MetaboNews -- October 2017
MetaboNews Masthead
Published in partnership between
TMIC and the Metabolomics Society
Issue 74 - October 2017

CONTENTS:


Online version of this newsletter:
 http://www.metabonews.ca/Oct2017/MetaboNews_Oct2017.htm
TMIC Services
TMIC Services

Welcome to the seventy-fourth 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 Consortium and Software Spotlight article titled "PhenoMeNal—An easy to use, scalable and cloud-based e-infrastructure to process and analyse metabolomics data".
This issue of MetaboNews is supported by:

Chenomx -- Metabolite Discovery & Measurement
Chenomx Inc.

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Metabolomics Society Logo

Metabolomics Society News

CONFERENCE CORNER 

Metabolomics 2018
The 14th Annual Conference of the Metabolomics Society will be held in Seattle, Washington, USA from the 25-28th June 2018. The Society’s annual conference consistently features the latest and greatest advances in metabolomics science, and, in 2018, we converge on Seattle, a world-class metropolis set within wild, beautiful, natural surroundings. Further details will be released regularly at http://metabolomics2018.org/.

Seattle, USA

Deadline extension for Expressions of Interest to host the 2020 Metabolomics Conference in Asia
The Metabolomics Society is calling for interested members in the Greater Asia region to express their interest in hosting the 2020 annual Metabolomics Society meeting (http://metabolomics2020.org/). Please send notice of your interest using this form by 15th October 2017.

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 is responsible 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 (metabolomics@askusa.com).

Appointment of new Conference Committee Chair
Many thanks on behalf of the entire Board of Directors to Darren Creek for all of his hard work and careful stewardship of the Conference Committee!  Darren helped the Society navigate several successful conferences, including the Dublin and Brisbane conferences.  We are also happy to welcome Sastia Putri as our new conference committee chair!   

Asian Oceania Metabolomics Forum
Researchers from the Asia Pacific region gathered for the first Asia Oceania Metabolomics Forum in the Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok Thailand. The forum was hosted by Assoc. Prof. Dr. Pravit Akarasereenont from the Faculty of Medicine Siriraj Hospital, Mahidol University. The delegates consisted of 25 participants from nine countries, namely Australia, New Zealand, Korea, Indonesia, Japan, Singapore, Malaysia, China and Thailand. Two board members of the Metabolomics Society, Dr. Darren Creek (Australia) and Dr. Sastia Prama Putri (Japan), were also in attendance. The objectives of the meeting were to exchange international knowledge and development in metabolomics research areas and to establish an international collaboration network among metabolomics researchers in the Asia Pacific Region. The research presented at the meeting highlighted some of the latest advances in metabolomics applications including topics specific to this region, providing novel insights regarding tropical diseases, traditional medicines, and local foods. The meeting concluded with an initial plan to build a communication network and sustain cooperation among the researchers in this region.

1st Asia Oceania Metabolomics Forum

MEMBERS CORNER

Election of Directors
We are pleased to announce that the following have been elected to the Board of Directors of the Metabolomics Society for 2017:
Dr Sastia Prama Putri, Osaka University (Japan) and Teknologi Bandung (Indonesia, re-elected for 2nd term) and Dr Horst Joachim Schirra, University of Queensland (Australia, newly elected). In addition, Dr Charmion Cruickshank-Quinn, University of Colorado Denver (USA) joins the Board as the newly elected chair of the Early Career Members Network.
 
We congratulate all the new directors on their election and look forward to working with them over their two-year term starting October 1, 2017. The Board would particularly like to thank all those who stood for election this year, and would encourage all members—whether on the Board or not—to engage with the Society’s mission, for example by joining a task group (see Board & Committees page of website).
 
We thank all those Directors who are leaving the Board for their service and commitment to the Society over the last few years: Dr Darren Creek and Dr Stacey Reinke. 
 
Thank you to all who took part in the election. As always, your active participation is important for the health and future of the Society!
 
