MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 55 - March 2016

CONTENTS:


Online version of this newsletter:
 http://www.metabonews.ca/Mar2016/MetaboNews_Mar2016.htm
TMIC Services
TMIC Services

Welcome to the fifty-fifth issue of MetaboNews, a monthly newsletter published in partnership between The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/) and the international Metabolomics Society (http://www.metabolomicssociety.org/), to keep metabolomics researchers and other professionals informed about new technologies, software, databases, events, job postings, conferences, training opportunities, interviews, publications, awards, and other newsworthy items concerning metabolomics. MetaboNews represents the one-stop-shop for the very latest and most critical news about the science of metabolomics. In this issue, we feature a Metabolomics Spotlight article titled "Shaping a Computational Mass Spectrometry Community for Metabolomics", and a metabolomics interview with Krista Zanetti of the National Institutes of Health.
This issue of MetaboNews is supported by:

Metanomics Health
    
Chenomx -- Metabolite Discovery & Measurement    
mzCloud
Metanomics Health GmbH
Chenomx Inc.
mzCloud

Advertising
 Would you like to advertise your metabolomics hardware, software, products, and services to over 2,800 MetaboNews readers worldwide? We offer a variety of advertising options. Please consult the MetaboNews advertising brochure for details.


Free Subscriptions: Our subscriber list is managed using Mailman, the GNU Mailing List Manager. To subscribe or unsubscribe, please visit http://www.mailman.srv.ualberta.ca/mailman/listinfo/metabonews.
Newsletter Archive: Current and back issues of MetaboNews can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).
 Content Suggestions/Feedback: We always appreciate your feedback on how we can make this newsletter better (metabolomics.innovation@gmail.com).
Metabolomics Society Logo

Metabolomics Society News

CONFERENCE CORNER
2016 Metabolomics Society Conference, Dublin
June 27 – June 30, 2016
Registration and abstract submissions are now open for the annual Conference of the international Metabolomics Society. The conference will showcase the best of metabolomics science from all disciplines and features Jeremy Nicholson, Luke O’Neill, Ines Thiele, and Tsutomu Masujima as plenary speakers. Additional keynote speakers include Soren Engelsen, Michael Schmidt, Karsten Hiller, Tuulia Hyötyläinen, Melissa Fitzgerald, and Krista Zanetti. Details of the six workshops planned for the first day are also available at the website. 

Register at www.metabolomics2016.org before March 31st to secure early-bird prices and book your accommodation at http://metabolomics2016.org/venue/hotel-information to secure a room.

Student and Early Career members of the Society are eligible for travel awards. See http://metabolomics2016.org/submission/awards for application details.

Call for Expressions of Interest (EOI) to Chair the 2018 Metabolomics Conference:
The Metabolomics Society is calling for interested members in the American region (North, Central, or South America) to express their interest in hosting the 2018 annual Metabolomics Society meeting (http://metabolomics2018.org/).

Please send notice of your interest using the EOI form by 15th March 2016. You should name individuals who will be key to forming a Local Organizing Committee (LOC) and outline the scientific plan for the conference. The LOC will report to the Metabolomics Society Board, assist A-S-K staff* and the Board in selection of a suitable venue, and organize the conference. The tasks of the LOC are to ensure regional and national support for the conference, to assist the Society in administrative planning, and most importantly, to chair and manage the scientific aspects of the conference. The LOC is also responsible for selecting, and administering, an International Organizing Committee, which in turn is responsible for determining the scientific content of the meeting. Please complete the application form outlining your ideas to maximize the scientific quality and outreach of the conference. For further enquires please contact the Society via A-S-K Associates (metabolomics@askusa.com). *A-S-K Associates is the Society’s administrative firm.


 MEMBERS CORNER
 Membership News for 2016
Attention students and early-career scientists! A large number of travel awards are available for the annual meeting of the Metabolomics Society, Metabolomics 2016, in Dublin. However, to be eligible for consideration for the awards, you must be a paid member by March 27, 2016. Please join or renew your membership at our convenient site.
TASK GROUPS CORNER
Data Standards Task Group

General Announcements for related standards activities:

Metabolomics Data Infrastructures Survey

The PhenoMeNal project is developing an open-source e-infrastructure for the processing, analysis, and information-mining of medical molecular phenotyping and genotyping data that will be generated by metabolomics applications. The project is publicly funded by the European Union's Horizon 2020 Programme. For more information, please see http://phenomenal-h2020.eu

To gain a better understanding of the requirements for data infrastructures for metabolomics research, PhenoMeNal has commissioned a survey to gain insight into current practices, future needs, and opinions, on how metabolomics research data is managed, published, and disseminated. We would be grateful if you could contribute to the survey at the link below.

