MetaboNews Masthead

MetaboNews
Issue 16 - December 2012

CONTENTS:


Online version of this newsletter:
http://www.metabonews.ca/Dec2012/MetaboNews_Dec2012.htm

Welcome to the sixteenth issue of MetaboNews, a monthly newsletter for the worldwide metabolomics community. In this month's issue, we feature a Software Spotlight article on metAlign 3.0, a handy metabolomics tool for preprocessing mass spectrometry data. As of the May 2012 issue, we introduced a new section called MetaboInterviews that features interviews with metabolomics experts from around the world. This issue includes an interview with Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism, European Bioinformatics Institute. This newsletter is being produced by The Metabolomics Innovation Centre (TMIC, http://www.metabolomicscentre.ca/), and is intended 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. We hope to provide enough useful content to keep you interested and informed and appreciate your feedback on how we can make this newsletter better (metabolomics.innovation@gmail.com).

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

 Software Spotlight

1) Software Spotlight

 Wageningen UR Logo

Data analysis strategy through metAlign eyes

Feature article contributed by Arjen Lommen, Senior Scientist Metabolomics, RIKILT - Institute of Food Safety, Wageningen UR, Netherlands

The bottleneck in metabolomics is still data analysis. The analytical instrumentation has evolved. Experiments are now highly automated and can output huge amounts of raw data in a relatively short time. It is easy to get swamped in data. Therefore in a full-cost calculation of a metabolomics experiment (presuming adequate samples are already present), data analysis costs will in general by far outweigh the measuring costs and also be the rate-determining factor in reporting results.

Obviously, the simplest way of cutting back on data-analysis time is to make sure that the data are of excellent quality. Badly designed or performed experiments are an expensive waste of time. But still, even with ideal experiments you need a lot of time to extract the signals, compare data and identify compounds.

Currently there are two ways of doing this. One way is a targeted analysis of a predefined set of compounds. The other is untargeted analysis, which entails comparison of all signals over different measurements, finding the interesting differences and then trying to do identification. Free (and probably better than commercial) packages that help in this are, for example, metAlign (http://pubs.acs.org/doi/abs/10.1021/ac900036d), XCMS, and mzMine. All three handle LCMS data with different mass precision. MetAlign, however, allows for the highest mass precision and also handles GCMS well. Most of the identification work is extra.


Scheme of metAlign and related software

Figure 1. Scheme of metAlign and related software.

While XCMS for instance has gone towards a web application (http://pubs.acs.org/doi/abs/10.1021/ac300698c), metAlign will remain a local application. MetAlign 3.0 (http://link.springer.com/article/10.1007%2Fs11306-011-0369-1) is now ten times faster on a modern consumer PC (around 1000 Euros) than 2 years ago; it now can use all the processors of a PC. It therefore will scale with future consumer PC developments, unlike most other programs which still use one processor even if more are available. Fumio Matsuda at RIKEN is now running metAlign routinely on twenty-four cores on a 64-bit W7 PC (ten minutes for 2.1 GB of raw GC-MS data). The point is that metAlign is a good and very fast alternative to web applications and avoids the necessity of uploading huge amounts of data. It is easy to increase computing power and speed at a low cost and still be independent. An important thing remains, that import is flexible (different machines and formats) and that export can easily be used and built on.

Identification is still a very big challenge if no reference compound or entry in a spectral library is present. Interesting signals from untargeted analysis and multivariate analysis therefore have to be filtered or clustered as much as possible before identification can proceed. Based on metAlign 2 platforms are available, i.e., http://prime.psc.riken.jp/lcms/ and http://link.springer.com/article/10.1007/s11306-011-0368-2?null. Because of the high costs of absolute de novo identification (preparative isolation and additional full study with NMR is required), it is extremely important to have high quality signal leads. Checking leads is therefore required. Important developments here are GCxGC-TOF-MS for improved separation and cleaner mass spectra and high-resolution UPLC-MS or perhaps high-resolution GC-TOF-MS for more accurate mass and therefore better elemental composition analysis. For that matter, even LCxLC-MS is not that far away anymore as well as coupling GCxGC or LCxLC to high-resolution mass spectrometers. Post sub-ppm enhancement of mass accuracy for LC-Orbitrap-MS may help http://www.springerlink.com/content/1h1714h537p574t5/.