Sincerely,
Julian Griffin (President), Krista Zanetti (Secretary) and Nichole Reisdorph (Treasurer) Metabolomics Society Officers
Board of Directors
Words from the Chair
This month I wanted to warn members of a number of conferences going under names very similar to our own international meeting, Metabolomics 2018. There is only one major international meeting that the Society is holding in 2018 and that is in Seattle. My reason for warning people is that there are a number of rather unscrupulous organizations that attempt to clone meeting titles and attract the unwary scientist to their meetings. We have had stories of presenters being alone in empty rooms for their sessions, so we really do not recommend these meetings! If you want to go to a meeting where world leaders in metabolomics will be present, block out the dates 25th-28th June, 2018 for Seattle; it’s never too early to consider what might go into the abstract for a talk or the very popular poster sessions. Alternatively, read below for some of the excellent regional meetings our affiliates put on. Finally, if you can’t find a meeting that quite fits your interests, why don’t you consider partnering with the society to deliver that meeting? We have funds to help put on a meeting, be it flying in a guest speaker or paying for student bursaries. Please speak to us if you think there’s a need for a particular workshop or symposium.


TASK GROUPS CORNER

Data Quality Task Group
The Data Quality Task Group (DQTG) is evaluating its planned activities for the next year. If you have any input or ideas about issues that the DQTG should address, please send them to dan.bearden@noaa.gov and rbeger@nctr.fda.gov.


INTERNATIONAL AFFILIATES CORNER

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

The French-speaking Fluxomics and Metabolomics Network will organize from October 2nd to October 5th a joint conference with French societies of Proteomics and Mass Spectrometry (SMMAP 2017) taking place in the Paris Area (Disneyland Paris).

More than 530 scientists have already registered for this event!

Ten international keynote speakers will give talks on plant metabolomics, fluxomics and cancer, lipidomics, bioinformatics, and society and science.

SMMAP 2017

https://smmap2017.sciencesconf.org/
 Spotlight

Consortium and Software Spotlight

 PhenoMeNal Logo

PhenoMeNal—An easy to use, scalable and cloud-based e-infrastructure to process and analyse metabolomics data

 Feature article contributed by Ralf J. M. Webera,b, Mark R. Vianta,b, James Bradburya, Philippe Rocca-Serrac, Pablo Morenod, Namrata Kaled, Claire O'Donovand, Christoph Steinbecke, and PhenoMeNal Consortium.

aSchool of Biosciences and bPhenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT, UK.
cUniversity of Oxford e-Research Centre, Department of Engineering Science, 7 Keble Road, OX1 3QG, Oxford, UK.
dEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
eFriedrich-Schiller-University, Jena, Germany.

PhenoMeNal (Phenome and Metabolome aNalysis, http://phenomenal-h2020.eu) project1,2, is a comprehensive, scalable, standardised, secure, and sustainable e-infrastructure that enables metabolomics researchers to process and analyse both small and large-scale metabolomics datasets. The e-infrastructure, funded by the European Commission's H2020 programme (grant agreement number: 654241), offers a solution to the challenges being faced by those handling, processing and analysing complex and large-scale metabolomics datasets. The computational services provided within PhenoMeNal enable researchers to further improve the understanding of the causes and mechanisms underlying health, healthy ageing and disease. While PhenoMeNal is primarily intended for human health applications, it can be applied across a wide range of metabolomics applications in biological, agricultural, environmental sciences.
We are excited to announce the first stable release of the PhenoMeNal e-infrastructure (Release Bucetin). Its open source App Library (https://portal.phenomenal-h2020.eu/app-library) showcases the PhenoMeNal service catalogue with a wide range of tools available for metabolomics data analysis. More information regarding the current and future releases can be found on the PhenoMeNal GitHub pages, including guidance on how to integrate other open source tools into the platform. The PhenoMeNal project is actively looking for user feedback and contributions from the community.

Screenshot of the project

Figure 1. Screenshot of the project website

Why do I need PhenoMeNal?