Survey link: https://www.surveymonkey.co.uk/r/metabolomics-data

Contact:
David Johnson (david.johnson@oerc.ox.ac.uk)
Philippe Rocca-Serra (philippe.rocca-serra@oerc.ox.ac.uk)


HUPO-PSI meeting 2016 announcement
The HUPO Proteomics Standards Initiative defines community standards for data representation in proteomics to facilitate data comparison, exchange, and verification. In metabolomics, we share many such formats, most notably, mzML, mzTab, ProteoWizard, etc. The success of the PSI standards is only achieved through wide participation from the broader community, including metabolomics community, so please consider participating and contributing to this important effort. Registration is free as the workshop is supported by several grants.
For more information, visit (or contact Reza.Salek@ebi.ac.uk): http://www.psidev.info/content/hupo-psi-meeting-2016

INTERNATIONAL AFFILIATES CORNER
Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.anzmn.org
ANZMN president Dr Oliver Jones and Professor Ewan Blanch hosted Professor Roy Goodacre (University of Manchester) at RMIT University from 11th Feb to 3rd March under the RMIT International Visiting Fellowship scheme. Professor Goodacre is well known in metabolomics, having helped establish the Metabolomics Society and being a director of the Metabolic Profiling Forum, as well as the founding Editor-in-Chief of Metabolomics (established 2005). While in Melbourne he gave lectures at RMIT (https://www.eventbrite.com.au/e/enhancing-metabolomics-shining-light-on-metabolism-tickets-21605888795) and the University of Melbourne (amongst several others), and set up several new collaborations with groups in Victoria.

Réseau Français de Métabolomique et Fluxomique (RFMF)
Visit http://www.rfmf.fr/

RFMF Logo
Registration has opened for the the 10th conference of the Francophone Metabolomics and Fluxomics Society (RFMF), to be held in Montpellier between the 30th of May and the 2nd of June 2016. More information can be obtained on the RFMF conference website: http://10-js-rfmf.sciencesconf.org/

Swiss Metabolomics Society (SMS)
Visit www.swiss-metabolomics.ch

The Swiss Metabolomics Society (SMS) is happy to announce the election of its organizing committee. On December 3rd 2015, in Basel, the SMS held its first general assembly meeting. Attending members elected the following to the board: Dr. Thomas Luke Simmons, President; Prof. Dr. Götz Schlotterbeck, Vice President; Dr. David Tonoli, Treasurer and Dr. Guido Sonsmann, Secretary. Drs. Patrick Kiefer, Endre Laczko, and Christian Berchtold were elected as our members-at-large.

In other news, the official SMS URL has been changed; please visit our new site: www.swiss-metabolomics.ch 


 
 Software Spotlight

Metabolomics Spotlight

Shaping a Computational Mass Spectrometry Community for Metabolomics

Feature article contributed by Sebastian Böcker1, Oliver Fiehn2,3, Steffen Neumann4, Reza M. Salek5, Emma L. Schymanski6
1Chair for Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany
2West Coast Metabolomics Center, UC Davis, 95616 Davis, California, USA
3King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
4Leibniz Institute of Plant Biochemistry, Dept. of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany
5Cheminformatics and Metabolism Group, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
6Eawag: Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600 Dübendorf, Switzerland

Mass spectrometry is the predominant analytical technique for detecting and identifying metabolites and other small molecules in large-scale metabolomics experiments. Huge technological advances in mass spectrometry and experimental workflows have occurred during the past decade, enabling novel investigations into biological systems beyond the metabolic level and towards comprehensive exposome analysis. These advances have resulted in a tremendous increase in both the amount and complexity of experimental data, such that both the data processing and identification of the detected metabolites and small molecules have become the most critical bottlenecks in high-throughput analysis. With advances in instrumentation sensitivity, accuracy, and throughput, metabolomics is currently at the edge of becoming a "big data" science and data analysts need to tackle this with resource-efficient methods. Analytics now needs to integrate bioinformatics, cheminformatics, and computer science in a more efficient way.

The Metabolomics Society established a Computational Mass Spectrometry Task Group in the beginning of 2015. The main objectives of the task group are to promote development and use of computational tools for data analysis of small molecules in metabolomics, natural products research, environmental and toxicology research, as well as other related areas. A distinguishing feature of this task group is its ties to CompMS.org, a joint initiative of the Human Proteome Organization (HUPO), the International Society for Computational Biology (ISCB), and now also the Metabolomics Society. The challenges in computational mass spectrometry are not unique to just one discipline and there are some excellent examples of successful workshops and training material for computational proteomics. The time is ripe to promote similar efforts for metabolomics.

