MetaboNews -- August 2016
MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society

Issue 60 - August 2016

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Aug2016/MetaboNews_Aug2016.htm

TMIC Services
TMIC Services

Welcome to the sixtieth 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 Fellowship Spotlight article by Masanori Arita and Donghan Li of the National Institute of Genetics (Japan) titled "Lipoquality Project and Travel Fellowship to Visit Japan", and a metabolomics interview with Reza Salek of EMBL-EBI.


This issue of MetaboNews is supported by:

Metanomics Health
   
Chenomx -- Metabolite Discovery &

                      Measurement
Metanomics Health GmbH

Chenomx Inc.

Advertising
Would you like to advertise your metabolomics hardware, software, products, and services to 2,900 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 ([email protected]).


Metabolomics Society Logo

Metabolomics Society News


USE YOUR VOTE!!  New Directors of the Metabolomics Society
Voting is now open for new Directors of the Board of the Metabolomics Society. This year, we have 15 international scientists standing for 6 positions, as well as 3 Directors standing for re-election. All members (both student and standard) are eligible to vote, so please use this opportunity to influence the governance and future direction of your Society.

To vote, visit http://metabolomicssociety.org/2016-election and sign in with your membership email address. Voting ends August 26. It only takes a few minutes, so don’t miss your chance!



CONFERENCE CORNER

2016 Metabolomics Conference… the biggest metabolomics conference ever held in Europe
The 2016 Metabolomics Conference in Dublin was a rewarding and enjoyable event for nearly 900 attendees that gathered to discuss cutting-edge metabolomics research. The final programme included almost 600 high quality poster and oral presentations, and the latest technological advances were on show from our corporate sponsors. In addition to the science, the social events were a highlight of the conference, with excellent networking events including the conference dinner at Ireland’s national sports stadium (Croke Park) and dedicated early-career events. Check out the full abstract listing and photos of all the action at http://metabolomicssociety.org/events/past-society-conferences

Save the Date now for the 2017 Metabolomics Conference
The 13th annual conference of the international Metabolomics Society will be held from June 26-29, 2017, in Brisbane, Australia. The conference will cover all aspects of metabolomics science, with featured themes to include Systems Biology and Identification of Novel Metabolites. Keep an eye on http://metabolomics2017.org for future updates.

Would you like to host the 2019 Metabolomics Society Conference in Europe?
The Metabolomics Society is calling for interested members in the European region to express their interest in hosting the 2019 annual Metabolomics Society meeting (http://metabolomics2019.org/). Please send notice of your interest using this form by September 10, 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 and assist A-S-K staff to select a suitable venue and organize the conference. The tasks of the LOC are to ensure national and regional support for the conference, to assist the Society in administrative planning and, most importantly, to chair and organize the scientific management of the conference, including forming an International Organizing Committee that has the responsibility for scientific aspects of the meeting. Please complete the application form outlining your ideas to maximize the scientific quality and outreach of the conference. For further enquiries, please contact the Society via A-S-K Associates ([email protected]).


MEMBERS CORNER

Early-career Members Network (EMN)
The EMN is dedicated to and run by early-career scientists who are members of the Metabolomics Society and are from academia, government, or industry. The network aims to provide a forum for metabolomics researchers at the start of their professional career.

Announcement of Opportunity: Applications sought from at least 5 additional early-career scientists to expand the EMN.
Deadline: August 15, 2016

Background
We are inviting at least 5 early-career researchers to join the early-career committee of the Society's new Early-career Members Network (EMN). The mission of the EMN is to recognize the value and importance of our early-career members, to ensure that their views are heard and acted upon, ultimately improving their experience in metabolomics science and our community. We are looking for creative thinkers to address challenges, such as, how do we help early-career scientists enter and engage with our scientific community? What mechanisms can we construct to allow student contributions (talks and posters) to be openly discussed in a safe environment, where senior scientists can teach and advise, and where no question is too basic? What activities and benefits can we develop to encourage students and postdocs to want to join (and remain members of) the Metabolomics Society even in years when they do not attend the annual conference? What training courses are required? How else can the Society serve its early-career members?

Eligibility
We welcome applications from students conducting higher degrees (Masters, PhDs) in a metabolomics discipline or from those within 5 years of their PhD who are actively engaged in metabolomics science. As an international society we encourage applications from all continents. Successful applicants must be members of the Metabolomics Society (or immediately become members upon joining the task group).

