Workshops

More workshops will be added as they become available.

Please click on the image to see it full size.
Click here to download a PDF version of the schedule.

Workshop Agenda 3 22 17

June 25 At the University of Queensland St. Lucia

Sunday 13:00 - 15:00

MetaboTools: Analysis of metabolomic data in the context of the metabolic model

Organiser: Maike Aurich, Université du Luxembourg

Note: This is the first of two sessions held on Sunday.
Constraint-based metabolic models consider in detail the metabolite transformations that appear in living cells at steady-state. They can be used to predict intracellular flux routes connecting metabolites cells consume to byproducts they release (exo-metabolome). MetaboTools provides extensive support for the analysis of extracellular metabolomic data in the context of the metabolic model. We will provide lectures at the beginning of the workshop to ensure a basic common understanding of the constraint-based modeling and analysis (COBRA) approach. Hands-on training of a computational workflow of data preparation, integration, and model analysis will allow the participants to get first hand experience on the requirements, analysis possibilities, and the limits of the intra-model analysis of exo-metabolomic data using MetaboTools. The workshop is designed for participants with limited experience in metabolic modeling and programming.

 

ANZMET Round Table + Peer Sessions

Organiser: Devin Benheim, La Trobe University

The ANZMET conference, founded in 2016, is fundamentally a community-driven event designed to foster an all-inclusive, engaging and rich interpersonal process through a blend of traditional presentations, peer-driven roundtable discussion and facilitated peer sessions. ANZMET is now the officially supported conference of the Australia & New Zealand Metabolomics Network (ANZMN).

The ANZMET-hosted workshops are designed to replicate the foundation experiences of the ANZMET conference—namely, the roundtable discussion and the peer session. The full ANZMET conference employs these two modalities in sequence - as both an introductory and networking tool (roundtable) and facilitated yet spontaneous topical peer-driven discussion (peer session).

The roundtable discussion will allow an informal atmosphere and fulfils three broad purposes:

  1. Defines and models an active, interactive, and safe conference environment.
  2. The roundtable provides a structured forum for attendees to meet and learn about each other’s affiliations, interests, experience, and expertise.
  3. The session uncovers topics researchers want to discuss and share, as well as indicating the level of interest in each topic.

One principal aim of the roundtable is to determine the topic(s) of discussion in proceeding peer-sessions, organized by way of popular vote at the conclusion of the roundtable session.
The peer sessions are attended by those interested by the set of available topics and are facilitated by one or several volunteer members of the community. One of three roles may befall a given volunteer: (1) Willing to facilitate the session, (2) prepared to be a panellist/presenter during the session and (3) expertise in the session topic.

 

EMN Workshop: Experimental Design in Metabolomics: How to get started?
This workshop will showcase experts discussing the core goals of experimental design in metabolomics. Possible solutions for commonly encountered challenges in both planning metabolomics studies and selection of suitable analytical strategies including quantification and data quality considerations will also be addressed.

 

Sunday 15:30 - 17:30

MetaboTools: Analysis of metabolomic data in the context of the metabolic model

Organiser: Maike Aurich, Université du Luxembourg

Continuation from Sunday morning session
Constraint-based metabolic models consider in detail the metabolite transformations that appear in living cells at steady-state. They can be used to predict intracellular flux routes connecting metabolites cells consume to byproducts they release (exo-metabolome). MetaboTools provides extensive support for the analysis of extracellular metabolomic data in the context of the metabolic model. We will provide lectures at the beginning of the workshop to ensure a basic common understanding of the constraint-based modeling and analysis (COBRA) approach. Hands-on training of a computational workflow of data preparation, integration, and model analysis will allow the participants to get first hand experience on the requirements, analysis possibilities, and the limits of the intra-model analysis of exo-metabolomic data using MetaboTools. The workshop is designed for participants with limited experience in metabolic modeling and programming.

 

Network medicine approaches for the analysis of metabolomics data

Organisers: Jessica Lasky-Su, The Ohio State University, Rachel Kelly, Brigham and Women's Hospital Harvard Medical School

Network medicine is a rapidly emerging field that integrates systems biology and network science in the study of complex disease. It provides a holistic approach to better understand disease through the identification and investigation of linear and nonlinear relationships and networks of interacting components. Network medicine and its underlying concepts have numerous applications in many different biological contexts for the study of disease etiology, diagnosis, phenotyping and treatment.

Network medicine is particularly well-suited to the study of metabolomics datasets. This workshop will provide an introduction to the concepts of network medicine, an overview of network approaches in the analysis of metabolomics data, a discussion of the utility of networks in integrative omics studies, an opportunity for hands-on network visulization and an exploration of the advantages and potential pitfalls of such approaches.

 

EMN Workshop: MS Metabolomics Data Processing
Processing large amounts of untargeted metabolomics data can be daunting, and the publicly available software tools rarely include an easy-to-understand walk-through. Participants will learn about several open source tools for analyzing their untargeted LC/MS and GC/MS data and how to get their spectra and raw data in the format needed for statistical analysis. The workshop will explain XCMS, CAMERA, and associated tools to process untargeted metabolomics data by providing examples, and demonstrating how to use the software. There will be a focus on practical skills and pitfalls so that the participants have an understanding of how to approach their data and answer their questions after the workshop.

