Computer skills
Linux® Bash and shell commands lab
Learn how to harness the power of the command line with our Linux® Bash lab specially designed for column and keyword manipulation on biology PDB files !
In this field of biology, where data is often massive and complex, skill in file manipulation and keyword searches becomes essential to effectively analyze and visualize this data.
We teach you the basics of Bash, a powerful tool used in Unix and Linux environments, which will allow you to automate repetitive data tasks, run serial analyzes and much more.
For those new to programming or looking to expand your skills, our tailor-made practicals will guide you through practical examples and concrete exercises on files and directories using shell and AWK.
Give your scientific career a competitive edge by acquiring these essential data manipulation basics with our Linux Bash training!
Lab 1: Cleaning PDB files and automating execution tasks, duration 8 hours
Lab 2: Extraction, Clustering and joining on result files, duration 8 hours
Lab 3: Basics of the AWK language and lowest energy extractions, duration 8 hours
Price of lab: 1 093 USD including tax, per unit
Languages: English or French
Python3™lab
Python3™ benefits from an active and diverse developer community meaning that there are a plethora of resources, libraries and modules available for a wide variety of demands. Being widely used in industry in general, it guarantees to be an interesting support due to its constant evolution, which is why we integrate it into our training.
The analytical exploration of Alzheimer's disease will support this practical work. You will have the opportunity to acquire specialized skills in advanced sorting manipulation, with an emphasis on the syntactic clarity and versatility of this language. Through this training, you will be able to master techniques for managing files containing complex data, such as the molecular structures of proteins involved in the pathogenesis of Alzheimer's disease. By manipulating this data using Python™, you will be able to extract relevant information, identify meaningful structure-function relationships, and create detailed visual representations to better understand the underlying mechanisms of disease. This scientific approach will allow you to manipulate interesting data and contribute significantly to understanding research in this area.
These applications can be run on various operating systems such as Windows®, macOS® and Linux®, providing great flexibility for users.
Practical 1: Introduction, duration 8 hours
Practical 2: Sorting, duration 8 hours
Practical 3: Performance, duration 8 hours
Price of lab: 1 093 USD including tax, per unit
Languages: English or French
AutoDock / Autodock Vina lab
This intensive lab, led by bioinformatics experts, is designed to provide you with an in-depth understanding of the theory and practice behind molecular docking via Autodock. You will learn to use it and its suites to predict the molecular interactions between target proteins and their ligands, as well as to interpret and analyze the results of your simulations.
Here's an overview of what you'll learn:
Understand the fundamentals of molecular docking.
Master Autodock commands and its advanced features.
Efficiently prepare your protein and ligand structures for simulation.
Optimize simulation parameters for accurate results.
Analyze and interpret docking results to guide drug design.
Explore real-world use cases and case studies for practical application.
Whether you are a bioinformatics researcher or graduate student, this training will provide you with the skills needed to excel in molecular docking with Autodock and stand out in your field.
Molecular docking lab: duration 16 hours
Price of lab: 2 187 USD including tax
Languages: English or French
CHARMM™lab
Advance in molecular modeling with our training specially designed for the study of RNA and DNA involved in cystic fibrosis on CHARMM™. During this intensive training, you will master the key words of this language, including (the modules are translated into French, if French-speaking). You will thus be able to concentrate on the manipulations and equations of forces that you will apply to RNA and DNA.
This practical work requires knowledge of thermodynamic physics and organic chemistry at the level of three university years.
NAMD lab
Developed by the University of Illinois at Urbana-Champaign, NAMD is widely used in biophysics, biochemistry, and computational biology research to study various molecular processes, such as protein conformation changes, protein-ligand interactions , membrane dynamics and much more.
NAMD is a molecular simulation software that primarily focuses on the molecular dynamics of large-scale biological systems. Its name stands for “NAnoscale Molecular Dynamics”. Designed to be fast and scalable, NAMD is often used to simulate complex biomolecular systems such as proteins, nucleic acids, and cell membranes.
This lab requires knowledge of thermodynamic physics and organic chemistry at a three-year university level.
NAMD uses advanced approximation techniques to accelerate molecular dynamics simulations, such as the interaction network method (interaction-mesh Ewald), thus making it possible to study large systems on significant time scales.
Our training will guide you through each step of the simulation process, from preparing systems to analyzing known Lyme disease outcomes, allowing you to understand the biophysical interactions interacting with data already known about this disease.
Lab 1: Getting started with all the modules and the spirit of the software package, duration 16 hours
Lab 2: Modeling and calculation of free energies, duration 8 hours
Price of lab: 2 187 USD including tax, per unit
Price of lab: 3 269 USD including tax, both
Languages: English or French
GROMACS lab
This training will provide you with an in-depth understanding of GROMACS, covering the following aspects:
Introduction to GROMACS: Understand the basic principles, its history, its applications and its importance in biomolecular research.