Time Commitment
There is much exciting work to be done and much to achieve! Therefore we anticipate a contribution of up to two hours per week (on average). If the Early-career Members Network organises sessions at conferences or other events, time commitments will increase accordingly. Note also that the existing members of the EMN committee span many time zones, so some conference calls may occur early or late in the day. No dedicated travel will be required for the EMN committee discussions. The appointment to the EMN committee is for one year initially, and may be extended up to two years. It is your responsibility to discuss this commitment with your supervisor(s) prior to applying.
 
Application Procedure
Please send the following, in one document (.docx or .pdf), to the EMN committee ([email protected]).
  1. One-page resume with relevant experience in developing and leading networking activities (e.g., student rep for other societies) plus your research experience in metabolomics (e.g., presentations, publications, etc.)
  2. Up to 300 words on why you fit the role and up to an additional 300 words (one page in total) on what ideas you are passionate about developing as part of the Early-career Members Network. Applications will then be reviewed by members of the Metabolomics Society’s Strategy Task Group and the existing EMN committee members, and successful candidates will be notified by the end of September 2016 to start in October 2016.
12th Annual International Metabolomics Conference, Dublin, Ireland

EMN Workshops: The EMN hosted two highly anticipated workshops: (1) Career Development and (2) The Importance of Experimental Design. First up, in the morning session Professor Julian Griffin (University of Cambridge, UK) opened the Career Development workshop with an insightful recollection of his own academic career, as well as motivating tips for EMN members wishing to follow the same path. The second speaker, Sinead Cullen (Life Science Recruitment, Ireland) provided helpful recommendations for selling oneself in the science industry job market. In the afternoon, the Experimental Design workshop took place. Professor David Broadhurst (Edith Cowan University, Perth, Australia) provided a fast-paced overview of the importance of estimating uncertainty in metabolomics experiments. Using computer simulation he guided us through the importance of sample size, variance and effect size in study design. Dr. Rick Dunn (University of Birmingham, UK) then followed with a valuable discussion of the necessary analytical and quality assurance aspects to be considered in metabolomics experiments. The third and final speaker, Dr. Julia Kuligowski (Health Research Institute La Fe, Spain), explained quality control (QC) through data cleaning and how QC-based signal correction can be employed to improve data quality. Both workshops were well attended, with interactive question and answer sessions following each. The workshops received many positive responses and the EMN would like to thank everyone involved.

Early Careers parallel sessions: Two parallel sessions (of one hour and 20 minutes each) were allocated for Early Careers (ECs)/young scientists’ presentations. The EMN committee members chaired the two parallel sessions: Aoife O’Gorman and Fidele Tugizimana (session 1), Justin van der Hooft and Stacey Reinke (session 2). The two sessions were well attended and the presenters, mostly PhD candidates, gave excellent talks. The presentations included evaluation of metabolite extraction methods, food metabolomics, finding biomarkers for disease prognosis and finding bioactive natural products with pharmaceutical benefits, to name a few; and these were the ongoing research projects of the presenters. The senior scientists in the audience were eager and happily to ask questions and provide inputs where necessary. The EMN chairing of the sessions put the presenters visibly at ease and such sessions, in which ECs are given a platform to share their research projects and receive constructive inputs from their peers and senior scientists, were one of the excellent successes of the conference, consolidating also the networking of young scientists/ECs that the EMN committee serves.

Social Events: The EMN hosted two social events. The meeting was kicked off in high spirit on Sunday evening with the Society's early career members meeting up at a meet-and-greet in the heart of Dublin. During the conference the EMN also hosted a reception at the conference venue where Mark Viant entertained with the history of EMN activities seen from the perspective of the chair of Metabolomics Society board. The new metabolomics forum (www.metabolomics-forum.com) was also introduced with positive feedback. The events were well-visited and gave the EMNs good opportunity to interact with each other and the Society board members.

Please feel free to contact us via [email protected] if you have any suggestions or comments regarding our planned activities this year (i.e., online webinars and workshops). If you think you have a great idea for a new activity we should organise then please share it with us; the EMN can only be a success with your support and ideas!

Membership News for 2016
WARNING: If you registered for Metabolomics2016 as a non-member, but have not confirmed your membership using the link provided, you may not be able to vote in the upcoming elections. Please make complete your membership registration process!


TASK GROUPS CORNER

Industry Engagement Task Group
If your company is not a Corporate Member of the metabolomics Society, please encourage the appropriate person to consider this. There are multiple benefits to our Corporate Members and the support of important companies helps the Society support the whole metabolomics community. Please consider supporting the Society through a Sponsorship for Metabolomics 2017, in Brisbane!

