Bioinformatics Applications in
Precision Medicine, Agriculture & Environment

16-27 Octber 2022, Biotechnology Research Center CRBt, Constantine

About The Workshop

  • Registration
  • Applications Deadline : 1th October 2022

    About The Event

    This workshop aims to provide Basics & Hands-On-Training in computational methods & Artificial intelligence methods to analyze and explore omics and multi-omics data such as (Genomics, Transcriptomics, Epigenomics, Metagenomics, etc.) & to drug design such as QSAR & Virtual Screening. Participants will also be introduced to the latest trends of Deep Learning applications in bioinformatics and clinical data analysis as well as standards and practices (FAIR Guiding Principles).

    Topics

    - Metagenomics Data Analysis

    - Machine Learning Applications

    - NGS Data Analysis

    - Deep Learning Applications

    - Biostatistics

    - Clinical Data Analysis

    The workshop is totally free of charge.

    Keynote Speakers

    Speaker 1

    Pr. Ammar AZIOUNE

    Head Of CRBt

    Speaker 3

    Pr. Kamal BOUKHALFA

    Professor @ ENSIA

    Pr. Fariza TAHI

    Pr. Fariza TAHI

    Professor @ Université Evry-val-d'essonne

    Dr. Hadj Ahmed BELAOUNI

    Dr. Hadj Ahmed BELAOUNI

    Associate Professor @ ENS KOUBA

    Workshop Lecturers

    Dr. Khalid BOUHEDJAR

    Dr. Khalid BOUHEDJAR

    Scientist @ CRBt

    Dr. Abdelbasset BOUKELIA

    Dr. Abdelbasset BOUKELIA

    Scientist @ CRBt

    Amine BELAIDI

    Mr. Amine BELAIDI

    Principal Engineer @ CRBt

    Dr. Rabah LEBSI

    Dr. Rabah LEBSIR

    Associate Professor @ University of Guelma

    Dr. Mouna CHERIET

    Dr. Mouna CHERIET

    Scientist @ CRBt

    Dr. Hadj Ahmed BELAOUNI

    Dr. Hadj Ahmed BELAOUNI

    Associate Professor @ ENS KOBA

    Dr. El Hassen MOKRANI

    Dr. El Hassen MOKRANI

    Associate Professor @ UC1

    workshops

    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.

    24-26 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

    Phylogenetics is the study of the evolution of life as reflected in the relationships between taxa. Phylogenetics is a very powerful tool that allows biologists in all fields to organize and retrieve biodiversity data, as well as make predictions based on the most recent common ancestor. Using observable and testable evidence, this methodology is based on cladistics and attempts to reconstruct the evolutionary history of taxa. This exciting field knew tremendous improvements with the rise of the NGS technologies, leading to high quality, and comprehensive genomic datasets that allowed high resolution phylogenomic super-trees. During a series of lectures and hands-on session, we shall have a look to the basics of the phylogenetic analyses and their application in modern bacterial taxonomy.

    17-19 October 2022

    Bacterial genomics

    Open discussion

    Bacterial pangenomes (lecture)

    Open discussion

    Introduction to Phylogeny (lecture)

    One gene phylogenetic analysis (hands-on session)

    Genomics and bacterial taxonomy (lecture)

    Phylogenomic analysis (hands-on session)

    One gene phylogenetic analysis (hands-on session)

    1. Genomic Dataset preparation

    2. GBDP phylogenomic trees

    3. ANI-based dendrogram

    4. Open discussion

    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.

    24-26 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.

    24-26 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

    Committees

    Pr. Ammar AZIOUNE Director of CRBt

    - 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

    Workshop Venue

    Workshop venue location info and gallery

    Contact Us

    Address

    UV 03 BP E73, Ali Mendjli Nouvelle Ville, Constantine

    Phone Number

    +213 (31) 77.50.37/39