 The PhenoMeNal e-infrastructure helps to address a number of technical challenges researchers are confronted with when they process or analyse metabolomics data.
  1. Tools and workflows: One of the common challenges researchers face is installing complex scientific software and their dependencies and "connecting" those tools together, whilst dealing with data standards and conversions. This task typically requires fairly advanced expertise in bioinformatics, which is often not available within metabolomics research groups. PhenoMeNal packages an extensive collection of tools and workflows that are directly available within the PhenoMeNal Cloud Research Environment (see below) and preconfigured to work without any additional technological knowhow.
  2. Capacity to handle large datasets: The size of datasets collected by research centres, facilities, groups and industry is significantly growing, making moving data around a time-consuming and complex process. PhenoMeNal bypasses this paradigm, allowing users to bring the computational infrastructure to the source of the data.
  3. Scalable infrastructure: PhenoMeNal provides a scalable infrastructure which helps the user to avoid the complexity of setting up a (high performance) computer cluster and networks. In essence, users get their own cluster with the relevant tools and software preinstalled and ready to do metabolomics data processing and analysis. This is achieved by launching PhenoMeNal on-demand on either a local compute cluster or a public cloud as provided, for example, by Amazon Web Services or Google Cloud Platform.
  4. FAIR capable: The PhenoMeNal infrastructure is also concerned with ensuring proper data reuse while complying in Ethical Legal and Social Implications (ELSI) requirements specific to the field of clinical phenotyping. By embedding additional ELSI metadata profiles in Investigation/Study/Assay (ISA) metadata files and offering full provenance tracking, PhenoMeNal assists its users in preserving and enabling dataset dissemination, and archiving in institutional repositories. It therefore delivers a key component to the creation of an infrastructure supporting Findable, Accessible, Interoperable, and Re-usable (FAIR) data.3
Services provided by PhenoMeNal

PhenoMeNal’s Cloud Research Environment

The PhenoMeNal Cloud Research Environment (CRE) is a virtual computing infrastructure that can be installed on demand by anyone who has access to a cloud computing provider. This means that after installing our CRE in a cloud, the user has access to a small cluster with many metabolomics data analysis tools and workflows.
The main workflow system in PhenoMeNal is Galaxy, which comes with a user-friendly Graphical User Interface (GUI) for workflow authoring and execution of tools and workflows. Galaxy has emerged as one of the leading open source workflow platforms in Metabolomics and other fields of life sciences.4,5,6
The PhenoMeNal Galaxy instance operates within a CRE, which allows users to run tools in an interoperable and scalable manner. It is designed as a computational architecture with services being implemented as virtual machines (i.e., emulation of multiple computer systems) and tools as Docker containers (i.e., lightweight, stand-alone, executable package of a piece of software that includes everything needed to run it), including a scheduler (Kubernetes) to manage the jobs initiated by the Galaxy user interface.

A public PhenoMeNal CRE, with an open installation of Galaxy featuring all the PhenoMeNal tools, is available for users to try the infrastructure without any need for cloud provider access or credits. The PhenoMeNal Portal gives users the power to create their own PhenoMeNal CRE, getting the same tools as shown in the public CRE, in private and public clouds (e.g., Google Cloud Platform, Amazon Web Services) through a simple set of steps on a user friendly graphical interface. This means that users do not need any computational skills in cloud computing or bioinformatics to have their own PhenoMeNal CRE. They only need access or credits with a public or private cloud provider (among those supported).
For expert computational users, PhenoMeNal also provides documentation to deploy on local hardware (laptop, workstation, server) and academic computing centre (OpenStack; which will also be available soon through the Portal in a user friendly manner).

Interaction between the user with credits on a cloud provider

Figure 2. Interaction between the user with credits on a cloud provider, Amazon Web Services (AWS) in this example, the PhenoMeNal Cloud Research Environment (CRE) Portal and a user created CRE. The user requests the creation of a CRE to the Portal, which in turns creates the CRE on the cloud tenancy of the user. Once the CRE is active, the user can run metabolomics data processing and analysis.