Data Standards Task Group
Data standards task group is planning to collaborate with ABRF-MRG2016 on data analysis reproducibility exercise. To find out more or get involved, see announcement below: 

ABRF-MRG2016 Metabolomics Research Group Data Analysis Study
We are pleased to announce the second Metabolomics Research Group Study. One of the major bottlenecks in the field of metabolomics is the varied application of bioinformatics and statistical approaches for pre and post-processing of global metabolomic profiling data sets collected using high-resolution mass spectrometry platforms. Our study design recapitulates a typical metabolomics experiment where the goal is difference detection of features between two groups.
The primary goal of this study is to examine reproducibility and optimal data analysis strategies for metabolomics studies, by comparing a consortium of analyses using the same dataset. In addition, this study will provide participants with an opportunity to evaluate their approaches with regard to the following:
For study details and materials please consult the attached pdf and the following Bioshare link:
http://bioshare.bioinformatics.ucdavis.edu/bioshare/view/tthvputgo2am4yo/
Deadline for returning MRG2016 Study results is October 1, 2016!!!
For more details, visit https://abrf.org/research-group/metabolomics-research-group-mrg
The ABRF Metabolomics Research Group: Chris W. Turck (Chair)
Max Planck Institute of Psychiatry, Tytus Mak – NIST, Maryam Goudarzi Georgetown University, Amrita K. Cheema Georgetown University, Andrew Patterson - Penn State University, and Christopher Colangelo (EB Liaison) - Primary Ion

Data Quality Task Group
The Data Quality Task Group welcomes our two newest members, Krista Zanetti and Susan Sumner. Check it out!



INTERNATIONAL AFFILIATES CORNER
Australian & New Zealand Metabolomics Network (ANZMN)
Visit http://www.anzmn.org

As part of his 2016 ANZMAG Lectureship 2016, Professor David Wishart (University Alberta, Edmonton) gave a 3-day course on NMR-based metabolomics from Wednesday, August 3 to Friday, August 5, 2016, at the University of Queensland. The course covered the whole pipeline of NMR-based metabolomics, including methods, statistical data analysis, databases, etc. As with other
Australia and New Zealand Society for Magnetic Resonance (ANZMAG) courses, the lectures were taped and will be uploaded to the ANZMAG YouTube channel (https://www.youtube.com/user/ANZMAG/playlists). Please find a flyer for the course online at https://www.dropbox.com/s/xhjvhkt9ylyx7rb/ANZMAG_Course_Flyer_updated.pdf?dl=0 with all the details on it.



 
Software Spotlight

Fellowship Spotlight


Lipoquality Project and Travel Fellowship to Visit Japan

Feature article contributed by Masanori Arita1,2 and Donghan Li1
1.    National Institute of Genetics, Mishima, Japan
2.    RIKEN Center for Sustainable Resource Science, Yokohama, Japan

1.    Lipoquality research consortium

Lipid researchers in Japan recently launched a 5-year project called “Lipoquality” (Project Leader: Makoto Arita, RIKEN Center for Integrative Medical Sciences) to identify and quantify various lipid classes to clarify their function through a multitude of detection methods including mass spectrometers (https://sites.google.com/site/lipoqualityjpn/). Since this program is based in Japan, all researchers are Japanese and documentation is in Japanese. However, to reduce the language barrier, this program also includes access to an international liaison office as part of the research fellowship.

2.    Fellowship details

The purpose of this fellowship is to advance the lipid research of applicants while contributing to the research of the Lipoquality project. The fellowship supports travel to Japan for 1 to 3 months and short-term visits to a research conference or meeting are not allowed. We currently offer the following seven research topics, but these are merely provided as examples and one can submit his or her own research plan.

1.    Non-targeted lipidomics using LC-MS/MS (RIKEN IMS / CSRS)
2.    Wide-targeted lipidomics for oxidized lipids (RIKEN IMS / CSRS)
3.    Electron-microscopic methods to observe distribution of membrane lipids (Nagoya University)
4.    Imaging mass spectrometry (Hamamatsu University School of Medicine)
5.    Wide-targeted analysis of eicosanoids (Juntendo University)
6.    Detection of GPCR activation by lipid ligands (Juntendo University)
7.    Real-time imaging of protein modification on membranes (Osaka University)

If you are interested and want to engage in lipid research for a couple of months, please visit our website and check your eligibility (https://sites.google.com/site/lipoqualityjpn/liaison-office). When your proposal is accepted, we will provide you (1) a round-trip air ticket (discount economy fare only, subject to our regulations), (2) a settling-in allowance of about 5000 Yen / day, (3) and research consumables of up to 500,000 Yen per visit. The flight and accommodations will be determined through discussion with your host researcher, and the consumable supply is upon request from your host laboratory. Although restrictions may apply, there is little obligation required on the part of the program participant and any person, including graduate students, can visit us.