The trouble with GCxGC-TOF-MS and LCxLC-TOF-MS is that the data sets are very large and information rich. This adds tremendously to the data analysis work load. This seems to add up to a situation in which the increase in separation is out-balanced by the extra data handling. If high-resolution MS is added to this technology the data size will not only grow beyond what we can handle on a 32-bit operating system, but data-analysis time will again increase. The paradox is that it is technologically possible, but the data handling is not or extremely tedious.

So, again there is a great need to come up with solutions for speeding up data handling. And as with metAlign 3.0 the obvious thing is to scale up by using more processors on a PC. We realized this with metAlignID for high-throughput targeted analysis in GCxGC-TOF-MS (http://www.sciencedirect.com/science/article/pii/S0021967312014689). This tool was developed for routine residue and contaminant analysis in GCxGC-TOF-MS. Within one hour it is now possible to convert, pre-process and search 30 GCxGC-TOF-MS files for 560 compounds on a standard quad core consumer PC.


redms viewer interface with two GCxGC-TOF-MS files loaded

Figure 2. The redms viewer interface with two GCxGC-TOF-MS files loaded. This program can read in up to a 100 files due to their small size.


A nice feature of all the pre-processing is that the size of data files is decreased ca. 100-fold. If storage of data profiles in databases or transfer through internet is an issue, this will certainly help. We recently have developed a beta-version of a viewer, which is capable of displaying these small data files. The viewer and examples of pre-processed GCxGC-TOF files and a sub-ppm corrected file are in this link: https://dl.dropbox.com/u/75158272/viewer.zip

These small pre-processed files can not only be easily stored, but can also easily be searched in a fast way (see given metAlignID and sub-ppm reference) and will not give memory problems. Furthermore, the same small files (but not GCxGC-TOF) can be used for alignment and untargeted strategies as well as unlimited targeted searches.


ppm error vs. mass of ten UHPLC Orbitrap in metAlign-processed data files

Figure 3. ppm error vs. mass of ten UHPLC Orbitrap in metAlign-processed data files (50000 resolution) after post-acquisition sub-ppm enhancement. 1535 experimental masses (including adducts) are obtained from a mix of 103 compounds at different concentrations. Outliers and errors in assignment are easily spotted.


ppm error vs. 10log (intensity) of 10 UHPLC Orbitrap

Figure 4. ppm error vs. 10log (intensity) of 10 UHPLC Orbitrap in metAlign-processed data files (50000 resolution) after post-acquisition sub-ppm enhancement. 1535 experimental masses (including adducts) are obtained from a mix of 103 compounds at different concentrations. Outliers and errors in assignment are easily spotted.


The current efforts based on metAlign output are going towards automation and combining sub-ppm enhancement of LC-Orbitrap-MS data (easier method and more routine), cleaning data for adducts, analysing isotope pattern information, elemental composition according to 7 golden rules (http://www.biomedcentral.com/1471-2105/8/105/), fragment searches and analysis and coupling to databases. Perhaps MS fragment prediction will also come into play. One important aspect will also be quality of mass precision, which is resolution but also intensity dependent. The second is the accuracy/correction of the calculated number of carbons, which is resolution-, mass-, and intensity-dependent in Orbitrap data. For both these quality aspects we will be obtaining distributional information over hundreds to thousands of mass peaks using very fast searching programs.

Besides untargeted approaches focusing on extracting important signals, we believe that highly-automated instrumental screening (large scale targeted analysis) like in residue and contaminant analysis will become very important in making metabolomics more cost-effective.

More information about MetAlign and Downloads: http://www.metalign.nl/



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

 MetaboInterview Icon

2) MetaboInterviews
MetaboInterviews, a new section as of May 2012, 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 Dr. Christoph Steinbeck, Head of Cheminformatics and Metabolism, European Bioinformatics Institute.


Christoph Steinbeck
Head of Cheminformatics and Metabolism, European Bioinformatics Institute, Hinxton, Cambridge, UK
Christoph Steinbeck 
Biography
Christoph Steinbeck received his diploma and doctoral degree in chemistry from the University of Bonn. After a postdoc at Tufts University in Boston, MA, USA, Dr. Steinbeck led the Structural Chem- and Bioinformatics Workgroup at the newly founded Max-Planck-Institute of Chemical Ecology in Jena, Germany. In the Fall of 2002, he moved to the Cologne University Bioinformatics Center (CUBIC) as head of the Research Group for Molecular Informatics. In December 2003, he received his "Habilitation" in Organic Chemistry from Friedrich-Schiller-University in Jena, Germany.