PhenoMeNal App Library

The PhenoMeNal App Library provides a service catalogue of free tools available within the PhenoMeNal CRE. Currently the App Library includes a wide range of MS and NMR-based tools, including popular data-processing and analysis tools and packages such as XCMS, rNMR, CAMERA, BATMAN, MetFrag, univariate, and multivariate statistics, among many other tools in metabolomics. All these tools are available via the Galaxy workflow environment installed in the Cloud Research Environment (described above), and whenever possible rely on MSI or HuPO-PSI vetted data standards (ISA7,mzML8,nmrML9).

The current PhenoMeNal CRE Galaxy workflow environment (Release Bucetin) features:
 The PhenoMeNal consortium is currently working to make the Cloud Research Environment, which users can create on their own cloud accounts (which is exactly equivalent to the publicly available CRE), more resilient, fast and secure. More tools and workflows are being added and tested, including tools from the well tested Workflow4Metabolomics and Galaxy-M initiatives, with whom PhenoMeNal closely collaborates with. The deployment technology is also being tried currently for other use cases, such as proteomics, increasing the critical mass of active developers. Internal users are also using the infrastructure for real research and clinical data analysis problems, feeding back issues to be fixed that come up in the real day-to-day operation.

The consortium values the importance of providing an environment that users find easy to use. As such, a third round of usability testing (UX) will start soon to improve both the PhenoMeNal Portal and the PhenoMeNal Cloud Research Environment.

Screenshot of PhenoMeNal App Library

Figure 3. Screenshot of PhenoMeNal App Library accessed via PhenoMeNal portal: https://portal.phenomenal-h2020.eu/home. The App Library showcases all the available tools inside any created PhenoMeNal Cloud Research Environment.

User Support and Training

The PhenoMeNal online training page offers tutorials on PhenoMeNal Cloud Research Environment deployment, workflow creation and tools usage.

Screen shot of PhenoMeNal online user training

Figure 4. Screen shot of PhenoMeNal online user training: Online tutorials and demos for the different tools can be found at the PhenoMeNal YouTube channel, Wiki, and online training pages.

Now that PhenoMeNal e-Infrastructure is operational, the consortium has increased its efforts to establish links with the metabolomics and wider scientific communities to form a strong user base for the services offered, including face-to-face training activities and Workshops. Please, follow us on twitter (@PhnmlH2020) or Latest News section on our website to stay up-to-date with our activities. You can also contact us via email or use our Online Feedback Form.

Can I contribute to PhenoMeNal?

PhenoMeNal explicitly encourages feedback and contributions from the community. The cloud-based infrastructure for metabolomics and phenomics data processing and analysis has a global scope and is not limited to Europe. Simple user feedback can be provided via the PhenoMeNal help desk. Active participation in the development can be channelled through the PhenoMeNal GitHub pages (https://github.com/phnmnl). PhenoMeNal provides a generic process for any computational omics tools for deployment in cloud environments and aim to move beyond the scope of metabolomics and phenomics as soon as possible. We envision the current infrastructure to grow into a global, inclusive and meritocratic community of developers interested in scalable and cloud-based workflow for metabolomics, proteomics and genomics data analysis.

Upcoming Activities
 References
  1. http://phenomenal-h2020.eu/home/about/partners-3
  2. http://www.metabonews.ca/Jan2016/MetaboNews_Jan2016.htm#spotlight
  3. http://phenomenal-h2020.eu/home/2017/03/10/metabolomics-implementation-network-european-open-science-cloud-launched/
  4. Giacomoni F, Le Corguillé G, Monsoor M, et al.: Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics. Bioinformatics. 2015; 31(9): 1493–5. [PMID: 25527831]
  5. Davidson RL, Weber RJ, Liu H, et al.: Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. GigaScience. 2016; 5: 10. [PMID: 26913198]
  6. Weber RJ, Lawson TN, Salek RM, et al.: Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy. Metabolomics. 2017; 13(2): 12. [PMID: 28090198]
  7. "ISA tools | Standardizing metadata for scientific experiments." http://isa-tools.org/. Accessed 14 Sep. 2017.
  8. "mzML—a Community Standard for Mass Spectrometry Data." 17 Aug. 2010, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013463/. Accessed 14 Sep. 2017.
  9. "nmrML." http://nmrml.org/. Accessed 14 Sep. 2017.