A notable event last year was a full-day pre-Metabolomics Society conference hackathon organised by Emma Schymanski (Eawag, Switzerland), Gert Wohlgemuth, Diego Pedrosa, and Oliver Fiehn (UC Davis, USA). The 30 hackathon participants divided into three different groups initially, discussing ideas related to data analysis workflows, data visualisation, and general licensing. In the afternoon, hands-on work was performed on “MassBank/data exchange & standardization”, “metabolite structure identification”, and “software communication”. The hackathon inspired related discussions during and after the conference, including conversations about the “spectral hash”. This spectral hash key will not only support mass spectrometry but can in principle can be extended to other types of spectra such as NMR, UV, IR, or Raman spectra.

During the 2015 Metabolomics Society conference in San Francisco, the Computational Mass Spectrometry task group had its inaugural meeting as an informal “birds-of-a-feather” gathering. Approximately 25 scientists participated in this event to discuss the next steps of the group. Several topics of interest were identified, ranging from collaborations on software development to avoid duplication in efforts such as raw data access or cheminformatics basics, and on discussion towards reviewing guidelines for software publications. Following the initial workshop there will be online meetings, phone conferences, and workshops. All parties interested are encouraged to participate in the discussion forum at www.metabolomics-forum.com/viewforum.php?f=30 and are invited to join subsequent events that are planned around the globe.

The U.S. National Institute of Health acknowledged these efforts by organizing a follow-up workshop “Beyond the Known Metabolome: Discovery and Identification of Biologically-Relevant Small Molecules” on November 17th, 2015, in Bethesda.

Participants of the birds-of-a-feather meeting

Figure 1. Participants of the birds-of-a-feather meeting in the Hyatt Regency in San Francisco/Burlingame, USA, during the Metabolomics Society Conference 2015.

In autumn 2015, Emma Schymanski, Juho Rousu (Aalto University, Finland) and Sebastian Böcker (with help from Tobias Kind and Oliver Fiehn, UC Davis, US) organized a Dagstuhl seminar on Computational Metabolomics1 in Saarland, Germany. Dagstuhl seminars are highly renowned in the Computer Science community, and are intended to foster discussion, exchange expertise, and initiate collaborations for specific research topics. The seminar brought together 30 participants from both the experimental and the computational side. The dynamic schedule consisted of overview talks and breakout sessions, covering the experimental-computational continuum in mass spectrometry and metabolomics data in applications. Overall, the seminar was considered a huge success by the participants. The seminar participants found that while the (lack of) public availability of data is holding back progress, several good initiatives are on the way. A follow-up seminar is planned for 2017.

Future metabolomics studies will grow ever larger, encompass many thousands of samples, which can amount to petabytes of data per year. New developments are underway in building new infrastructure to support large-scale computational metabolomics studies; one such example is the EU Horizon 2020 funded PhenoMeNal2 project that strives to assemble the required e-infrastructure for tomorrow’s metabolomics data.

The Metabolomics2016.org conference in Dublin in June is one event ahead that will also contain a lot of computational mass spectrometry efforts. The sessions planned range from "Advances in Statistical Tools"  by the conference organisers, to "New Approaches for Identification of Metabolites applying MS and NMR" (Session team: Witting/Dunn), "Network and Pathway Analysis for Metabolomics" (Session team: Willighagen/Jourdan), and "Computational Mass Spectrometry"  (Session team: Neumann/Böcker). There are also workshops on "Computational Workflows and Workflow Engines" (Workshop lead: Christoph Steinbeck), "Workshop On Data Sharing and Standardisation" (Workshop team: Reza Salek et al.), and "metaRbolomics: The R toolbox for Metabolomics" (Workshop team: Stanstrup/Neumann). Likewise, there will be an "Informatics: Metabolomics" session, chaired by Sebastian Böcker, at the ASMS Conference in Texas (June 5-9)3, and a non-target analysis conference (nontarget2016) organised by Eawag in Switzerland (May 29-June 3)4.

More such workshops and opportunities to participate will be highlighted and presented on the Metabolomics Society web page in the future. We look forward to your participation and interactions for a growing computational mass spectrometry community in metabolomics.   

References


Please note: If you know of any metabolomics research programs, software, databases, statistical methods, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe at metabolomics.innovation@gmail.com.
 MetaboInterview Icon

MetaboInterview
This section features interviews with prominent researchers in the field of metabolomics. The aim of these interviews is to shed light on metabolomics researchers around the world and give them an opportunity to share their metabolomics story. In this issue, we feature an interview with Krista Zanetti.
Krista A. Zanetti

 Program Officer in the Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences at the National Cancer Institute, National Institutes of Health
Krista Zanetti
Biography

Krista Zanetti is a Program Officer in the Epidemiology and Genomics Research Program (EGRP), Division of Cancer Control and Population Sciences at the National Cancer Institute (NCI), National Institutes of Health. Dr. Zanetti earned her Ph.D. in Nutrition in 2003 from Cornell University and joined the Cancer Prevention Fellowship Program at the NCI. During the first year of her fellowship, she earned an M.P.H. at the Johns Hopkins Bloomberg School of Public Health. Dr. Zanetti then conducted primary research in the Laboratory of Human Carcinogenesis in the NCI’s Center for Cancer Research from 2004 to 2010. Since joining EGRP in 2010, Dr. Zanetti’s primary focus has been building infrastructure and capacity to support metabolomics in population-based research. Most recently, she spearheaded collaborative efforts to establish the trans-NIH international COnsortium of METabolomics Studies (COMETS) that brought together 25 prospective cohorts and three well-established consortia from the U.S., Europe, Asia, and South America.