Lipoquality Logo 


3.    Future Directions

The fellowship program continues for the next few years and we plan to accept up to 5-6 researchers each year depending on our budget. The purpose is to establish a long-term research partnership among institutions. Laboratories collaborating with members of the Lipoquality core groups are therefore prioritized. We also welcome project-wide collaboration. We will organize an international symposium next year, which could be a joint collaborative event. We look forward to collaborating with you by using the novel analysis technologies on lipids.


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 metabolom[email protected].

 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 Reza Salek.

Coordinator Scientific Curation: Metabolomics and Molecular Informatics, European Bioinformatics Institute (EMBL-EBI), UK
Reza

                  Salek


Biography

Reza got his PhD in Molecular Biophysics and Biochemistry from University College London, UK. He started working in the field of metabolomics in University of Cambridge, over time moving from lab experimental settings towards data analysis and data handling. In the past, he has worked as Scientific Investigator at the Medical Research Council, Cambridge UK. In 2012, he joined EMBL-EBI and currently work as the Coordinator Scientific Curation. At EMBL-EBI, they host the MetaboLights (http://www.ebi.ac.uk/metabolights/), the first general purpose repository for metabolomics data. For Reza, open access data sharing is of paramount importance to metabolomics growth, enabling the community to move a step closer to result reproducibility, a key objective for any scientific field. Here metabolomics standards can play a vital role (http://www.metabolomics-msi.org). Reza has had the opportunity to manage and coordinate a large EU infrastructure project on metabolomics data standards, COSMOS (Coordination of Standards in Metabolomics, http://cosmos-fp7.eu/); this project has re-ignited standards effort within community leaders, in a more bottom-up approach. Such efforts, combined with data sharing in MetaboLights, would benefit the community substantially. Professionally, he's a member of the Cambridge Systems Biology Centre, Cambridge Neuroscience, and Cambridge Cancer Centre. He's the main organizer of the “EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists 2012
 - 2016", giving him the opportunity to work with a group of talented and excellent instructors/tutors in metabolomics that share the same passion for metabolomics data handling. He’s one of the directors of the Metabolomics Society, chairing the data standards task group and website committee. He is also one of the directors of the Metabolic Profiling Forum (MPF), where the Metabomeeting conference series are hosted to promote the discussion and debate of the latest developments in metabolomics. Additionally he is Associate Editor for Frontiers Metabolomics Journal.


Metabolomics Interview (MN, MetaboNews; RS, Reza Salek)

MN: How did you get involved in metabolomics?

RS: I started working in the field of metabolomics at the University of Cambridge, and later moved to the Medical Research Council, Cambridge UK. Initially, I began in lab-based research, particularly investigating neurodegenerative diseases, type 2 diabetes, and breast cancer. Gradually over time I moved from a lab setting to the data side, data analysis, and data handling. I joined EMBL-EBI in 2012, where we host MetaboLights (http://www.ebi.ac.uk/metabolights/) [1], the first general purpose repository for metabolomics data and derived experiments. We work on facilitating data sharing, data standards, and setting up data analysis pipelines and workflows. Once enough datasets and the right tools are available, we can then move toward generating new knowledge from existing data.

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

RS: Open access data sharing is of paramount importance to the metabolomics community growth, enabling us to move a step closer to result validation and reproducibility [2], and to generate new knowledge from existing data. Data sharing relies on a standards framework for growth. We have now MetaboLights and COSMOS (Coordination of Standards in Metabolomics, http://cosmos-fp7.Eu/) [3] that have re-ignited the standards effort within the community, on more pragmatic and application-based approaches. The accumulative and collective knowledge of experiments over time in public domain repositories should enable us to explore metabolic consensus across species, or relevance to diseases, and to bring the ability to mine and integrate the results, all of which are activities that we pursue in our institute. Curating various types of experimental datasets has exposed us to a variety of different data types and experimental settings, providing good insight on common practices and methods used in metabolomics. I suppose the most important part is networking with a large number of labs and groups working in metabolomics.

