Silico Drug Design: Bioactive Molecules). At Université Paris-Cité (semesters 1,3) and Università degli studi di Milano (semester 2), students gain solid knowledge on therapeutic targets (biological macromolecules), Biochemistry and advanced skills on computer modelling of target interactions with molecules. For example, in silico approaches such as biostatistics and data analysis, Python programming, structural bioinformatics, molecular dynamics and modelling, docking methods, and virtual screening are addressed.

2. Chemoinformatics and Physical Chemistry. At Università degli studi di Milano (year 1) and at University of Strasbourg (year 2), students learn methods for the modelling and simulation of biomolecules, the fundamentals of chemoinformatics and databases, and the basics of physical chemistry and NMR spectroscopy. They also acquire the capacity to apply computer-aided approaches and develop software to solve complex chemical problems.

3. Chemoinformatics for Organic Chemistry. At Universidade Nova de Lisboa (year 1) and at University of Strasbourg (year 2), organic chemistry provides essential concepts for Chemoinformatics such as molecular structure and design, reactivity, mechanisms and spectroscopy. In addition to Chemoinformatics and IT courses, Lisbon offers a program with courses in organic synthesis, bioorganic analytical chemistry, medicinal chemistry, physical organic chemistry and entrepreneurship.

4. Chemoinformatics for Biophysical and Computational Chemistry. At University of Ljubljana (year 1) and at University of Strasbourg (year 2), students will learn about the latest developments and best practices in decision making using data and models for drug and material design. They will also learn the basics of modelling biophysical events using real examples. Throught practice, students learn the algorithms required for scientific programming.

5. Suspended until further notice Ultra Large Chemical Library Design and Virtual Screening. At Taras Shevchenko National University of Kyiv, Chemoinformatics tools are effectively applied for the design of target-focused compound libraries up to the enumeration of chemical libraries containing over hundreds of billions of tangible compounds requiring dedicated technologies for virtual screening. This track focuses also on molecular recognition in biological processes, on implementation of structural analysis technologies and rational design of compound libraries with a predetermined mechanism of action.

6. Suspended until further notice Chemoinformatics and Materials Informatics. At Bar-Ilan University (year 1) and at University of Strasbourg (year 2), students will apply chemoinformatics methodologies to chemistry and materials sciences, with emphasis on renewable / green energy (e.g., solar cells). Specific attention is put on the 3D structures of molecular systems (e.g., materials) using different levels of theory (e.g., DFT calculations, force fields) and on relevant descriptors for these systems. The course expands on construction of and navigation in compounds / materials spaces, through predictive models for key properties.

The Master thesis

Students do their internship in the institution of their choice, European or extra-European, academic or industrial. They can also choose one partner of the consortium that they did not visited before. The defence of the research project will be organized in Strasbourg.

The Diploma

At the end of the program, the Student will receive a Master degree from the university where he passed his first year and the university where he passed the second year. He will also receive a certificate about his participating in the joint Erasmus Mundus Master Degree in ChEMoinformaticplus, and a joint Diploma Supplement.

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