Dr. Steinbeck is editor-in-chief of the Journal of Cheminformatics, a director of the Metabolomics Society, lifetime member of the World Association of Theoretically Oriented Chemists (WATOC), past chairman of the Computers-Information-Chemistry (CIC) division of the German Chemical Society, and member of various editorial boards and committees.

Today, he is Head of Cheminformatics and Metabolism at the European Bioinformatics Institute (EBI) in Hinxton, Cambridge, UK. His group develops open chemistry databases for the biosciences, such as ChEBI, the dictionary and ontology of Chemical Entities of Biological Interest, the EnzymePortal, and the MetaboLights database, a repository and reference database for Metabolomics. They further develop a number of the leading open source software packages in chem- and bioinformatics, including the Chemistry Development Kit (CDK), a Java library for chem- and bioinformatics.

The Steinbeck group’s research is dedicated to natural products research, the elucidation of metabolomes by means of computer-assisted structure elucidation and other prediction methods, the reconstruction of metabolic networks, and algorithm development in cheminformatics.


Metabolomics Interview (MN, MetaboNews; CS, Christoph Steinbeck)

MN: How did you get involved in metabolomics?

CS: I started my career as an analytical chemist and NMR spectroscopist in natural products structure elucidation. I was then able to combine this with my old passion for computer science and started to develop software systems for computer-assisted structure elucidation of natural products. That turned me into a chem- and bioinformatician over the years and I now lead the cheminformatics and metabolism team at the European Bioinformatics Institute (EMBL-EBI). Metabolomics is a field uniquely combining my interest in molecular biology, analytical chemistry and chem- and bioinformatics and my central goal here at the EBI is now to help develop good databases and data analysis methods for metabolomics, and to help build the bridges into other areas of biomedical data.

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

CS: On the scientific side, metabolomics experiments give insights into many diverse aspects of phenotypes of organisms, covering areas such as nutrition, exercise, general lifestyle, disease, etc. Clearly, only a combination of metabolomic, other phenotypic, as well as genomic information will allow deeper insights in areas such as personalised medicine or simply the understanding of basic biology. That again requires extensive and rich data collections of geno- and phenotypes and that is where my involvement starts. Metabolomics is the youngest and least mature of the large omics areas and we only now see the emergence of national and global data management efforts.

MN: What key metabolomics initiatives are you pursuing at your research centre or institute? What is happening in your country in terms of metabolomics?

CS: My team at the EBI was able to secure funding for building MetaboLights (http://www.ebi.ac.uk/metabolights or just http://metabolights.org), the first open-access, cross-species, cross-application database for metabolomics experiments maintained by one of the large open-access data providers in molecular biology. The repository part of the database, which stores primary research and meta-data in metabolomics, is up and running and we now work on the reference layer, which will provide curated information about individual metabolites, their analytical chemistry, and biological roles. MetaboLights will engage in a network of data sharing with similar efforts elsewhere in Europe, the United States, Canada, and Asia.

As a second major initiative, complementing our work on MetaboLights, I'm coordinating the COSMOS consortium (http://cosmos-fp7.eu), a European-Commission-funded network of fourteen partners to work on the next wave of standards, workflows, and data management in metabolomics. We just had our launch meeting in Barcelona in the second week of October 2012. While the partners are all European, this is really a global effort and a significant portion of the funding goes into inviting the global stakeholders to our meetings.

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

CS: On a strategic level, I hope to help contribute to the network of global data resources that will eventually allow us to truly deliver on personalized medicine. One of my goals is to build resources that link metabolic phenotypes in humans to their general pheno- and genotypes. The government in the United Kingdom has just announced the creation of the National Phenome Centre, which will be a significant step towards capturing richer data about human phenotypes on a molecular level. As a first step, I want to develop MetaboLights into one of the the leading general purpose databases for metabolomics.

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

CS: I think its greatest strength is also probably its greatest weakness. Metabolomics data is incredibly rich in information. The time resolution is high, and metabolomics data are influenced by our genetic makeup, our microbiome, our lifestyle, our nutrition, drugs that we take and so on and so forth. We still have a significant way to go until we have enough data to really understand the complex composition of metabolomes, what influences it and how. Once that is done, and we are currently seeing in the genome sciences how long that can take (it was not enough to complete a handful of reference genomes to truly understand variation), metabolomics has the potential to become a routine diagnostic method which, in conjunction with the personal genome, will give unprecedented insights into the state of an organism.

MN: What do you see as the greatest barriers for metabolomics? What improvements, technological or otherwise, need to take place for metabolomics to really take off?