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.
Metabolomics Current Contents

Metabolomics Current Contents

Recently published papers in metabolomics:

MetaboNews

MetaboNews 

15 Sep 2017
Introducing Metabolomics Association of North America and its Board of Directors

A new scientific society, the Metabolomics Association of North America (MANA), was launched in July 2017 after a successful call for members. The new society already has a membership of >190 active researchers in the field of metabolomics. The mission of MANA is to promote the growth and development of the field of metabolomics (broadly defined as the systems-scale study of biochemical intermediates in biological systems), particularly on the continent of North America. MANA will work to provide opportunities to develop collaborations among North American researchers to grow the metabolomics community, to create connections between academia and industry in the field of metabolomics, to provide opportunities for presentation of research achievements and for workshops, to promote the publication of meritorious research in the field and other activities that support the growth and excellence of metabolomics sciences.

We would like to take this opportunity to announce that, with the overwhelming support of its founding members, Metabolomics Association of North America (MANA) moved forward with its formal incorporation and elected its first board of directors this past summer. This came after much careful discussions with the Metabolomics Society (MS) over different models for establishing MANA including a chapter model, an affiliate model, and a subsidiary model of MS. In the end, it was decided that an initial independent path for MANA would be best while making every effort to connect with MS at various levels. MANA is committed to work with MS and with many other organizations to bring connections nationally and internationally. The seven elected board members are charged with the task of coordinating the first phase of growth of MANA. Each of board members will lead a function within MANA as noted below per the approved bylaws:
 
Dr. Mark Styczynski – President (three year term)
Dr. Oliver Fiehn – Treasurer (five year term)
Dr. Dan Jones – Secretary (four year term)
Dr. Maryam Goudarzi – Vice-President (two year term)
Dr. Susan Murch – Officer (three year term)
Dr. Arthur Edison – Officer (three year term)
Dr. Rima Kaddurah-Daouk – Officer (three year term)
 
In their first communication with members since the election, MANA board members reiterated that It is important for the association to represent all aspects of research and applications of metabolomics. MANA aims to have input from academia, industry, government, not-for-profit, and for-profit organizations, as well as instrument providers, to shape the path forward. The board members will work closely with the rest of the members and the community to set the stage for what they wish to achieve over the next five years. MANA board members seek to enable and empower many to lead different functions and they will be reaching out to the members of the association shortly.
 
For future updates and information, please see our new website: https://metabolomicsna.org/

Metabolomics Events

Metabolomics Events 

12-13 Oct 2017
Quality Assurance and Quality Control in Metabolomics
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This two-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.

Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/quality-phenotyping.aspx or contact bmtc@contacts.bham.ac.uk.
12-13 Oct 2017
Mayo Clinic Metabolomics Symposium
Venue: Leighton Auditorium, Siebens Building, Mayo Clinic, Rochester, Minnesota, USA
Register today for the Mayo Clinic Metabolomics Symposium October 12-13, 2017 – Siebens Building, Leighton Auditorium, Rochester, Minnesota.

Featured speakers include Mayo Clinic experts and:
  • Dr. David Wishart, University of Alberta, Canada
  • Dr. Daniel Raftery, University of Washington
  • Dr. Thomas Caskey, Baylor College of Medicine
  • Dr. David Pagliarini, University of Wisconsin, Madison
  • Dr. Clary Clish, Broad Institute of MIT and Harvard University
Metabolomics 2017 Symposium Agenda

Registration links:

Mayo Clinic Metabolomics Symposium  *You will be required to create a profile. Speakers and vendors do not need to register.