Metabolomics Interview (MN, MetaboNews; KZ, Krista Zanetti)

 MN: How did you get involved in metabolomics?

KZ: The focus of my Ph.D. work was nutritional biochemistry, but I changed gears during my postdoctoral fellowship and earned an M.P.H. concentrating in epidemiology and biostatistics. After I completed my M.P.H., I spent the remainder of my postdoctoral training focusing on the genetic and molecular epidemiology of cancer, which allowed me to capitalize on both my basic science and epidemiology skill sets. As I moved into my current position as a Program Officer, I realized that my training positioned me quite well to lead efforts that support metabolomics research with an epidemiology study design component. In 2011, I organized a meeting that took place at the National Institutes of Health (NIH) titled “Think Tank on the Use of Metabolomics in Population-Based Research.” Since then, my primary focus has been in this area.

MN: What are some of the most exciting aspects of your work in metabolomics?

KZ: My main role is to build capacity and infrastructure for the successful application of metabolite profiling to population-based studies, such as case-control studies and prospective cohorts. There are a number of challenges in the field that need to be addressed in this particular area, so it is very exciting to develop and implement initiatives to tackle these barriers.
MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

 KZ: The Metabolomics Common Fund Program is one of the key initiatives currently ongoing at the NIH (http://commonfund.nih.gov/metabolomics/index), which supports comprehensive metabolomics resource cores, training, technology development, reference standards synthesis, data sharing, and international collaboration.

Additionally, the trans-NIH COnsortium of METabolomics Studies (COMETS, http://epi.grants.cancer.gov/comets/) was established in 2014, and currently includes 25 prospective cohorts and three established consortia from the United States, Europe, Asia, and South America. The COMETS mission is to promote collaborations among the various prospective cohort studies that perform metabolite profiling of individuals and follow them for a range of outcomes.

MN: What is happening in your country in terms of metabolomics?

KZ: The establishment of six NIH-funded Comprehensive Metabolomics Resource Cores through the Metabolomics Common Fund has allowed institutions to expand and improve their capacity to conduct metabolomics studies. Additionally, the training programs funded by the NIH Metabolomics Common Fund program have aided a significant number of U.S. scientists through mentored research grants, development of courses and workshops, and offering online training. In turn, more of the U.S. scientific community is beginning to appreciate what can be accomplished through metabolomics, broadening the field for greater public health impact.

 MN: How do you see your work in metabolomics being applied today or in the future?

 KZ: The establishment of COMETS, which was an initiative co-developed with Drs. Steven Moore and Joshua Sampson from the National Cancer Institute, is already making an impact. We now have a number of investigators working together to tackle barriers in the field such as data harmonization across cohort studies. In the future, we expect that COMETS will embark on projects that, not only make significant contributions to biomarker discovery, but also develop methods for data analysis and integration that will help advance the field as a whole.

 MN: As you see it, what are metabolomics' greatest strengths?

KZ: Metabolites correlate with the most downstream biochemistry; and in turn, more closely represent the disease phenotype than genomic, transcriptomic, or proteomic data. Therefore, metabolomics has the potential to help us understand the functional implications of the vast amount of data produced through investments in genomic and transcriptomic projects.

 MN: What do you see as the greatest barriers for metabolomics?

 KZ: From an epidemiology perspective, the lack of methods for data harmonization and integration across laboratory platforms and analytical techniques is a significant barrier for leveraging existing data. The development of these methods would allow researchers to more effectively collaborate, rapidly scale up sample sizes for biomarker discovery, and improve our confidence in meta-analyses of these data.

More generally, only a small fraction of metabolites in the human metabolome have been identified and characterized. Therefore, we are working with truly limited information for novel biomarker discovery.

 MN: What improvements, technological or otherwise, need to take place for metabolomics to really take off?

KZ: Advances in compound identification would make a significant impact on the field. Improved identification and characterization of unknown metabolites would allow us to more consistently link observations to the underlying biochemistry. In turn, this would create a greater capacity for disease risk assessment, screening, diagnosis, prognosis, predictive response to therapy, and provide much needed mechanistic insight.

 MN: How does the future look in terms of funding for metabolomics?