CS: I can only comment on this from a bioinformatician's standpoint. There is certainly still a lot to be learned through good old-fashioned science that digs into individual metabolomics experiments and comes up with a particular finding; but I also feel that we can learn a lot from "big data", large-scale omics studies on large cohorts, which lead to publicly accessible datasets, subsequently analysed by a large number of bioinformaticians worldwide. These types of big data projects in metabolomics, analogous to the 1000 genomes project and its followers, are yet to come and are, in terms of experimental design, certainly much more demanding.

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

CS: I guess we all feel that these are difficult times for science funding. On the other side, we are lucky that metabolomics is currently seeing a second wave of big funding, both in Europe as well as in the United States. The funding of a number of Regional Comprehensive Metabolomics Resource Cores (RCMRC) in the United States plus a national repository is very good news, and a number of countries in Europe continue to invest in National metabolomics infrastructures. I hope that metabolomics will benefit from being the youngest and least developed of the three large omics areas and will still be able to retrieve significant funding in the coming years.

 MN: What role can metabolomics standards play?

CS: Standards are absolutely crucial. They enable data sharing and analysis as well as the creation of free tools. This again lowers the barriers for worldwide access to this data. Other scientific areas have very nicely demonstrated the importance of the creation of open standards, and metabolomics is no exception. I very much hope that COSMOS, building on earlier metabolomics standards initiatives, will be instrumental toward this end.

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

CS: I would like to motivate researchers in metabolomics to engage in data deposition and data sharing. We will soon arrive at a situation where funders and publishers will demand data deposition in one of the large repositories such as MetaboLights. We understand that dataset acquisition is costly and that datasets are extremely valuable assets for researchers, which is why we will have embargo periods for deposited data that allow researchers to mine their own data as long as necessary. No individual lab, however, is able to understand and leverage the true potential of every dataset they are producing and it is just very important that as much of the high-quality metabolomics data produced worldwide is made publicly available so that others can mine the data and discover new knowledge.
Biomarker Beacon

3) Biomarker Beacon

Feature article contributed by Ian Forsythe, Editor, MetaboNews, Dept of Computing Science, University of Alberta, Edmonton, Canada

Metabolomics is an emerging field that is complementary to other omics sciences and that is gaining increasing interest across all disciplines. Because of metabolomics' unique advantages, it is now being applied in functional genomics, integrative and systems biology, pharmacogenomics, and biomarker discovery for drug development and therapy monitoring. More than 95% of today's biomarkers are small molecules or metabolites (MW <1500 Da), which can be used for disease testing, drug testing, toxic exposure testing, and food consumption tracking. While standard clinical assays are limited in the number and type of compounds that can be detected, metabolomics measures many more compounds. Since a single compound is not always the best biomarker (diagnostic, prognostic, or predictive), healthcare practitioners can use metabolomic information about multiple compounds to make better medical decisions. Global metabolic profiling is now being used to determine clinical biomarkers in assessing the pathophysiological health status of patients.

In the following two recent studies, metabolomic approaches were used to develop biomarker tools for the identification of biomarkers associated with ovarian cancer and response to neoadjuvant chemotherapy for breast cancer, respectively.
  1. Zhang T, Wu X, Ke C, Yin M, Li Z, Fan L, Zhang W, Zhang H, Zhao F, Zhou X, Lou G, Li K. Identification of potential biomarkers for ovarian cancer by urinary metabolomic profiling. J Proteome Res. 2012 Nov 19. [Epub ahead of print] [PMID: 23163809]

    In this paper, the research team sought to identify candidate biomarkers of epithelial ovarian cancer (EOC). The investigators utilized ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) to evaluate urine samples from 40 pre-operative EOC patients, 62 benign ovarian tumors (BOT) patients, and 54 healthy controls. Combining this approach with partial least-squares discriminant analysis or principal component analysis, they managed to obtain good separation between EOC vs. BOT and EOC vs. healthy controls. They identified 22 metabolites that were altered in the EOC patients including pseudouridine, N4-acetylcytidine, L-histidine, imidazol-5-yl-pyruvate, 3-indolelactic acid, 3'-sialyllactose, and 3-sialyl-N-acetyllactosamine. These identified metabolites could potentially be used to develop a convenient, non-invasive diagnostic test for ovarian cancer.
  1. Wei S, Liu L, Zhang J, Bowers J, Gowda GA, Seeger H, Fehm T, Neubauer HJ, Vogel U, Clare SE, Raftery D. Metabolomics approach for predicting response to neoadjuvant chemotherapy for breast cancer. Mol Oncol. 2012 Oct 25. pii: S1574-7891(12)00101-9. doi: 10.1016/j.molonc.2012.10.003. [Epub ahead of print] [PMID: 23142658]