MN: What key metabolomics initiatives are you pursuing at your research centre or institute?

RS: Besides development of the MetaboLights repository, where we are currently incorporating data analysis tools, other major active collaborations are working on lowering the barrier of data submission, as well as the promotion and development of open data standard formats. We are actively working on mzML2ISA, nmrML2ISA, and imzML2ISA, a set of tools that can automatically generate ISATab metadata files from metabolomics raw XML data files.  In addition, I am actively involved with development of nmrML, mzTab, and qcML data formats, for reporting metabolite identification and quality control metrics. Besides the teamwork efforts within our institute we greatly rely on collaborating with external research partners, as well as industry, to integrate and adapt existing tools to analyse, visualize data, and to support data submission-compatible formats. Another active area is in capturing data analysis parameters and workflows (such as Galaxy) in MetaboLights. Such efforts would ideally get us closer to data analysis reproducible results. This is also an active collaboration with tool developers and those working on workflow environments to capture data analysis parameters systematically. In our institute we are also working with our project partners on setting up cloud-based collaborative infrastructure to handle and manage large-scale metabolomic clinical data analysis pipelines (see PhenoMeNal project). I also have a personal interest in cross omics data fusion and integration although this work is quite challenging and at the early stages; nevertheless it holds great potentials.

Click on the thumbnail below to view a larger version of the image

MetaboLights

              Thumbnail

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

RS: Metabolomics in the UK is quite strong and there are many well known groups both nationally and internationally. Currently in UK, national investment in a metabolomics network is missing. We need a similar initiative to RFMF in France or Metabolomics Australia. There is however the Metabolic Profiling Forum (MPF), which has successfully hosted UK and European-based MetaboMeetings since 2005. MetaboMeeting provides a venue for networking, interaction, and presentation of the latest research. Maybe in the future MPF can play a central role for even wider collaborative projects and sharing of resources? Another area that the UK metabolomics community is doing well is in training and courses in metabolomics. Many universities and research institutes have several, typically week long, training courses, where skills levels range from beginner to advanced, and cover a range of topics from lab-based work to data analysis. At EMBL-EBI, I have organised the “EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists” annually since 2012, giving me the opportunity to work with groups of talented, excellent instructors/tutors in metabolomics that share the same passion for metabolomics data handling.

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

RS: I hope to see growth in data sharing and standards in metabolomics; currently a very small percentage of available research metabolomics data (assuming that 50% of ~50,000 or so publications have data) have been shared publicly. The number of publically available data is smaller in metabolomics than any other omics; for example, we have roughly 700 public and private metabolomics datasets, while for proteomics, there are about 6,000 and even more for transcriptomics—nearly 70,000 datasets (http://www.omicsdi.org/). We are seeing an increase in the number of multi-omics data submissions across EMBL-EBI, making it possible to perform data integration or meta-analysis across different omic fields. (You can find more than 4,000 such examples from new EMBL-EBI Omics Discovery Index tool: http://www.omicsdi.org/ 
[4]). Once large interoperable datasets are available that are highly curated, and in a standard format, new or existing data analysis tools could be brought to data (rather than data to tools), integrating with it in the future. Such setup, or cloud computing, would enable researchers to explore and navigate data and provide the ability of mining new information or to generate new knowledge, going beyond what currently is possible with limited data.

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

RS: As we all know, metabolomics is multidisciplinary by nature. This makes metabolomics fascinating whilst at the same time quite challenging. Essentially, I believe that metabolomics is a team effort, requiring the skill sets of different individuals coming together to address a particular challenge. Metabolomics has wide and diverse applications that can potentially provide cheap and fast means for diagnosis, profiling, and classification. Once a model has been established, data can be acquired in near real-time; processed and analysed, making metabolomics an ideal tool for diagnosis or monitoring, with huge industry applications.
Metabolomics, combined with tracer labelled results, flux modelling,  or imaging, has another strength; it can provide dynamics, mechanistic, and spatial information on the biology, which is far more informative than a classical approach. We could see metabolomics playing a greater role in personalized medicine, single cell measurements, and real-time data collection.