KZ: As mentioned earlier, the NIH has invested significantly in the field through the Metabolomics Common Fund Program, which aims to increase national capacity in metabolomics. Future funding will depend on advances in the field, including both technological and methodological advances, key scientific discoveries, and the general funding climate, so there will be many factors at play in the years to come.

 MN: What role can metabolomics standards play?

 KZ: Standardization has a very important role in the field. If standards are not in place that encourage researchers to, not only report methods of data acquisition, study design, and data processing and analysis in detail, but in a similar standardized form or structure, it limits the ability to reproduce and validate results. It also creates barriers for data sharing which limits our ability to leverage existing resources. Overall, lack of standards has the potential to significantly slow down scientific discovery and other advances.

MN: Do you have any other comments that you wish to share about metabolomics?

KZ: Many of the challenges that we currently face in the field of metabolomics are more effectively tackled with collaborative efforts, such as COMETS, COSMOS (http://cosmos-fp7.eu/), and the Metabolomics Common Fund. We must leverage resources and data in a collaborative manner if we hope to advance the field in a more rapid fashion and accelerate scientific discovery.

 
Please note: We are open to suggestions for our MetaboInterviews section. Please send suggestions for future interview candidates to Ian Forsythe at metabolomics.innovation@gmail.com.
Metabolomics Current Contents

Metabolomics Current Contents

Recently published papers in metabolomics:

MetaboNews

MetaboNews
9 Feb 2016
ABRF Metabolomics Research Group Research Study

The ABRF Metabolomics Research Group invites you to participate in its second study with a focus on strategies for the analysis of metabolomics data collected with high resolution mass spectrometry. For study details and materials, please use the following hyperlink:
http://bioshare.bioinformatics.ucdavis.edu/bioshare/view/tthvputgo2am4yo/
Metabolomics Events

Metabolomics Events
21-23 Mar 2016

Clinical & Pharmaceutical Solutions through Analysis
Venue: The UF Clinical & Translational Science Institute, Gainesville, Florida, USA

Make plans to attend the 2nd Annual Metabolomics Symposium on Clinical & Pharmaceutical Solutions through Analysis (CPSA Metabolomics 2016). This unique event is highly interactive and dedicated to the needs of the clinic. The program features updated perspectives and experiences on clinical and pharmaceutical analysis. Imagination and stimulating discussion are central to each CPSA Metabolomics session and event.

Goal
The goal of CPSA Metabolomics is to provide in-depth review of innovative technology and industry practices through open discussion of industry-related issues and needs. This annual event is specifically geared to the needs of professionals attempting to keep pace with faster development times and technology marketing managers attempting to benchmark emerging trends.

Program
The CPSA Metabolomics symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The program will highlight speakers and sessions that provide real-world experiences with new technologies and critical insights into current issues and future needs. Education and specialized training are the foundation of all CPSA events.

Each session at CPSA Metabolomics will address the current industrial landscape and the global need to bring products to market faster. The program chairs will promote discussion and exchange of experiences, ideas, and visions so that current processes that involve analytical measurement can be benchmarked and future strategies may be developed.

For more information, visit http://www.cpsa-metabolomics.com/2016/index.shtml
28 Mar-1 Apr 2016

Hands-on LC-MS Data processing and Statistics 2016
Venue: UC Davis, CA Alumni Center, California, USA

The course will include:

  • Exercises on identification of unknowns by cheminformatics software workflows (incl. CFM-ID, MassFrontier, and various databases and small software routines)
  • Untargeted data processing and exercises on MS-DIAL software
  • Data normalizations and transformations with and without internal standards and Quality Controls
  • Multivariate and univariate statistics (MetaboAnalyst and other software)
  • Pathway mapping (MetaboAnalyst and MetaMapR)

For more information, visit http://metabolomics.ucdavis.edu/courses-and-seminars/courses
30 Mar to 1 Apr 2016

The Australian & New Zealand Metabolomics Conference (ANZMET 2016)
Venue: La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia

The inaugural ANZMET conference is an exciting, peer-driven event! It is designed to foster an all-inclusive, engaging and rich interpersonal process through a blend of traditional presentations, rapid-fire postgraduate presentations, poster sessions, a roundtable discussion, and topical peer sessions.

Its aim is to promote collaboration, innovation, and community-building in metabolomics across private and government sectors by open engagement of all researchers and institutions throughout Australia and New Zealand. The conference is actively supported by the Australia & New Zealand Metabolomics Network (ANZMN), in conjunction with the Metabolomics Society and Metabolomics Australia. Several keynote speakers will present at the conference, including Professor David Wishart amongst others.
For further details, visit http://www.anzmet.org/.
3-7 Apr 2016

Microscale Separations and Bioanalysis: MSB 2016
Venue: Queen’s Landing, Niagara-on-the-Lake, ON, Canada

We invite you to join us for the 32nd International Symposium on Microscale Separations and Bioanalysis (MSB 2016), which is the premier forum for the discussion of cutting-edge research on the frontiers of separation science relevant to human health and the environment. If you are currently incorporating microscale separations like capillary electrophoresis, nano-LC, multidimensional separations, ion mobility spectrometry, microfluidics and lab-on-a-chip devices into your research, then this is a meeting you will not want to miss!