    Not all women benefit from chemotherapy for breast cancer. In this study, the researchers aimed to identify metabolites that predict response to neoadjuvant chemotherapy for breast cancer. This group used nuclear magnetic resonance (NMR) spectroscopy, liquid chromatography-mass spectrometry (LC-MS), and statistical analysis methods to profile serum samples from patients with complete (n=8), partial (n=14), and no response (n=6) to chemotherapy. The research team narrowed their set of diagnostic biomarkers for response to chemotherapy for breast cancer down to four metabolites: three from NMR (threonine, isoleucine, glutamine) and one from LC-MS (linolenic acid). These newly identified biomarkers could be used to develop more personalized treatment regimens for patients with breast cancer.
Metabolomics Current Contents

4) Metabolomics Current Contents

Recently published papers in metabolomics:
MetaboNews

5) MetaboNews
16 Nov 2012
New whale shark study used metabolomics to help understand shark and ray health

New research from Georgia Aquarium and Georgia Institute of Technology provides evidence that a suite of techniques called "metabolomics" can be used to determine the health status of whale sharks (Rhincodon typus), the world's largest fish species. The study, led by Dr. Alistair Dove, Director of Research & Conservation at Georgia Aquarium and an adjunct professor at Georgia Tech, found that the major difference between healthy and unhealthy sharks was the concentration of homarine in their in serum—indicating that homarine is a useful biomarker of health status for the species.

The paper, "Biomarkers of whale shark health: a metabolomic approach", which is published in the journal PLOS ONE, is especially significant to the veterinary science community because the study documents the results of a rare opportunity to collect and analyze blood from whale sharks. The paper also comprises the only work yet carried out on biochemistry of the world's largest fish. "This research and its resulting findings are vitally important to ensuring Georgia Aquarium's and the scientific community's care, knowledge, and understanding of not only whale sharks, but similar species of sharks and rays," said Dr. Greg Bossart, Senior Vice President of Animal Health, Research & Conservation and Chief Veterinary Officer at Georgia Aquarium. "The publishing of this clinical research provides a greater opportunity for scientists and Zoological professionals to understand the Animals in our care and can be used to help wild populations, which puts us ahead of the curve in the integrated understanding of animal biology."

Source: Phys.Org
 
14 Nov 2012
New centre to bring metabolomics to the clinic

Imperial College London has set up a new research centre, called the Imperial Clinical Phenome Centre, that will apply the latest metabolomics technology to the real-time diagnosis of disease.

The new centre will look to develop novel technologies and methods for analysing the metabolites in bodily fluids such as blood and urine as a way to diagnose disease and determine its progression, as disease can have an important effect on metabolite composition. These novel technologies and methods with be based on liquid chromatography, capillary electrophoresis, mass spectrometry and NMR spectroscopy. However, they will be adapted for use in the clinic or operating theatre, providing physicians and surgeons with useful, real-time diagnostic information.

For example, Zoltan Takats, a reader in medical mass spectrometry at Imperial, is developing an 'intelligent knife' that can analyse the smoke produced when an electrically-heated surgical blade cuts into tissue during an operation. Research shows that the profile of the chemicals in the smoke can provide detailed information about the disease state of the tissue, such as whether it is cancerous, or otherwise diseased or non-viable.

"These analytical technologies are now very mature and are immensely powerful for telling us about someone's physical condition and disease state," said Jeremy Nicholson, head of the Department of Surgery and Cancer at Imperial. "Bringing them fully into the clinical setting will help doctors make a more informed diagnosis, choose the best treatment based on the individual characteristics of the patient, and monitor their progress more precisely. It is the dawn of a new age of 'precision medicine'."

The centre is being jointly funded by the National Institute for Health Research (NIHR), the Imperial Biomedical Research Centre and the analytical instrument companies Waters and Bruker. It will be equipped with three nuclear magnetic resonance spectrometers and six mass spectrometers, and will work closely with the existing Medical Research Council-NIHR Phenome Centre, which uses metabolomics data for population screening.

Several researchers involved with the new centre, including Nicholson and Takats, have written a review that appears in the latest edition of Nature highlighting the promise of metabolomics for disease diagnosis.