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


RS:
Metabolite identification and correctly reporting it [5], and wide adoption of quantified measurements are still amongst the major challenges in metabolomics. Open data standards formats, particularly mzTab, which I’m very keen on, could potentially address several such issues particularly in reporting identification confidence and steps taken to calculate the measurements. Reproducibility and cross validation of results are also ongoing challenges, mainly due to the multifactorial nature of metabolomics experiments, from instrumental settings to analytical chemistry variations, all the way to data processing, analysis, and statistics. Wider adoption of workflows could tackle this problem and help address some of the issues. Another major challenge would be the ever increasing data size and volume of data produced, particularly for Phenome Centres or others working on high-resolution imaging. A larger part of data files carry signals that lack any metabolic information and are mainly composed of instrumental, chemical, or analyte noise. Extracting relevant knowledge from raw data files would reduce this data volume, while retaining the knowledge part of the dataset. Still this area needs substantial work and engagement with industry, before getting caught in the exponential growth of data.
 

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

RS: Improvements are gradual and happening all the time and are continuous in terms of instrumentation accuracy, precision, and automation. I would hope to see more automation in data acquisition and data processing, similar to what is taking place now for genomics. Once such variation in data collection and processing are minimised, with the right analysis tools, we could expect to do more robust everyday application of metabolomics. Noninvasive continuous monitoring of certain metabolites within devices that can warn us before levels of certain metabolites or biomarkers reach crucial levels, also has great potential, e.g., current glucose monitoring systems used for diabetic patients to warn for low or excessive levels of glucose in the blood; such measurements need to quantified to be useful.


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


RS: Compared to genomics, metabolomics funding is proportionally a lot smaller but metabolomics can equally deliver diagnosis. Some such metabolites are already used in everyday applications (e.g., newborn metabolic screening). Many metabolites can play an important measurement to assess an environmental or agricultural impact, both of which are areas with huge potential growth and investment. Although any future prediction is flawed, for now I believe we can expect growth in overall funding; lucky whoever gets it! Another indication is the increase in the number of high profile journal publications and public media coverage of metabolomics. On top of this, it seems that the business sector is predicting annual market growth in this sector.

MN: What role can metabolomics standards play?

RS: Everyone knows standards are important but not many want to do it! Joking aside; as we all know, standards are necessary for data reproducibility and facilitate result validation. Standards have several aspects, ranging from reporting standards (i.e., minimum reporting guidelines), open data formats, to chemical standards. Standards need to cover and cope with an ever growing variety of technologies, methods, and analysis platforms. There has been a lot of work in the past on reporting guidelines, and work is currently ongoing in terms of metadata capture and open data formats. Technologies are constantly evolving so we need more funding and continuous work in this area. Some of our thoughts are nicely summarised in the article ("Data standards can boost metabolomics research, and if there is a will, there is a way." Metabolomics 12.1 (2016): 14). Our efforts, in conjunction with my role as the chair of the Metabolomics Societies Data Standards Task Group, is to work closely with leaders in this area, both from the metabolomics and proteomics communities as well as industry, to establish and promote community-wide standards.

Data

              Standards in Metabolomics
For more details see [2].


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

RS: Working together with Jan Stanstrup, we have now merged and revitalised the metabolomics forum, and hope to bring society activities to public domain discussions, for better engagement with society members and the general metabolomics community, as well as a venue where one can post his or her questions. Visit the forum at http://www.metabolomics-forum.com/

References
  1. Haug, Kenneth et al. "MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data." Nucleic acids research (2012): gks1004.
  2. Rocca-Serra, Philippe et al. "Data standards can boost metabolomics research, and if there is a will, there is a way." Metabolomics 12.1 (2016): 14.
  3. Salek, Reza M et al. "COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access." Metabolomics 11.6 (2015): 1587-1597.
  4. Perez-Riverol, Yasset et al. "Omics Discovery Index - Discovering and Linking Public Omics Datasets." bioRxiv (2016): 049205. (bioRxiv)
  5. Salek, Reza M et al. "The role of reporting standards for metabolite annotation and identification in metabolomic studies." GigaScience 2.1 (2013): 13.

 
Please note: We are open to suggestions for our MetaboInterviews section. Please send suggestions for future interview candidates to Ian Forsythe at [email protected].

Metabolomics Current

                                Contents

Metabolomics Current Contents


Recently published papers in metabolomics:
Metabolomics Events

Metabolomics Events

12-16 Sep 2016


2nd Metabolomics Sardinian Summer School: "How to bridge metabolomics and genomics"

Venue: Polaris Technology Park, Pula, Sardinia, Italy

Course Objectives
The Summer School will offer students theoretical sessions with lectures by experts, and hands-on data analysis aimed to deepen the theoretical and practical knowledge for using the main tools available to integrate metabolomics data.