Installation and Configuration: Learn how to install and configure GROMACS on different platforms, including personal computers.
Principles of Molecular Simulation: Understand the theoretical foundations of molecular dynamics and Monte Carlo simulations, as well as the algorithms used in GROMACS.
Preparing Simulation Systems: Learn how to prepare molecular systems for simulation, including creating force topologies and preparing input files.
Running Simulations: Master the commands and command line options to run molecular simulations, optimizing performance and interpreting the results.
Simulation Data Analysis: Learn how to analyze simulation results using tools built into GROMACS as well as other processing and visualization software.
Advanced applications: Explore advanced applications of GROMACS such as simulation of membrane systems, drug binding calculations.
VMD lab
Whether you are a researcher in biophysics, computational chemistry or structural biology, this training will provide you with the essential skills to master the analysis and visualization of complex molecular structures. You will learn to visualize and manipulate proteins, nucleic acids, lipids.
With VMD, you will be able to graphically represent the three-dimensional structure of your molecules, calculate molecular properties and create dynamic animations to represent molecular dynamics. Our training will guide you through every feature of VMD, from manipulation of structures to advanced analysis of simulation results.
Our bioinformaticians offer you an immersive experience that will revolutionize your approach to molecular visualization and open up new research perspectives in the exciting field of structural biology!
VMD Lab : duration 10 hours
Price of lab : 1 093 USD including tax
Languages : English or French
PyMOL® lab
Developed by Schrödinger®, PyMOL® offers a wide range of features for visualization, including various representation modes (wireframes, surfaces, rods, etc.), annotation tools, measurement and analysis tools , as well as advanced features for creating animations and generating high-resolution screenshots.
PyMOL® is primarily molecular visualization software used for the graphical representation and analysis of molecular structures in structural biology, biophysics and computational chemistry. It allows visualization of proteins, nucleic acids, ligands, protein-ligand complexes, membranes and other types of molecular structures with high precision and flexibility.
It is widely used in academic and industrial research to study the structure and function of biomolecules, to design new drugs and to visualize the results of molecular simulations. It is also used in education to teach molecular biology and structural chemistry by providing interactive visual representations of molecules.
In summary, PyMOL® is a powerful and versatile tool for molecular visualization, providing researchers with an intuitive and efficient way to explore and analyze molecular structures at the atomic scale.
Lab 1, duration 10 hours
Lab 2, duration 10 hours
Price of lab: 1 093 USD including tax
Languages: English or French
Chimera® lab
Chimera® is a molecular visualization and modeling software widely used in the field of structural biology, biophysics and computational chemistry. Developed by the University of California, San Francisco (UCSF), Chimera® offers a wide range of capabilities for the analysis and manipulation of molecular structures.
Key features of Chimera® include 3D visualization of biomolecular structures such as proteins, nucleic acids, and protein-ligand complexes, as well as representation of molecular surfaces, electron density maps, and other types of interesting data.
These labs will allow you to perform molecular modeling operations such as modifying structures, superimposing molecules, building structures of protein-protein or protein-ligand complexes, and much more. You will use advanced tools for analyzing structures, including measuring distances and angles, calculating accessible areas, finding structural patterns, and creating highly customizable graphical representations.
Cytoscape® lab
Cytoscape® is a widely used open-source software platform for the visualization, analysis and manipulation of complex networks, such as biological networks, protein-interaction networks and many others.
Developed by the Institute of Systems Biology in Seattle, Cytoscape® offers a user-friendly interface and powerful features for exploring the structure and dynamics of biological networks. Users can import network data from various sources, such as public databases or local files, and visualize them as interactive graphs.
Microsoft Word® lab
Developed by Microsoft Corporation, you will be introduced to the main components of Microsoft Word®, a word processing program widely used for creating and formatting documents, such as reports, letters, etc.
Discover our training on Microsoft Word®, specially designed for those who encounter difficulties with the software's many functions and shortcuts! This training will help you master Word® in a simple and effective way. We'll walk you through every essential feature, from creating and formatting documents to adding images, tables, and charts. You'll learn how to use the layout tools to create professional, attractive documents, as well as the review features to collaborate with other users on projects. We'll also focus on effectively using autocorrect, numbering, bulleted lists, and text styles to save time and improve the consistency of your documents.
Price of lab: 1 093 USD including tax
Languages: English or French
ggplot2® lab
ggplot2® is a charting library in R, developed by Hadley Wickham. This library is based on the principle of "Grammar of Graphics", which provides a coherent and systematic approach to constructing graphics by decomposing graphic elements into different layers.
We will introduce ggplot2® as a utility that allows users to create complex and aesthetically pleasing graphs using a set of simple and intuitive functions. It provides great flexibility to customize every aspect of the chart, including colors, shapes, legends, scales, etc.
ggplot2® is widely used in the field of data analysis and visualization, especially in the context of data science, academic research and the publication of scientific results.