 
9 Nov 2012
Salk's $300M Campaign to Fuel Genomic Medicine, Replace Waning NIH Funds

The Salk Institute for Biological Sciences has launched a campaign to raise $300 million in private funding to support a new genomic medicine initiative, as well as new cancer, aging, and neuroscience programs.

Speaking at a press conference yesterday, Salk's Chair of the Board of Trustees, Irwin Jacobs, said the institute has already raised $150 million from private individuals and foundations during a quiet phase of campaign fundraising that began in 2009.

This six-year effort, the first such campaign in the institute's 53-year history, is aimed at bridging the gap left by flagging funding from the National Institutes of Health. Nine years ago, NIH funding made up two-thirds of the Salk's budget, but now it accounts for less than 50 percent, the institute said.

The Campaign for Salk will support research efforts across a wide range of the institute's missions, including Alzheimer's disease, Parkinson's, obesity and diabetes, spinal cord injuries, crop studies, and others.

The Genomic Medicine Initiative that Salk plans to fund will focus on research in three general areas: metabolism and physiology, cancer, and stem cells.

"This type of initiative is going to be transformative to the Salk — to the present as well as in the future," Ron Evans, a professor in the Salk Gene Expression Laboratory, said during the press briefing.

Evans said the initiative "is really underpinned by our interest in wanting to understand the nature of chronic disease and chronic illnesses ... [including] diabetes, heart disease, cancer, neurodegeneration."

"We will delve into the genome, and use cutting-edge, state-of-the-art technologies to try to understand the nature of stress, and the impact of stress on our genes, and how our bodies respond to the environment when things go wrong," Evans added.

The Genomic Medicine Initiative will create several new core facilities at Salk focused on genome sequencing, proteomics, chemical and systems biology, bioinformatics, and metabolomics, as well as a therapeutics development resource for pursuing new drug targets in preclinical and proof-of-principal trials.

The genome sequencing core facility will provide complete genomics solutions and services for use in next-generation projects involving de novo genome sequencing, targeted re-sequencing, metagenomics, transcriptome profiling, and epigenetic marker sequencing.

The bioinformatics core facility will house both genome sequencing and computing capacities, and it will host databases and biostatisticians for storing and analyzing genomic data.

The metabolomics core will provide mass spectrometers and chromatography tools and expertise for use in studies of lipids, metabolites, and metabolic pathways.

The metabolism and physiology studies will involve metabolomic profiling, studies of the aging genome, epigenetics studies of chronic inflammation and angiogenesis, and they will focus on important pathways and molecules that could be used in new treatments.

Salk's stem cell initiative will focus on identifying gene regulatory networks that control stem cell development and on determining how these genes can be manipulated to make stem cells useful as model systems or as treatments. Researchers also will perform genome sequencing-based studies of the role of DNA modification in reprogramming and generating stem cells.

Through the cancer initiative, Salk researchers will seek to define cancer genomes and the mutations involved in cancer development and disease progression — an effort that will produce knowledge that will be integrated into the stem cell and metabolomics initiatives.

"Our goals are to build on our current strengths and expand into new areas that have been opened up by the human genome sequence and by new imaging technologies," explained Tony Hunter, Salk professor of molecular and cell biology.

"We will continue to build more accurate models of human cancers, like glioblastoma and lung cancer, to study the process of metastasis, and test our ideas for new cancer drugs," Hunter said.

Source: GenomeWeb

Please note: If you know of any metabolomics news that we should feature in future issues of this newsletter, please email Ian Forsythe (metabolomics.innovation@gmail.com).

Metabolomics Events

6) Metabolomics Events
3-6 Dec 2012

Metabonomics Shortcourse 2012 - Metabolic Phenotyping in Disease Diagnosis & Personalised Health Care
Venue: Imperial College London, South Kensington Campus, London, UK

We are organising a metabolic phenotyping short course at Imperial College London. The course will be held on the 3rd-6th Dec, 2012.