Main Topics
  • Cancer: genes or metabolism?
  • Chemometric analysis
  • Data Processing ad softwares
  • Molecular Hypotheses from Dynamic Metabolomics Data
  • Omics integration
  • Omics and nutrition
  • Statistical methods for biomarkers discovery
  • Translating big data from genes and metabolites into molecular knowledge
Daily lectures and hands-on sections, plus poster and oral presentations from participants

Target Audience
The Summer School is targeted to researchers at an early stage in their career, from Biological Sciences, Health Sciences and other different background (Including bioinformatics and mathematics) who are interested in learning about both technical and cheminformatics tools to integrate metabolomics data.

Applications               
The course is funded by the Regional Sardinian government and registration will be free of charge for all attendees. Selection will be based on CV and a letter stating the motivations for attending the course and future research plans of candidates. A letter of reference from the current supervisor must also be attached to the application. Registration includes course material, lunches and coffee breaks (not accommodation expenses). For selected participants contribution or reimbursement will be considered.

Organizing Committee
Summer School Secretariat: [email protected]

For detailed information about the Summer School in Sardinia, visit http://sites.unica.it/metabolomicaclinica/events/.

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.

10-12 Oct 2016


Max Rubner Conference on Food Metabolomics

Venue: Karlsruhe, Germany

We are pleased to announce the second international Max Rubner Conference on Food Metabolomics to be held from October 10th -12th, 2016, at the Max Rubner-Institut, the German Federal Research Institute of Nutrition and Food, in Karlsruhe, Germany.

For further information and registration details, please visit https://www.mri.bund.de/de/ueber-das-mri/veranstaltungen/max-rubner-conference/2016/.

12-14 Oct 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 3-day course will provide a comprehensive overview of dealing with complex biological samples for LC-MS analysis. The course is targeted towards students and researchers who are actively applying metabolomics in their research. The course will be led by experts in the field and include
  • An overview of 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 clean up methods
  • 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 [email protected].

15-16 Oct 2016


Mayo Clinic Metabolomics Workshop

Venue: Siebens Building, Rochester, Minnesota, USA

Mayo Clinic will host a Metabolomics Symposium from October 15 to October 16 on the Rochester, Minn., campus. The event will feature presentations on the practice and theory of metabolomics applications, the latest research in metabolomics and networking opportunities. The workshop is open to beginning and established researchers, students and postdoctoral fellows.

New this year: A focused workshop is available to a limited group of individuals based on availability.

Scholarships for scholars and junior faculty are available.

For further information and registration details, please visit https://matrix.secureserverdot.com/metabolomics_2016/home_live1.htm.

3-4 Nov 2016


Metabolite identification with the Q Exactive and LTQ Orbitrap

Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 2-day course will provide a hands-on approach to teach the latest techniques and tools available to perform metabolite identification. We will apply these tools on the Q Exactive and LTQ Orbitrap mass spectrometry family. The course is targeted towards students and researchers who are actively applying metabolomics.

The course will be led by experts in the field and include significant hands-on experience using both the Q Exactive and LTQ Orbitrap instruments to perform,
  • Data dependent acquisition
  • Data independent acquisition
  • MS/MS and MSn data acquisition
The course will finish with a session on the tips and tricks from the experts and an opportunity to ask questions.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/metabolite-identification.aspx or contact [email protected].

23-25 Nov 2016


Metabolomics with the Q Exactive

Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK

This 3-day 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 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 and using the Q Exactive mass spectrometer in your studies
  • Polar and non-polar sample preparation for profiling and targeted studies
  • 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 [email protected].

28 Nov to 2 Dec 2016


Workflow4Experimenters (W4E) Course 2016

Venue: ABiMS platform, Roscoff, France

Using Galaxy and the Workflow4metabolomics infrastructure to analyse metabolomics data

Overview: Pre-processing, statistical analysis, and annotation of metabolomics data is a complex task. The Workflow4metabolomics online infrastructure provides a user-friendly and high-performance environment with advanced computational modules for building, running, and sharing complete workflows for LC-MS, GC-MS, and NMR analysis (Giacomoni et al., 2015).

Goals:
During this one-week course, participants will learn how to use the W4M infrastructure to analyze their own dataset.Morning sessions will be dedicated to methodology and tools. Afternoon sessions will be devoted to tutoring.