 

June 26 At the Brisbane Convention & Exposition Centre (BCEC)

Monday 8:45 - 10:15

EMN Workshop: Statistical Considerations and Pathway Analysis Strategies for Metabolomics Datasets
Over the past decade, major advancements in untargeted and targeted metabolomics technologies have enabled high-throughput analysis of 1000s of biochemical perturbations associated with various organismal processes and pathological conditions. Statistical analysis of large datasets remains a bottleneck. Furthermore, the successful integration and interpretation of metabolomic datasets requires adequate background knowledge of associated biochemical pathways, an aspect that may not be attributed to all scientists, particularly those that are new to the field. The primary intents of this workshop are to 1) highlight important statistical/chemometric considerations for metabolomic datasets and 2) provide education on biochemical pathway mapping approaches. This workshop is primarily targeted towards beginners in the metabolomics field, including early-career researchers, but also everyone who is using metabolomics to complement their own existing research.

 

Diet and Health

Organisers: Lee Gethings, Waters Corporation, David Heywood, Waters Corporation, Antonietta Wallace, Waters Corporation

Application of OMIC workflows, particularly metabolomics has shown to provide insight into health and food as well as the complex relationship which exists between both. Understanding bioavailability of food in the body for short and long term wellbeing is of increasing interest. New research is emerging based on advances from technology and metabolomic standpoints, to understand the nature of disease, nutritional diet and the role diet plays physiologically.

This interactive workshop will provide in-depth discussion regarding technological advances from an LC-MS, ambient ionisation and informatic perspective. Integration of these technologies into metabolomic workflows will be presented by leading academic and industrial users, demonstrating how these approaches can be used to better understand the complex relationship between diet and health.

 

Data Sharing, Standardisation and Workflow for reproducible analysis in Metabolomics

Organiser: Reza Salek, EMBL-EBI

Reproducing results in any science is quite challenging. In the field of metabolomics, for results to become reproducible, descriptions of an investigation in a manuscript are not sufficient. To surpass this, and increase the chance of result reproducibility, standard frameworks for data sharing and sharing of experimental data are invaluable. We now have several data sharing platforms such as MetaboLights and Metabolomics Workbench that aim to make use of such standards to promote data-sharing. In this workshop, we will discuss data sharing as well as metabolomics data formats, much of which are adopted from the efforts in the proteomics HUPO-PSI initiative. Examples and application of data formats such as mzMl and nmrML would be given. We will also present and discuss mzTab developments for metabolite identification. We will also demonstrate how emerging metabolomics data sharing platforms can promote open, accessible data sharing standards. Finally we will discuss computational workflows for metabolomics data analysis within the PhenoMeNal e-infrastructure. We hope to make the metabolomics community aware of such efforts and ideally how to get involved.

 

Hybrid Ion Mobility MS

Organiser: Endre Laczko, FGCZ UZH / ETH

Hybrid Ion Mobility – Mass Spectrometry systems (IMS – MS) are known for many years. Today, IMS-MS systems are available from several vendors (TofWerk, Waters, Agilent, Bruker, ABSciex, Thermo may follow soon), however they are still rarely used for metabolomics. In this workshop the currently available IMS-MS types will be presented and their use for metabolomics will be discussed. Further, it will be explained how an IMS-MS method is set up and how the resulting data is analysed. Exemplary cases will allow the participants to valuate IMS-MS metabolomics data in comparison to metabolomics data from other systems currently in use. It is planed to include a Q&A session and to explore the interest for an IMS user group.

 

Monday 10:30 - 12:00

EMN Workshop: Career Development
In this workshop you will meet speakers from academia and industry that will provide career development advice for early-career scientists. We hope to make attendees more aware of career options that they may not have otherwise considered and give them the opportunity to interact with individuals in these fields directly. Topics will include choosing the right career path and how to systematically work towards your preferred path. The speaker will use their own experience to formulate actionable career progression advice for early-career scientists. In addition to the main speakers, the workshop will include a panel discussion where the audience can ask questions to a panel of scientists at different career stages.

 

Clinical Biomarkers

Organiser: Nick Rattray, Yale University

Metabolomics as a translational tool within the clinical has made vitally important in areas such as early detection and diagnosis of disease, prognosis of drug action and therapeutic evaluation. The purpose of this workshop is to overview the experimental workflow used within the biomarker development pipeline and will include insights from experts in the field of metabolomics who will give examples of their experiences and provide tips and advice to new-comers in the field and help explain how to overcome the issues of complexity

 

Metabolite Identification Annotation

Organiser: Rick Dunn, University of Birmingham and Phenome Centre Birmingham

Metabolite annotation and identification are key components of any untargeted metabolomics workflow to enable the delivery of biological knowledge and impact from analytical data. The processes applied to annotate or identify metabolites are numerous and are dependent on the complexity of sample, analytical platform applied and quality of data acquired. Based on the reported spectral evidence, a confidence level of a unique identification or more ambiguous annotation is given to a detected peak. The development of reporting standards and in particular of confidence levels for metabolite annotation and identification was initiated in 2007 by the Metabolomics Standards Initiative [Sumner et al. Metabolomics, 2007, 3, 211] and these reporting standards are currently being assessed and revised.. In this workshop a panel of experts will provide their insights in to the complexities and solutions for metabolite annotation applying NMR spectroscopy, gas/liquid chromatography-mass spectrometry and imaging mass spectrometry followed by a Q&A session to allow the metabolomics community to question the experts.

 

Advances in High Throughput Targeted Metabolomics Analysis

Organisers: Alex Apffel, Agilent Laboratories, Judith Denery, Amyris, Inc.

In the last several years a number of approaches have be developed to increase the throughput of targeted metabolomics analysis. Each has advantages and disadvantages in terms of speed, sensitivity and specificity. Each has also been developed in a specific application context and designed to meet the needs of that application. This workshop will explore a number of these approaches while explaining how the technology serves the needs of the specific application area.