Course Features:
  • Hands-on data analysis workshops
  • Panel discussions with experts from academia and industry
  • Lectures on topics including
    • NMR spectroscopic tools
    • Mass spectrometry approaches
    • QC strategies and study design
    • Data analysis and interpretation
Short Course Programme 2012 Dec [PDF]

Prices
  • Academics: £475
  • Industry: £975
  • Students: £295
Online Booking
  • Available NOW here.
Contact
For more information, please contact:
For more information, visit http://www1.imperial.ac.uk/surgeryandcancer/divisionofsurgery/biomol_med/education/short_courses/metabonomicsshortcourse/
27 Jan-1 Feb 2013

Gordon Research Conference on Plant Lipids: Structure, Metabolism & Function
Venue: Galveston, Texas, USA

The third Plant Lipids GRC is scheduled for Jan. 27 - Feb. 1, 2013 in Galveston, Texas. The program for the meeting has been assembled around the theme of “Emerging and advancing research areas in plant lipid metabolism and signaling”. Presentations will focus on elucidation of lipid signaling and lipid metabolic mechanisms, strategies to enhance production of economically important plant products, and new lipid imaging strategies. The GRC on Plant Lipids will bring together experts working to create and disseminate new research tools, discovering fundamental paradigms for lipid-mediated regulation of development, physiology, and stress responses and developing new understanding of lipid storage and homeostasis. We are anticipating much discussion of basic and applied research on plant lipids.

For the first time, a pre-conference Gordon Research Seminar (GRS) , January 26-27, 2013 at the same location, is being organized by investigators at the graduate student and postdoctoral levels for investigators at the graduate student and postdoctoral levels. This seminar is intended to provide (1) background that will enhance understanding of science presented at the subsequent conference, (2) opportunities to share research and to network with peers and experts in the field, and (3) peer and expert feedback and supportive suggestions about ongoing research.

For more information, visit http://www.metabolomicssociety.org/scientific_events and http://www.grc.org/programs.aspx?year=2013&program=plantlipid
25 Feb-1 Mar 2013

EMBO Practical Course on Metabolomics: Bioinformatics for Life Scientists
Venue: European Bioinformatics Institute, Cambridge, CB10 1SD, UK

Overview:
Is it right for me?
This course is aimed at advanced PhD students and post-doctoral researchers who are planning to improve their ability or learn new techniques in metabolomics and applying optimal data analysis methods using various bioinformatics tools in their research. The aim of this course is to familiarize the participants with advanced data analysis and data fusion methodologies and provide hands-on training on the latest analytical approaches and abilities to visualized and map metabolic changes on the relevant pathways.

What will I learn?
Lectures will give insight into how biological knowledge can be generated from metabolomics experiments and illustrate different ways of analyzing such data using variety of open source and freely available tools. Practicals will consist of computer exercises that will enable the participants to apply statistical methods and different analytical and data processing software to the analysis of metabolomics data under the guidance of the lecturers and teaching assistants. Familiarity with the technology such as data acquisition with NMR and MS is required. Ideally also some experience with R/Bioconductor (basic understanding of the syntax and ability to manipulate R objects) and the Unix/Linux operating system.

What will it cover?
The course covers optimal study design for metabolomics experiments, various data analysis methods, usage of online databases and resource as well theoretical a practical approaches on data fusion. Other topics will include: visualization of metabolomics data on metabolic pathways, methods of identification of unknown compounds, differential expression, data quality and reproducibility assessment using statistical analysis and optimal experimental study design.

For more information, visit http://www.ebi.ac.uk/training/course/embo-practical-course-metabolomics-bioinformatics-life-scientists.
8-10 Apr 2013

2nd International Conference and Exhibition on Metabolomics & Systems Biology
Venue: Hilton Suites Chicago/Northbrook, USA

OMICS Group invites you to attend the 2nd International Conference and Exhibition on Metabolomics & Systems Biology which is going to be held during April 08-10, 2013 at Hilton Suites Chicago/Northbrook, USA.

Metabolomics-2013 is a remarkable event which brings together a unique and International mix of large and medium pharmaceutical, biotech and diagnostics companies, leading universities and clinical research institutions making the conference a perfect platform to share experience, foster collaborations across industry and academia, and evaluate emerging technologies across the globe.

2nd International Conference and Exhibition on Metabolomics & Systems Biology will serve as a catalyst for the advances in the study of Metabolomics & Systems Biology by connecting scientists within and across disciplines at sessions and exhibition held at the venue, creates an environment conducive to information exchange, generation of new ideas, and acceleration of applications that benefit research in Metabolomics & Systems Biology.