Mayo Clinic Optional Focused 4-hour Workshop Friday, afternoon, October 13 (limited availability, not open to Mayo Clinic Employees)

Cost:

$50 Course Registration – Mayo Clinic Employee
$150 Course Registration – Scholar/Junior Faculty
$275 Course Registration - Standard
$100 Optional Hands-on – Limited Attendee Workshop

Attendees are invited to display posters at the conference reception on Thursday evening. Awards for excellence will be given to first place ($300), second place ($200) and third place ($100).  Vendor opportunities are available and will be displayed during the entire workshop as well. Please contact Jacquelyn Gosse for vendor information.
 
Mayo Clinic is one of six federally funded Regional Comprehensive Metabolomics Resource Cores (RCMRC) to support medical research using metabolomics - the comprehensive and quantitative analysis of molecules (metabolites) that define the metabolic signatures of living systems. This symposium was made possible through grant number U24DK100469 from the National Institute of Diabetes and Digestive and Kidney Diseases and originates from the National Institutes of Health Director’s Common Fund.

For more information, contact Jacquelyn Gosse.
18-20 Oct 2017
Workshop in Environmental Omics, Integration and Modelling
Venue: CosmoCaixa, Barcelona, Spain
The aim of this workshop is to review the state-of-the-art and broaden the knowledge on high-throughput analytical methods, data integration and modelling in Environmental Omics and Toxicology.

The main workshop topics will be the following:
  • Transcriptomic and Genomic studies
  • Metabolomic and Lipidomic studies
  • Development of Chemometrics and Analytical Tools
  • Data Integration and Modelling
We are pleased to invite you to participate in this workshop that will promote knowledge exchange and creation of new relationships and future collaborations.

For more information, please visit http://wenvomics2017.info/.
24 Oct 2017
EMN Webinar “Using PhenoMeNal for your metabolomics data analysis on the cloud”
Venue: Online
For further details, please contact the PhenoMeNal team members at http://phenomenal-h2020.eu/home/help/.
30 Oct-3 Nov 2017
Hands-on targeted and untargeted LC-MS metabolomics
Venue: Aarhus University, Tjele, Denmark
PhD course at Department of Animal Science:
Hands-on targeted and untargeted LC-MS metabolomics with emphasis on measuring phytochemicals in plasma and urine

Level of course: Master, PhD and Postdoc

For further information and registration details, please visit http://anis.au.dk/uddannelse/hands-on-targeted-and-untargeted-lc-ms-metabolomics/.
6-8 Nov 2017
Metabolomics with the Q Exactive
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This three-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.

Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/q-exactive.aspx or contact bmtc@contacts.bham.ac.uk.
7-10 Nov 2017
Hands on Data Analysis for Metabolic Profiling
Venue: Imperial International Phenome Training Centre, Imperial College London, UK
Earlybird: £900
Standard: £1100

This 4-day course provides a comprehensive overview of data analysis for metabolic profiling studies with data acquired from NMR spectroscopy and Liquid Chromatography-Mass Spectrometry. It combines lectures and tutorial sessions to ensure a thorough understanding of the theory and practical applications.

Day 1: Introductory lectures and tutorials regarding the pre-processing of data acquired via NMR and LC-MS.

Day 2: Lectures and tutorials introducing exploratory chemometrics approaches, including PCA.

Day 3: Lectures and tutorials covering advanced chemometrics techniques including PLS and Orthogonal PLS.

Day 4: The next step - computational tools to aid metabolite identification and pathway analysis.

For more information, visit http://www.imperial.ac.uk/imperial-international-phenome-training-centre/courses/hands-on-data-analysis-for-metabolic-profiling/.
13-17 Nov 2017
Hands-on LC-MS for Metabolic Profiling
Venue: Imperial International Phenome Training Centre, Imperial College London, UK
 
Earlybird: £1750
Standard: £1950

This week long course covers how to perform a metabolic profiling experiment from start to finish. It will cover study design, sample preparation, the use of mass spectrometry for global profiling, targeted methodologies and data analysis.

Day 1: Introductory lectures in mass spectrometry and chromatography, study design and sample preparation, followed by preparation of biological samples for analysis on subsequent days.