To ensure a stimulating yet intimate environment for discussions, MSB 2016 will be limited to 275 delegates. We invite you to browse our conference website (www.msb2016.org) to learn more about our exciting scientific program.
4-6 Apr 2016

Metabolomics with the Q Exactive
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This three-day hands-on course will introduce you to using the Q Exactive mass spectrometer in your metabolomics investigations. The course is aimed at students and researchers with minimal previous experience of applying liquid chromatography-mass spectrometry (LC-MS) in metabolomics. The course will be led by experts in the field and include lectures, laboratory sessions and computer workshops to provide:
  • An introduction to metabolomics, LC-MS and using the Q Exactive mass spectrometer in your studies
  • Sample preparation for analysis of polar and lipid metabolites in metabolic profiling and targeted studies
  • Instrument methods and data acquisition for profiling and targeted studies
  • Data processing and data analysis
  • Introduction to metabolite identification
The course will finish with a question and answer session with a panel of experts.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/q-exactive.aspx or contact Dr Cate Winder (C.L.Winder@bham.ac.uk).
17-19 Apr 2016

4th Workshop on Holistic Analytical Methods for Systems Biology Studies
Venue: Aristotle University, Thessaloniki, Greece

This is the fourth in a series of successful meetings that started in Thessaloniki in 2008 and then moved to Athens and Patras.

We expect again high level presentations and an open, friendly atmosphere. We plan tutorial sessions on protocols, tips and tricks, live demonstration of software, and training session for small number of young participants with hands on PC.

The first day is devoted to fundamentals/methods/protocols, the second day to health/life sciences and the last day to food/plant/nutrition.

Topics:
  • Analytical Technologies for Metabolite Profiling: LC-MS, GC-MS, NMR
  • Informatics, Chemometrics, Validation
  • Biomarker Discovery: Disease, Drug Efficacy, Embryo Growth, Ageing, Physical Exercise
  • Food authenticity/geographical origin, Nutrition
  • Investigation of gut microbiota host-guest symbiosis
Information: info.metabolomics@gmail.com
Looking forward to seeing you in the historic port city of Thessaloniki.

For more information, visit http://bioanalysis.web.auth.gr/metabolomics.
18 Apr to 26 May 2016

Copenhagen School of Chemometrics - 2016 (CSC-2016)
Venue: Copenhagen, Denmark

  • CSC-2016 is FREE of charge for students at any level.
  • PhD students can obtain a maximum of 12 ECTS.
  • We will count with highly recognized chemometricians as lecturers/teachers: Frans van den Berg, Riccardo Leardi, Thomas Skov, Tormod Næs, Rasmus Bro, Age Smilde, Åsmund Rinnan, Evrim Acar, Federico Marini and Jose M. Amigo.
  • Bonus track: There is the possibility to attend the “Introduction to Matlab for Multivariate Data Analysis” PhD course (see flyer for more information).
The maximum number of participants will be 20 participants per seminar. Therefore, it's strongly recommend to contact Jose Amigo (jmar@food.ku.dk) as soon as possible for keeping your seat!

How to enroll in the CSC-2016? Please, send an e-mail to Jose Amigo (jmar@food.ku.dk) with the information requested in this flyer.
20-22 Apr 2016

Multiple biofluid and tissue types, from sample preparation to analysis strategies for metabolomics
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This three-day course will provide a comprehensive overview of dealing with complex biological samples for liquid chromatography-mass spectrometry (LC-MS) analysis. The course is targeted towards students and researchers who are actively applying metabolomics in their research and want to learn more about robust sample preparation and data acquisition. The course will be led by experts in the field and  will include:
  • An overview of sampling, quenching and extraction strategies for different biological samples
  • Hands-on sample preparation using different sample types
  • Hands-on HILIC and reversed phase LC-MS data acquisition
  • Solid phase extraction and liquid-liquid extraction
  • An overview of data analysis and metabolite identification
  • An opportunity to ask questions and seek advice to prepare samples in your own research.
For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/sample-analysis.aspx or contact Dr Cate Winder (C.L.Winder@bham.ac.uk).
9-12 May 2016

Metabolomics Summer Workshop
Venue: Kellogg Eye Center (Kellogg Auditorium), located at 1000 Wall Street, Ann Arbor, MI, USA

The Michigan Regional Comprehensive Metabolomics Resource Core (MRC)2 is presenting a four-day Metabolomics Summer Workshop, May 9-12, 2016.