For more information, visit http://omicsgroup.com/conferences/metabolomics-systems-biology-2013/.
14-19 Apr 2013

54th ENC Conference
Venue: Asilomar Conference Grounds, Pacific Grove, California, USA

Come immerse yourself in cutting-edge NMR science at the beautiful Asilomar conference grounds by the sea!
  • Jan 11, 2013: Deadline for abstracts to be considered for short talks and early decision.
  • Jan 11, 2013: Deadline for student travel and Ritchey Award materials
  • March 8, 2013: Deadline for late poster abstracts
  • March 15, 2013: Deadline for Asilomar lodging and advance conference registration
General Information: http://enc-conference.org/Conference/GeneralInformation/tabid/144/Default.aspx
Preliminary Program: http://www.enc-conference.org/ConferenceDetails/Program/tabid/63/Default.aspx

For more information, visit http://www.enc-conference.org/.
1-4 Jul 2013

9th Annual International Meeting of the Metabolomics Society
Venue: Glasgow, Scotland

We are delighted to announce that the 9th Annual International Conference of the Metabolomics Society will be held in Glasgow, Scotland 1st – 4th July 2013 at the award-winning Scottish Exhibition & Conference Centre (SECC). This appealing combination of an excellent city location and the best scientific research will guarantee this a memorable conference.

We expect this to be the 'must attend' meeting in 2013 for researchers from around the world, where the best speakers in the world and rising stars of the future will present their work in a mixture of plenary and parallel sessions. The Metabolomics Society came into being with the development of the Metabolomics as a discipline and as a result provides a focus for the most varied aspects of the subject ranging from microbes to man. As a result of this it brings together a diverse mixture of scientists from many disciplines, which produces very stimulating meetings.

One of the main aims of the conference will be to create a unique platform for young scientists. Come and listen and talk to the top experts in the field.  Find out about the latest exciting technologies that can advance your own research, but most of all come and enjoy Scotland's largest and most vibrant city and the beautiful countryside around it.

We look forward to welcoming you to Glasgow in 2013!

Dave Watson
Chair, Local Organising Committee
Metabolomics Glasgow 2013


For more information, visit http://www.metabolomics2013.org/.
13-17 Aug 2013

Metabolic Signaling & Disease: From Cell to Organism
Venue: Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA

Abstract Deadline: May 31, 2013

Organizers:
Daniel Kelly, Sanford-Burnham Medical Research Institute
Mitchell Lazar, University of Pennsylvania
Susanne Mandrup, University of Southern Denmark

We are pleased to announce the first Cold Spring Harbor meeting on Metabolic Signaling & Disease: From Cell to Organism which will begin on Tuesday evening, August 13 and end at noon on Saturday, August 17, 2013.

Metabolic regulation is at the intersection of many scientific fields, ranging from basic biochemistry and molecular biology to physiology, to the study of disease pathogenesis. Currently, a major challenge for these diverse fields is to define commonalities and differences in metabolic pathways and their regulation, and determine the role of these processes for physiology and disease states. This meeting will fill an important gap by bringing together outstanding researchers focused on diverse pathways, cell types, or diseases with a common theme of understanding how metabolism is regulated in physiology and disease states.

For more information, visit http://meetings.cshl.edu/meetings/2013/metab13.shtml.

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

7) 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 4 issues (8 weeks) unless the position is filled prior to that date.

Jobs Offered

Job Title Employer Location Date Posted Source
Sales Representative
 Human Metabolome Technologies
 Cambridge, MA, USA 20-Nov-2012 Human Metabolome Technologies
Metabolomics Data Analyst
 Stemina Biomarker Discovery
 Madison, WI, USA 10-Nov-2012 naturejobs.com
Experimental Officer in NMR Metabolite Analysis
 University of Birmingham Birmingham, UK
 9-Oct-2012 Metabolomics Society
Director of Laboratory Operations
 Metabolon
 Durham, NC, USA 29-Oct-2012 Metabolomics Society
Postdoctoral positions in Advanced Metabolomics
 NIH West Coast Metabolomics Center, UC Davis Davis, CA, USA
 22-Oct-2012 Metabolomics Society
Postdoctoral Position in Metabolomics
 Georgetown University Washington, DC, USA
 22-Oct-2012 Metabolomics Society
Biomarkers of Inflammation and Malnutrition Using Metabolomics - Open Rank Position
 The Pennsylvania State University University Park, PA, USA
 22-Oct-2012 Metabolomics Society
Assistant Professor of Biology
 University of Virginia
 Charlottesville, VA, USA
 27-Sep-2012 Metabolomics Society


Jobs Wanted

This section is intended for very highly qualified individuals (e.g., lab managers, professors, directors, executives with extensive experience) who are seeking employment in metabolomics. We encourage these individuals to submit their position requests to Ian Forsythe (metabolomics.innovation@gmail.com). Upon review, a limited number of job submissions will be selected for publication in the Jobs Wanted section.

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