Days 2 and 3: Analysis of biofluids through global profiling and targeted analyses; an introductory session to liquid chromatography, followed by sessions on each of the newest QToF and TQ instrumentation. Instrument set up, method development and acquisition will be covered. We have set a maximum of 3 attendees per instrument allowing for hands-on participation by all.  Day 3 finishes with introduction to data analysis.

Day 4: Data analysis workshops where attendees will process the data acquired from the previous days, mixed with further statistics lectures, allowing for development of interpretation skills.

Day 5: Application lectures, tips, tricks and troubleshooting, optional trip to the MRC-NIHR National Phenome Centre.

For further information, please visit http://www.imperial.ac.uk/imperial-international-phenome-training-centre/courses/hands-on-lc-ms-for-metabolic-profiling/.
20-27 Nov 2017
2nd International Electronic Conference of Metabolomics (IECM-2)
Venue: Held online

Building in the success of the 1st International Electronic Conference of Metabolomics (IECM-1) in 2016, Metabolites (ISSN 2218-1989), a peer-reviewed, scientific journal, edited by MDPI AG, is proud to be the organizer and sponsor of the second International Electronic Conference on Metabolomics. Contributions dealing with any discipline promoting metabolism and metabolomics will be welcomed.

The conference will be held online (http://sciforum.net/conference/iecm-2) from 20–27 November 2017, enabling you to present your latest research to the scientific community and to have the opportunity to participate in fruitful exchanges of information with academic and industrial groups from all over the world. It is absolutely free of charge to participate as an author or a visitor; all you need to do is create an account on the home page. After the event, proceedings from the conference (abstracts) will be published in the online open access journal, Proceedings.

On behalf of our active scientific committee and dynamic editorial staff, we warmly invite you to join us at the second International Electronic Conference on Metabolomics and we look forward to posting your contribution.

Sincerely yours,

A/Prof Peter J Meikle

Chair of the 2nd International Electronic Conference on Metabolomics
Editor-in-Chief of Metabolites (ISSN 2218-1989)
NHMRC Senior Research Fellow
Program Head, Metabolism
Head, Metabolomics Laboratory
Baker IDI Heart and Diabetes Institute
75 Commercial Road, Melbourne VIC 3004
E-Mail: peter.meikle@bakeridi.edu.au
Website: www.bakeridi.edu.au

For further information, please visit http://sciforum.net/conference/iecm-2.
1 Dec 2017
Introduction to Metabolomics for the Clinical Scientist
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This one-day course in partnership with the Phenome Centre Birmingham will provide clinicians with an overview of the metabolomics pipeline, highlighting the benefits of the technique to the medical field. The course will provide an:
  • Introduction to experimental design and sample collection
  • An overview of both the analytical and computational methods applied in the field
  • Case studies and panel discussions with the experts
Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registrations details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/introduction-metabolomics.aspx or contact bmtc@contacts.bham.ac.uk.
6-8 Dec 2017
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
Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/sample-analysis.aspx or contact bmtc@contacts.bham.ac.uk.
11-13 Dec 2017
MetaboMeeting 2017
Venue: University of Birmingham, UK
Make plans to attend the 10th successful MetaboMeeting conference. The meeting will bring together research scientists and practitioners from all areas of application and development of metabolic profiling, covering a wide range of experience from early career scientists to experts from throughout the international metabolomics field. MetaboMeeting 2017 continues to highlight the work of its attendees through both oral platform presentation and poster sessions.
The deadline for oral presentation abstracts is 15th July 2017.
The deadline for poster abstracts is 1st October 2017.

For further information, visit http://metabomeeting2017.thempf.org/.
14 Dec 2017
Free Practical Course - PhenoMeNal e-infrastructure: taking metabolomics data processing and analysis to the cloud
Venue: University of Birmingham, UK
No registration cost. Register here.
14-15 Dec 2017
Metabolite identification with the Q Exactive and LTQ Orbitrap
Venue: Birmingham Metabolomics Training Centre, School of Biosciences, University of Birmingham, Birmingham, UK
This two-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.

Bursaries are now available for PhD students funded by the BBSRC, MRC, or NERC.

