The Training Workshops are now available, below you can find all the information about them.

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All Training Workshops will be on July 2nd;

80 seats are available for each training workshop. Seats will be assigned on a first-come, first-served basis.

Teachers: Dr. Erica Nocerino (University of Sassari, Italy) and Dr. Fabio Menna (Fondazione Bruno Kessler, Trento, Italy)

Length: Tuesday July 2, 2024 Time: 09:00-13:00

Participants knowledge required: Although not necessary, a prior knowledge of photogrammetry, surveying and positioning techniques would be a plus.

Participants devices required: Laptop

Workshop description:

The three-dimensional structure and spatial arrangement of coral reefs are key for a healthy marine environment. Coral reefs’ complex architecture supports biodiversity, providing a habitat and shelter for a broad variety of marine organisms, including fish. Healthy coral reefs also act as natural barriers, protecting coastlines from the impact of storms and erosion. Environmental stressors, such as rise in water temperature, ocean acidification, and anthropogenic pressures, are constantly escalating, exposing coral reefs to increasingly extreme conditions.

Therefore, it has become globally imperative to put in place actions to monitor the health of coralligenous habitats. This necessarily involves monitoring the structural integrity of the coral reefs, i.e. understanding how their morphology evolves over time.

Geomatic techniques, including underwater photogrammetry, may constitute a crucial support in understanding the dynamics of changes in the three-dimensional reef architecture. These approaches may provide three-dimensional models and derived products, like for example orthophoto mosaics, from which to derive analyses of ecological interest. Indeed, recent times have seen a significant increase in studies applying photogrammetry to marine ecology. However, there is still need for standardized procedures and reliable methods to correctly estimate the potential accuracy of the derived measurements and statistics.

This tutorial aims at proving the participants with an introduction to the crucial aspects of underwater photogrammetry as 3D surveying technique and independent methods for the assessment of its accuracy potential.

The first part of the tutorial will cover the following aspects:

  • History of underwater photography and photogrammetry
  • Image formation underwater: optical considerations
  • Photographic aspects: light absorption, scatter, depth dependent white balance and colour correction
  • Flat vs Dome ports (from optical to geometric influences in underwater photogrammetry)
  • Camera calibration approaches: implicit vs explicit modelling
  • Platforms for underwater photogrammetry, from surface vehicles to scuba divers to ROVs and AUVs
  • Underwater visual odometry and SLAM
  • Mono, stereo and multi camera systems

The tutorial will be organized in two sessions: in the first two hours, we will cover the theoretical aspects, then the audience will be engaged in an interactive demo on underwater data processing.

Expected outcome:

It is anticipated that the participants will gain a working understanding of underwater photogrammetry, its strengths and current limitations in monitoring of coral reef ecosystems. The complex principles of optics, different geometric and colour calibration models will not be trivialized but simplified to enable the participants to efficiently employ them in ecological monitoring practice. Through examples of monitoring projects, participants will get insights on how to verify and validate the metric and colorimetric accuracy of the results obtained. The overview of currently available algorithms and platforms will be propaedeutically in understanding which tools are best suited to meet the needs of different monitoring needs. Attendees expect to engage in practical exercises in underwater data processing, applying theoretical knowledge to real-world scenarios. This will support them in replicating the experience gained from the workshop in their research and studies. Through theoretical sessions and practical exercises, they aim to contribute meaningfully to coral reef preservation and management, providing knowledge and tools that can be implemented in the operative practices of different user groups.

Teacher: Prof. Lukasz Jaremko (King Abdullah University of Science and Technology, KAUST, Saudi Arabia)

Length: Tuesday, July 2, 2024 Time: 14:00-18:00

Participants knowledge required: Those interested in conducting extensive research on small molecules would benefit from having a basic understanding of biology at the undergraduate level.

Participants devices required: Smartphone or tablet, laptop, Excell/OpenOffice Suite

Workshop description:

Metabolomics is the study of small molecules, or metabolites, within biological systems like cells, biofluids, tissues, or organisms, collectively known as the metabolome. Like genomics and transcriptomics, which focus on genetic and RNA information respectively, metabolomics examines metabolic substrates and products influenced by genetic and environmental factors. It provides a direct reflection of cellular biochemical activity, making it a powerful tool for understanding molecular phenotypes. Marine ecosystems, including coral reefs, are complex systems with intricate dependencies that cannot be fully understood without molecular and atomic-level knowledge. This workshop aims to bridge the gap between metabolomics and marine sciences, enabling the application of small molecule approaches to study these ecosystems effectively.

The course content comprises two main components:

  1. Theoretical Introduction (1 hour):
    • Overview of Small Molecules and Their Roles in Organisms and Ecosystems and Introduction to Metabolomics Techniques
  1. Practical (3 hours):
    • Data Types
    • Experimental Techniques and Data Comparison
    • Hands-on Experience with Computational Tools and Data Analysis.
    • Q&A session.

Metabolomics in Coral and Marine Ecosystems Workshop Outline:

Introduction to Metabolomics:

  • Understanding Small Molecules
  • Overview of the Metabolome and Metabolic Reactions

Importance of Metabolomics:

  • Exploring Applications in Coral and Marine Ecosystems

Designing a Metabolomics Study:

  • Experiment Design
  • Sample Preparation Design and Existing Techniques
  • Comprehensive Analysis Workflow Overview
  • Utilization of Mass Spectrometry and Nuclear Magnetic Resonance (NMR)
  • Comparative Analysis of NMR and MS Techniques
  • Data Processing Methods
  • Analysis and Interpretation of Results

Accessing metabolomics resources in your department and internationally

Conclusion and Summary

In conclusion, the complexity of ecosystems and organisms necessitates the integration of multiple methods simultaneously. Throughout this course, we will be working with integrated NMR and MS-derived datasets from organisms living in tropical seas, including the Red Sea and Papua New Guinea. Participants will gain practical experience in sample preparation, protocol development, data analysis, and more.

Expected outcome:

Upon completion of the course, you will:

  • Understand the significance and objectives of metabolomics.
  • Explain key principles underlying metabolomic study design.
  • Understand the principles of sample preparation for various experimental techniques.
  • Assess the strengths and weaknesses of various analytical techniques (MS and NMR) employed in metabolomics research.
  • Engage in discussions regarding contemporary applications of metabolomics.
  • Understand the publicly available software tools for analysing datasets.

The course is designed to cater to MS/PhD students, postdoctoral fellows, and professionals engaged in biological research who work with biological samples and seek to employ or enhance their utilization of small molecules to address their research inquiries. Whether attendees currently utilize small molecules in their research or aspire to do so in the future, the course offers valuable insights and practical knowledge applicable to a diverse range of biological research fields.