Registration: https://umichumhs.ut1.qualtrics.com/SE/?SID=SV_bPEVDn7I5wSEcwl
 
This workshop is intended for investigators seeking a solid foundation to expand their research using metabolomics.
Sessions include:
  • Study design
  • Sample collection
  • Analytical methods
  • Data processing, statistical analysis, and metabolite identification
  • Exploratory analysis with bioinformatics tools
  • Case study applications
  • Hands-on data analysis training, including statistical analysis and data visualization
After attending the workshop, you will be able to:
  1. Understand the principles of the analytical methodologies and data analysis techniques used in metabolomics.
  2. Use this knowledge to incorporate metabolomics into your research.
  3. Understand the reasoning behind data processing and statistical analysis.
  4. Gain a working familiarity with bioinformatics tools for exploratory analysis.
Costs per participant are $350 for internal U-M investigators and $750 for external investigators. Lunches are included.

If you have any questions about the workshop, please contact Terri Ridenour.
 
For more information, visit the MRC2 website.
26-27 May 2016

Informatics and Statistics for Metabolomics (2016)
Venue: Downtown Toronto, Canada

CBW will be hosting a Metabolomics workshop May 26-27 in downtown Toronto.

The workshop will cover many topics ranging from understanding metabolomics technologies, data collection and analysis, using pathway databases, performing pathway analysis, conducting univariate and multivariate statistics, working with metabolomic databases and exploring chemical databases. Participants will be given various data sets and short assignments to assist with the learning process.

For more information and to register, visit http://bioinformatics.ca/workshops/2016/informatics-and-statistics-metabolomics-2016.
30 May-2 Jun 2016

10th conference of the Francophone Metabolomics and Fluxomics Society (RFMF)
Venue: Montpellier, France

RFMF is pleased to announce the 10th conference of the Francophone Metabolomics and Fluxomics Society (RFMF), to be held in Montpellier between the 30th of May and the 2nd of June 2016. Every year since 2005, this conference gathers scientists who are interested in metabolomics and fluxomics, and more generally in the study of metabolism. This year, the main scientific themes are:
  • Ecotoxicology, environmental metabolomics and microbiology
  • Health: clinical applications, therapeutic monitoring, biomarker determination
  • Agricultural resources and food science
This conference is also a good opportunity to hear about recent developments in analytical methods/hardware and bioinformatics tools in metabolomics and fluxomics. The meeting will include:
  • Plenary lectures by renowned international invited speakers:
    • Prof. Arthur Edison (University of Georgia, USA)
    • Prof. Elizabeth Hill (University of Sussex, UK)
    • Dr. Kris Moreel (University of Gent, Belgium)
    • Dr. Patrick Kiefer (ETH Zurich, Switzerland)
  • Oral presentations
  • Flash communications associated with poster sessions
  • Thematic workshops and round-tables
The registration and submission interfaces will open on February 1st 2016. The deadline for abstracts to be considered for oral presentations is April 1st 2016. More information can be obtained on the website of the RFMF conference: http://10-js-rfmf.sciencesconf.org/
27-30 Jun 2016

Metabolomics 2016
Venue: Convention Centre, Dublin, Ireland

The 12th Annual International Conference of the Metabolomics Society will be held in Dublin from June 27-30, 2016. The conference venue is the Convention Centre Dublin, located conveniently in the city centre with easy access to the airport. In the historic, compact city centre there is lots to do and see, and visitors will love the rich selection of galleries, museums, restaurants, pubs and shops, not to mention the traditionally warm welcome from Dubliners.

The conference programme will cover all aspects of metabolomics under five broad themes: Metabolomics in Nutrition and Food Research, Metabolomics in Health and Disease, Advancing the Field, Environmental, Plant and Model Organisms.

For further details, visit http://metabolomics2016.org.
17-21 Jul 2016

4th Annual Workshop on Metabolomics
Venue: University of Alabama, Birmingham, Alabama, USA

The 4th Annual UAB Metabolomics Workshop, sponsored by the NIH Common Fund Metabolomics Program, will be held Sunday, July 17 to Thursday, July 21, 2016. Registration is now open (http://www.uab.edu/proteomics/metabolomics/workshop/workshop_july_2016.php) and will close on April 29, 2016. There will be slots for up to 40 registrants. An R25 grant from the NIGMS provides funding support for graduate students and postdoctoral fellows. Slots are also available for Faculty at all levels who wish to receive training in this rapidly growing complement to biomedical research.

Women, members of under-represented minority groups, and individuals with disabilities are strongly encouraged to apply.