Target audience: LC-MS, GC-MS and NMR experimenters (e.g., biologists, chemists)
Registration fee: 750 € (Academia) and 1400 € (Industry); Fees include accommodations but not travel expenses
Language: English
Pre-registration: Monday 30 May 2016 to Friday 15th July 2016 at Workflow4Experimenters course 2016
Contact: [email protected]

For further details, visit http://workflow4metabolomics.org/training/W4Mcourse2016.

8-10 Dec 2016


4th ICAN Conference Series on Precision Medicine in Cardiometabolic Diseases and Nutrition-Related Diseases

Save the date. Program and registration coming soon: http://www.ican-series.com/

12-13 Dec 2016

Quality Assurance and Quality Control in Metabolic Phenotyping

Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK


This 2-day course will provide a comprehensive overview of the application of quality assurance (QA) and quality control (QC) in metabolic phenotyping. The course is aimed at students and researchers who are actively working in the field. Experts who have developed the application of QA and QC procedures within the field will lead the course. It will include both theoretical and practical components to
  • Introduce QA and QC in metabolic phenotyping
  • The application of QA and QC in untargeted and targeted studies
  • Preparation of QCs and data acquisition
  • Data processing and reporting standards
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/quality-phenotyping.aspx or contact [email protected].

13-17 February 2017

EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists

Venue: European Bioinformatics Institute (EMBL-EBI) - Training Room 2 - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom


Application opens: Monday August 08 2016
Application deadline: Friday November 11 2016
Participation: Open application with selection
Contact: Maria Bacadare Goitia
Registration fee: £350

Overview
This course will provide an overview of key issues that affect metabolomics studies, handling datasets and procedures for the analysis of metabolomics data using bioinformatics tools. It will be delivered using a mixture of lectures, computer-based practical sessions and interactive discussions. The course will provide a platform for discussion of the key questions and challenges in the field of metabolomics, from study design to metabolite identification.

Audience
This course is aimed at PhD students, post-docs and researchers with at least one year’s experience in the field of metabolomics who are seeking to improve their skills in metabolomics data analysis. Participants ideally must have working experience using R (including a basic understanding of the syntax and ability to manipulate objects).

For more information, please visit https://www.ebi.ac.uk/training/events/2017/embo-practical-course-metabolomics-bioinformatics-life-scientists-3.

17-18 May 2017

Conference on Food and Nutritional Metabolomics for Health

Venue: The Ohio State University, Columbus, OH, USA


The purpose of this two-day event is to disseminate state-of-the-art knowledge in the field of food and nutritional metabolomics and foster networking and collaboration among colleagues and industry partners.

For more information please visit: https://discovery.osu.edu/focus-areas/foods-for-health/events/conference-2017.html.


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 ([email protected]).
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 ([email protected]). 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
Researcher Position
Centro Cardiologico Monzino Milan, Italy
8-Aug-2016
Centro Cardiologico Monzino
Postdoctoral Fellow in Metabolomics/Metabolite Identification
University of Missouri Metabolomics Center Columbia, USA
8-Aug-2016
University of Missouri
Metabolomics Research Specialist
St. Jude Children’s Research Hospital Memphis, Tennessee, USA 29-Jul-2016 Until filled
Metabolomics Society Jobs
Metabolomics Staff Scientist
St. Jude Children’s Research Hospital Memphis, Tennessee, USA 29-Jul-2016 Until filled Metabolomics Society Jobs
Director, Metabolite Profiling Core Facility
Whitehead Institute Cambridge, Massachusetts, USA 27-Jul-2016 31-Oct-2016 Metabolomics Society Jobs
Postdoctoral Fellow in Clinical Metabolomics
Concordia University Montreal, Canada
14-Jul-2016 31-Oct-2016 or until filled
Concordia University
Lecturer/Senior Lecturer in Systems Genomics
The University of Melbourne Parkville, Australia
30-June-2016 10-Aug-2016
The University of Melbourne
Senior Experimental Officer for Untargeted Analytics for SYNBIOCHEM Centre for Synthetic Biology
University of Manchester Manchester, UK
28-June-2016 10-Aug-2016
University of Manchester
Project Assistant Professor in Sustainable Food Security, Faculty of Life and Environmental Sciences
University of Tsukuba
Tsukuba, Ibaraki, Japan 24-June-2016 Until filled
Metabolomics Society Jobs
Two Postdoc positions Metabolomics/Bioinformatics
Leibniz Institute of Plant Biochemistry Halle, Germany
24-June-2016 31-Aug-2016
Leibniz Institute of Plant Biochemistry


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 ([email protected]). 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.


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 [email protected].

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