Bioinformatics Applications in
Precision Medicine, Agriculture & Environment

R is a simple programming environment that enables the effective handling of data, while providing excellent graphical support. RStudio is a tool that provides a user-friendly environment for working with R. The three days programming workshop with extensive hand-on-exercises will enable participants to programs in R, and its application in downstream biological data analysis.

29-31 October 2022

Introduction to R programming

1. Installing R and the R Commander
2. R Packages
3. Data types

Introduction to R commander

1. Data Input and Data Management
2. Descriptive Statistics
3. Simple Statistical Tests

Use R with R-Studio

1. Making the script
2. Handing of different data types
3. Hypothesis Testing
4. Descriptive statistics
5. Analysis of Variance (ANOVA)

This workshop focuses on how cheminformatics and Bioinformatics tools can be used in chemical research and drug design development. KNIME is an open platform for the entire data science process: data access and transformation, visualization, predictive analytics, and reporting. With KNIME and its dedicated Cheminformatics and Bioinformatics Extensions you can select from a wide range of cheminformatics functionality, which we will make use of in this workshop as well. In this session you will create your own interactive cheminformatics workflows that include: reading, converting, visualizing and saving chemical data. The examples will include building components for interactive visualization, clustering molecules based on the fingerprint similarity, running a similarity search.

Introduction to KNIME

1. Installing KNIME analytics
2. Nodes in KNIME
3. Data types

Chemoinformatics Extensions

1. RDKit toolkit
2. CDK toolkit
3. Indigo toolkit

Build Chemoinformatics Pipelines

1. Handing of different data types
2. Build KNIME Model
3. Machine learning in KNIME

Biopython is a Python package including many tools for bioinformatics and computational biology developed by an international team.
In this workshop, we focus on the implementation side of Bioinformatics basics using. Indeed, the three days programming workshop with extensive hand-on-exercises will enable participants to programs bioinformatics pipelines using BioPython, and its application in downstream biological data analysis.

Introduction to Python

1. Installing Python & Biopython
2. Variables Types
3. Oriented Object in Python

Biopython

1. Omics Data in BioPython
2. Basic bioinformatics pipelines
3. Applications

Data Banks in Biopython

1. Principal Packages
2. NCBI in Biopython
3. UNIPROT in Biopython

Molecular docking is the study of how two or more molecular structures (e.g., drug and enzyme or protein) fit together. In a simple definition, docking is a molecular modeling technique that is used to predict how a protein (enzyme) interacts with small molecules (ligands). The ability of a protein (enzyme) and nucleic acid to interact with small molecules to form a supramolecular complex plays a major role in the dynamics of the protein, which may enhance or inhibit its biological function. Drug design highly depends on knowledge and understanding of ligand-target interactions.

17-19 October 2022

Introduction to Molecular Docking

1. Principles of molecular docking.

2. Essential requirements of docking.

3. Optimization of 3D structure.

Basic steps of docking

1. Ligand and protein preparation

2. Ligand-protein docking and analysis

Machine learning is an AI application that allows systems to learn and improve without being explicitly programmed. Machine learning is interested in creating computer programs that can access data and use it to learn on their own. Deep learning is a subset of a larger class of machine learning methods that combine artificial neural networks and representation learning. In this workshop, we focus on the applications of machine learning and deep learning in bioinformatics, with extensive hand-on-exercises. Which, will enable to participants to solve real bioinformatics problems in many fields (Agriculture, Health, etc.) by integrating machine & deep learning algorithms using python environment.

29-31 October 2022

Introduction to Machine Learning

1. ML Basics
2. Supervised ML
3. Unsupervised ML
4. Semi Supervised ML

Introduction to Deep Learning

1. DL Basics
2. Predictive DL Models
3. Generative DL Models

ML & DL applications in Bioinformatics

1. ML & DL for Health
2. ML & DL for Agriculture
3. ML & DL for Clinical Data Analysis

Next-generation sequencing (NGS) technologies are now an essential component of almost all life sciences research and diagnostics. NGS data are typically processed by qualified bioinformaticians due to their volume and, more importantly, complexity. In this workshop, you learn the fundamentals of NGS data processing including the fundamental steps of NGS data analysis, such as raw data manipulation, quality control, and the removal of low-quality sequences, sequence adapters, artifacts, or other contamination. The end result should be complete mastery of the process, with the output being a set of high-quality data that can be used for further analysis.

29-31 October 2022

Introduction to NGS Data Analysis

1. Overview of NGS Data analysis
2. Introduction to Linux System
3. Navigation of Bash commands
4. Tools for NGS analyses

NGS Data Analysis Pipeline

1. Quality Control of NGS Data
2. Processing Raw NGS Data
3. Mapping & Annotating NGS data

NGS Data Analysis on Galaxy Platform

- REZGUI Abdelmalek CRBt Constantine

- BENKHEMISSA Abdelhamid CRBt Constantine

- BOURAS Ali CRBt Constantine

- FERDJANI Nabila CRBt Constantine

- DERGHOUT Nabil CRBt Constantine

- KHENNAOUI Hamza CRBt Constantine

- LEKHAL Moussab CRBt Constantine

- MENOUMES Moussa Djoubeir CRBt Constantine

- AFCIL Fatima Hasna CRBt Constantine

- BOUHEDJAR Khalid CRBt Constantine

- BOUKELIA Abdelbasset CRBt Constantine

- BELAIDI Amine CRBt Constantine

- BOUCHEHAM Anouar UC3 Constantine

- REZGUI Abdelmalek CRBt Constantine

- BOUKELIA Abdelbasset CRBt Constantine

- DEMS Mohamed Abdesslem CRBt Constantine

- BOUHEDJAR Khalid CRBt Constantine

- CHERIET Mouna CRBt Constantine

- YOUSFI Tarek CRBt Constantine

- BELAIDI Amine CRBt Constantine

- BELAOUNI Hadj Ahmed ENS Kouba Algiers

- LEBSIR Rabah University of Guelma Guelma

- MOKRANI El Hassen UMC Constantine

- BOUCHEHAM Anouar University Salah Boubnider Constantine