The metabolome, in distinction to the other –Omics, provides a better assessment of the exposure to the chemicals of life – it is truly intergenomic providing information on “metabolites” coming from ourselves or the model we’re using, the unique, non-human/mammalian compounds we consume as part of our food, compounds generated by the microorganisms that are part of “us”, and other compounds that are in the environments we live in. If ever precision medicine is able to deliver what is claimed it will, it has to include the metabolome context in which genes and proteins are operating.

The themes in this fourth year of the workshop are:
  1. Design of a metabolomics experiment
  2. Sample stability and extraction methods
  3. Analytical systems (nuclear magnetic resonance and gas- and liquid chromatography-mass spectrometry)
    • Targeted metabolomics
    • Untargeted metabolomics
    • Quantitative metabolomics
  4. Pre-processing of analytical data (Mzmine 2 and XCMSonline and Chenomx)
  5. Statistical analysis of the data (MetaboAnalyst, Simca, SAS)
  6. Metabolite databases (METLIN, HMDB, LIPIDMAPS, PubChem, ChemSpider)
  7. Identification of metabolites (MetaboSearch, MSMS analysis)
  8. Metabolite pathway analysis (Mummichog, KEGG, GeneGo, Ingenuity)
  9. Advanced elective sessions allow attendees to fine tune their training experience
    • Imaging mass spectrometry
    • isotope ratio analysis
    • Ion mobility
    • Using metabolomics software at the command line and based programs
For further details, visit http://www.uab.edu/proteomics/metabolomics/workshop/workshop_july_2016.php.
12-23 Sep 2016

2016 International Summer Sessions in Metabolomics
Venue: Campus UC Davis, CA, USA

The course will include:
  • Study design, including pitfall analysis and hidden biases in studies from microbial, plant, mouse and human cohort research
  • Sample preparation and quality control
  • In-laboratory detailed discussions standard operating procedures for GC-MS and LC-MS data acquisitions
  • Targeted metabolomics, including monitoring charts and use of isotope labeled internal standards
  • Exercises on flux analysis in cancer cells by isotope tracer analysis
  • Exercises on identification of unknowns by cheminformatics software workflows (incl. CFM-ID, MassFrontier, and various databases and small software routines)
  • Untargeted data processing and exercises on MZmine and MS-DIAL software
  • Data normalizations and transformations with and without internal standards and Quality Controls
  • Multivariate and univariate statistics (incl. Devium, MetaboAnalyst and other software)
  • Pathway mapping (incl. MetaboAnalyst and MetaMapR)
For further details, visit http://metabolomics.ucdavis.edu/courses-and-seminars/courses.

Please note: If you know of any metabolomics lectures, meetings, workshops, or training sessions that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).
Metabolomics Jobs

Metabolomics Jobs

This is a resource for advertising positions in metabolomics. If you have a job you would like posted in this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com). Job postings will be carried for a maximum of four issues (eight weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Posted Closes Source
Postdoctoral scholar
 Oregon State University Corvallis, OR, USA 26-Feb-2016 Until filled Metabolomics Society
Postdoctoral Fellowship in Metabolomics
 Lund University Malmö, Sweden
 23-Feb-2016
Lund University
Post-doctoral position (18 mo) in nutritional metabolomics
INRA Clermont-Ferrand, France 21-Feb-2016 15-Mar-2016
 Metabolomics Society
Assistant or Associate Professor or Professor -  Food and Nutritional Metabolomics Computational Biology
 Ohio State University
 Columbus, OH, USA 16-Feb-2016 18-Mar-2016
 Ohio State University
Cornell University Assist./Assoc. Professor in Plant Metabolomics
Cornell University Ithaca, NY, USA 1-Feb-2016 Until filled Metabolomics Society
Assistant Professor, Metabolomics
 Auburn University Auburn, AL, USA 21-Jan-2016 Until filled Metabolomics Society
Research associate 3 at the Metabolomics lab
 University of Miami
 Miami, FL, USA 12-Jan-2016 Until filled Metabolomics Society
use key word: P00007201
Proteomics and Metabolomics Facility, Research Associate I
 Colorado State University Fort Collins, CO, USA 4-Jan-2016 Until filled Metabolomics Society
Proteomics and Metabolomics Facility, Post-doctoral Scientist
 Colorado State University
 Fort Collins, CO, USA 4-Jan-2016 Until filled Metabolomics Society


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.
  • There are currently no positions being advertised.

Funding Opportunities
  • The University of Michigan Regional Comprehensive Metabolomics Resource Core (MRC)2 [PDF]

Free Subscription
To subscribe or unsubscribe, please visit http://www.mailman.srv.ualberta.ca/mailman/listinfo/metabonews. Please forward this newsletter to any interested colleagues or collaborators. Send your comments and feedback about this newsletter to metabolomics.innovation@gmail.com.

Back issues of this newsletter can be viewed from the newsletter archive (http://www.metabonews.ca/archive.html).