Date: Thursday, 21 November 2024

Time: 14:15-17:30

Delivery Mode: In-person or Online

 

  • Workshop #1

Title: Navigating the IRB Process: Ethical Considerations in Genomic Research

Instructor: Aisha Naeem

Description:
Genomic research holds immense promise for advancing personalized medicine and understanding human health, but it also presents complex ethical challenges. This session will delve into the ethical considerations that researchers must address when conducting genomic studies, particularly regarding human subjects protection, privacy, and the responsible use of genetic data. The workshop will provide practical guidance on navigating the IRB process, with a focus on preparing robust IRB applications that meet ethical standards for genomic research. Key topics will include informed consent, data confidentiality, and the challenges of working with secondary data. Through a combination of theoretical discussions and hands-on exercises, participants will learn how to balance ethical considerations with scientific advancement. By the end of the session, attendees will be equipped with the tools and knowledge necessary to ensure their genomic research is ethically sound and compliant with IRB regulations.

Delivery Mode: In-person

  • Workshop #2

Title: RNA-seq analysis using python and R

Instructors: Priyanka Thareja and Dr Priyanka Jain 

Description:
In recent years, bulk RNA sequencing has emerged as a crucial technique for unraveling gene expression patterns across different conditions, offering insights into disease mechanisms, cellular responses, and more. The motivation behind this workshop is to equip participants with practical skills to perform comprehensive bulk RNA-seq analysis, enabling them to analyze large transcriptomic datasets efficiently. The proposed content will cover the complete workflow, including quality control, read alignment, gene expression quantification, and differential gene expression analysis using Python’s pyrpipe library and Rsubread package, ensuring participants gain hands-on experience with both tools.

Delivery Mode: Online

  • Workshop #3

Title: Integrating Generative AI into BioInformatics Pedagogy through Experiential Learning and Design Thinking

Instructors: Bert Verhoeven and Vishal Rana

Description:
The integration of Generative AI into BioInformatics education is rapidly becoming essential as educational institutions strive to keep pace with technological advancements. This workshop is motivated by the need to equip educators with innovative tools and methods to enhance the learning experience in this highly technical field. As BioInformatics evolves, so too must the pedagogical approaches used to train the next generation of scientists. This session introduces attendees to the power of Generative AI and design thinking as frameworks for reimagining BioInformatics education. The workshop will focus on how experiential learning can be enriched through the use of AI-driven tools to create dynamic, student-centered educational experiences. Attendees will be guided through the design thinking process—empathising with learner needs, defining pedagogical challenges, ideating creative solutions, and prototyping AI-powered learning modules. In breakout sessions, participants will collaborate to develop AI-driven teaching tools tailored to BioInformatics, receiving hands-on experience in both the design and application of these technologies. The session will conclude with testing and reflection, offering insights into how iterative refinement and feedback can enhance both teaching strategies and student outcomes. This workshop is ideal for educators and researchers seeking to modernise their teaching methodologies and incorporate AI innovations into BioInformatics curricula. By the end, attendees will leave with actionable strategies and prototypes to enhance their educational practice using Generative AI and design thinking.

Delivery Mode: In-person

  • Workshop #4

Title: To snake or to flow: comparison of Snakemake and Nextflow

Instructor: Wai Yee Low

Description:
Computational pipelines are integral in bioinformatics, particularly for high-throughput sequenced data. While traditional Shell scripting is a common method, alternatives like Snakemake and Nextflow have gained popularity. Notably, the verkko assembler for assembling complete human telomere-to-telomere genomes uses a Snakemake pipeline whereas many workflows customised to the use of Oxford Nanopore Technologies long reads use Nextflow pipelines. This workshop addresses common queries such as the choice between Shell scripting and workflow management systems like Snakemake or Nextflow. By demonstrating variant calling with both Shell scripts and these systems, the workshop provides insights into factors to consider, including scalability. Pros and cons of each method underscore the idea that the optimal approach depends on specific task requirements and features.

Delivery Mode: In-person

  • Workshop #5

Title: Colaboratory, a Gateway for Bioinformatics and Innovation

Instructor: Ashfaq Ahmad

Description:
Colaboratory, or Colab, is a free development tool offered by Google. It provides public access to state-of-the-art Graphics Processing Units (GPUs) and Tensor Processing Units (TPUs), enabling them to run complex scripts that perform various predictions and analyses efficiently. It means that individuals can swiftly transform their innovative ideas into remarkable results, even without extensive computational resources. On the other hand, Machine Learning (ML) and Deep Learning (DL) models offer tremendous applications in various domains, including healthcare, finance, and, notably, Bioinformatics. The ability of these models to analyse large datasets and extract meaningful patterns can significantly accelerate the discovery and development of new medications. This workshop session is designed to provide you with a quick demonstration from the field of drug design. Initially, we will briefly learn about Colab and its usage. Moving forward, I will guide you through the process of predicting the biological activity of organic compounds using an Artificial Neural Network (ANN) implemented in Colab. In this 50–60-minute session, you will delve into the field of data science for drug design and innovation. Moreover, we will learn how to access and fetch data from a biological database containing assays. Collectively, Colab is a powerful tool that allows you to test and reshape your ideas before implementing them into practical solutions. It supports and imports all public libraries of Python seamlessly. I am excited to have you join this workshop and look forward to exploring the innovative intersection of technology and Bioinformatics, in particular drug designing.

Delivery Mode: Online

  • Workshop #6

Title:  Workshop on Chemcomputational Toxicity assessment tools for xenobiotics

Instructor: S. Shantkriti

Description:

In this workshop, the attendees will learn various freely available in silico toxicological assessment tools and software’s such as LAZAR, pKCSM, CarcinoPred-EL, PROTOX II, Pred- Skin, Pred-hERG, VEGA, Endocrine Disruptome for prediction of mutagenicity, AMES toxicity, hepatotoxicity, hERG inhibition and skin sensitization, Chemical carcinogenicity, toxicity, skin sensitization, cardiac toxicity, toxicity in bee, fish, Daphnia magna, biodegradability and persistence in soil and Water, endocrine disruption etc. The relative toxicity, mutagenicity and carcinogenicity of each case study compound will be analysed and compared using various in silico tools and software. Comparative toxicological assessments of in silico assessment with real time experimental data obtained from USA Food and Drugs Administration (USFDA) FAO/WHO standards etc. will also be performed. These chemical’s SMILES (Simplified Molecular Input Line Entry Systems) obtained from the PubChem database will be used to perform their in silico evaluation. Thus, this workshop will particularly focus at skill development in toxicological evaluation useful for bioinformatics education as well as research.

Delivery Mode: Online

  • Workshop #7

Title: Molecular dynamics of lipid embedded membrane receptors

Instructor: Ayesha Fatima 

Description: 
Molecular dynamics simulation of membrane embedded proteins is not a trivial matter and requires attention in preparing and running the complexes. Using examples of transmembrane proteins, this workshop will look into preparing and running simulations.

Delivery Mode: Online

  • Workshop #8

Title: Innovate to Cure: Mastering Computer-Aided Drug Design for Sustainable Solutions

Instructor:  Shefin Safeer P. M

Description: 
The urgent need for innovative drug discovery solutions in the face of complex health challenges and agricultural demands has never been more critical. Computer-Aided Drug Design (CADD) offers powerful tools to streamline and enhance the drug development process, enabling researchers to design more effective therapeutics with greater efficiency. As the agricultural biotechnology sector increasingly integrates biopharmaceutical approaches, equipping postgraduate students and researchers with CADD skills is essential for fostering a new generation of innovators capable of addressing global health and sustainability issues.

Delivery Mode: Online