23rd June


Effective Metabolomics Software: From Design to Practice

Dai-ichi Tsuru

Organizer: Saravanan Dayalan

Aim and Scope: Good design of scientific software is important. The care and awareness in using such softwareprograms were highlighted in 2006, when a group at Scripps had to retract five papers, including three from Science and one from PNAS due to a problem in their software program(Science 314, 1875;2006). As in other fields of life sciences, software is an intertwined part of Metabolomics. It plays a crucial role in all aspects of the workflow from data generation, management, processing, analysis, and to interpretation.

This workshop is aimed at both software users and developers, with the goal of teaching the fundamentals of efficient software design and development, and best practices in software usage. The speakers provide insights from developing a wide-range of metabolomics software programs.

10:50-11:05 Saravanan Dayalan (Metabolomics Australia, Australia)
11:05-11:20 Janna Hastings (EMBL-EBI, Cambridge UK)
11:20-11:35 Atsushi Fukushima (RIKEN-CSRS, Japan)
11:35-11:50 Jianguo Xia (University of Alberta, Canada)
11:50-12:10 General Discussion


Metabolomics Measurement Technology and Application (JST-NSF)

Marica Hall

Morning (Marica):

Organizers: Masanori Arita, Oliver Fiehn

Aim and Scope: Metabolomics covers wide range of topics and is effective not only in biomedical fields but also in energy or environmental sciences. This workshop introduces the four research projects under the program title “Metabolomics for a Low Carbon Society,” jointly coordinated by the U.S. National Science Foundation (NSF) and Japan Science and Technology Agency (JST) since 2011. Each talk covers the recent progress including the measurement methods for metabolite identification, software development, and metabolic signalling among plants, insects, and disease. The latter part is dedicated to the worldwide networking efforts.

10:50-11:05 Ryo Nakabayashi (RIKEN-CSRS, Japan)
11:05-11:20 Hiroshi Tsugawa (RIKEN-CSRS, Japan)
11:20-11:35 Sastia Putri (Osaka University, Japan)
11:35-11:50 Ryu Nakata (Kyoto University, Japan)

Introduction to Worldwide Networks
11:50-12:00 PAMM-NET RCN
Lloyd Sumner (Noble Foundation, USA)
12:00-12:10 Ring Trial Initiative and NIH common funds
Oliver Fiehn (UC Davis, USA)


Early-career Member Network of Metabolomics Society

Dai-ichi Tsuru

Abstract are available.
Organizers: The EMN committee of the Metabolomics Society
(Sastia Putri, David Liesenfeld, Thomas Payne, Ralf Weber, Justin van der Hooft, Nicholas Rattray, Evangelia Daskalaki, Gabriel Valbuena, Vincent Asiago)
Session I. Scientific writing and Grant writing: how to get published and funded in metabolomics

This session will deal with something all scientists often face during their career: writing. Three excellent speakers will share their view on how to effectively communicate your science using written language. The different roles these scientists have, i.e., journal editor, part of funding body, part of reviewing committee, promises a vivid and diverse setting of this first session of the workshop. The speakers will concentrate on technical aspects of writing and give some tips focused on early-career scientists. This session aims to provide early-career scientist with tools and resources to work on their writing skills.

Scientific writing
13:40-13:55 Royston Goodacre (University of Manchester, UK)
13:55-14:05 Q&A

Grant writing
14:05-14:15 Krista Zanetti (NIH, USA)
14:15-14-25 Eiichiro Fukusaki (Osaka University, Japan)
14:25-14:35 Q&A
14:40-15:25 Extended Coffee Break (1st floor, exhibition room)
A chance to for the early career members to connect with each other and mingle with top scientists in metabolomics field. Please move to the exhibition area of Dai-ichi Hotel (poster area).
Session II. Identification of unknown metabolites

This session is focused on one of the biggest hurdles facing metabolomics research nowadays. The annotation and identification of unknown metabolites many of you will be confronted with during your metabolomics experiments, is a challenging part of the metabolomics pipeline. In this session, three speakers will explain their approaches and views on this topic and show useful metabolomics databases. The first two speakers will focus on data analysis of gas chromatography coupled to mass spectrometry (GC-MS) spectra and liquid chromatography coupled to high-resolution MS (LC-MS), and the role of NMR in de novo identification will be briefly touched upon. The last speaker will highlight the different metabolomics repositories that are available to the community nowadays. 

This session aims to create an awareness of the different approaches that are out there and the current metabolomics databases that you can use to annotate and identify your metabolites of interest.

15:30-15:45 Oliver Fiehn (UC Davis, USA)
15:45-16:00 David Watson (University of Strathclyde, UK)
16:00-16:15 Ralf Weber (University of Birmingham, UK)
16:15-16:40 Interactive discussion


Metabolomics data standards, data capture and exchange

Marica Hall

Organizers: Reza Salek, Christoph Steinbeck, Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, and the COSMOS consortium
Session I. Data Standardization
13:40-13:55 Reza Salek (EMBL-EBI, UK)
13:55-14:20 Steffen Neumann
(Leibniz Institute of Plant Biochemistry, Halle Germany)
14:10-14:25 Kenny Billiau (MPI-MP Golm, Germany)
14:20-14:40 Philippe Rocca-Serra
Alejandra Gonzalez-Beltran
(Oxford e-Research Centre, UK)
14:40-15:00 Discussion and questions
Session II. Data Dissemination, Standardization and Exchange
15:20-15:50 Scott Edmunds(Gigascience) 
Rob Davidson (Gigascience)
Susanna-Assunta Sansone (Nature Scientific Data)
15:50-16:10 Reza Salek (EMBL-EBI, UK)
Philippe Rocca-Serra (Oxford e-Research Centre, UK)
16:10-16:25 Padma Maruvada (NIH/NIDDK, USA)
16:25-16:40 Discussion and questions

  • Agilent Technologies
  • Bruker Corporation
  • Human Metabolome Technologies
  • LECO Corporation
  • Shimadzu Corporation
  • Thermo Fisher Scientific, Inc.
  • Waters Corporation