For further information and registration details, please visit http://www.birmingham.ac.uk/facilities/metabolomics-training-centre/courses/metabolite-identification.aspx or contact bmtc@contacts.bham.ac.uk.
Late 2017
(To be confirmed)
Metabolic Phenotyping in Disease Diagnosis and Personalised Health Care
Venue: Imperial International Phenome Training Centre, Imperial College London, UK

Students: £500
Academic: £800
Industry: £1150

A lecture based course detailing an overview of metabolic phenotyping including the use of NMR spectroscopy and Mass Spectrometry, with insights from the experts at Imperial College and collaborators from all over the world. Lectures will cover data acquisition and analysis with some advanced statistical workshops for more hands-on participation for attendees. There will also be examples of real life applications from the research at Imperial College and their collaborators.

Day 1: Registration followed by session 1 which will cover an analytical technology (either NMR or MS) for metabolic profiling. A laboratory tour of the facilities will follow.

Day 2: Session 2 will cover the alternative analytical technique (NMR / MS) and will be followed by session 3 which will introduce the theory to statistical analysis.

Day 3: Session 4 covers more advanced chemometrics, such as OPLS and O2PLS and includes hands-on workshops. Session 5 will introduce metabolite identification in both NMR and MS and cover some tips and tricks to avoid common pitfalls.

Day 4: The final day will cover some of the real life applications of NMR and MS for metabolic phenotyping.

For further information, please visit http://www.imperial.ac.uk/imperial-international-phenome-training-centre/courses/metabolic-phenotyping-in-disease-diagnosis-and-personalised-health-care/.
8 Jan 2018
Metabolomics in Life Sciences
Learn about metabolomics principles and their applications in life sciences
Venue: Osaka University

About this course
This course is an introduction to metabolomics principles and their applications in various fields of life sciences.

We will provide a summary of all steps in metabolomics research; from experimental design, sample preparation, analytical procedures, to data analysis. The course also provides case studies of various kinds of research samples to attract students that are not familiar with metabolomics, providing them enough explanation to utilize metabolomics technology for their respective research fields.

Several examples of metabolomics applications will be introduced throughout the lectures. These include examples within food science and technology, metabolic engineering, basic biology, introduction to imaging mass spectrometry, and application in medical science.

No previous knowledge on metabolomics is needed but we recommend that students have an undergraduate-level understanding of Biochemistry, Analytical Chemistry, and Biostatistics, and that they learn about basic principles of multivariable analysis prior to taking this course.

For further information, please visit https://www.edx.org/course/metabolomics-life-sciences-osakaux-metab101x.
5-9 Feb 2018
EMBO Practical Course on Metabolomics Bioinformatics for Life Scientists
Venue: European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, UK

Application opens: Friday August 04 2017
Application deadline: Friday November 03 2017
Participation: Open application with selection
Contact: Emily Rees
Registration fee: £350 including accommodation & food
Apply now

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 to two years of 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 further information, please visit https://www.ebi.ac.uk/training/events/2018/embo-practical-course-metabolomics-bioinformatics-life-scientists-4.

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
Head of Business Development & Sales North America
 BIOCRATES Life Sciences AG
 Innsbruck, Austria 27-Sep-2017   BIOCRATES Life Sciences AG
Business Development Manager Pharma North America
 BIOCRATES Life Sciences AG Innsbruck, Austria 27-Sep-2017   BIOCRATES Life Sciences AG
Regional Business Development Manager North America BIOCRATES Life Sciences AG Innsbruck, Austria 27-Sep-2017
BIOCRATES Life Sciences AG
Postdoctoral Researcher Fellowship Gunma University Initiative for Advanced Research Gunma, Japan 24-Sep-2017 31-Oct-2017
 Karolinska Institutet
Faculty position in Biological Mass Spectrometry Michigan State University East Lansing, USA 20-Sep-2017 Until filled
 Michigan State University
Assistant Professor of Analytical Chemistry University of Florida Gainesville, USA 5-Sep-2017 25-Oct-2017
 University of Florida


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.

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