Computational mass spectrometry and metabolomics at the metabolomics conference 2016 in Dublin

Dear CompMS community,

one of the big events this year will be the annual conference of the international Metabolomics society in Dublin (27.-30.6.2016, see http://metabolomics2016.org/), where around 1000 people can be expected to attend. Last year we coordinated several proposals for workshops and sessions, and we are delighted that ALL THREE proposed sessions got accepted! Among the other scientific topics like the session on “Advances in Statistical Tools”, we expect to have these sessions related to #CompMS and computational metabolomics:

• New Approaches for Identification of Metabolites applying MS and NMR (Session team: Witting/Dunn)
• Network and Pathway Analysis for Metabolomics (Session team: Willighagen/Jourdan)
• Computational Mass Spectrometry (Session team: Neumann/Böcker)

There will also be these workshops :

• Computational Workflows and Workflow Engines (Workshop lead: Christoph Steinbeck)
• Workshop On Data Sharing and Standardisation (Workshop team: Reza Salek et al.)
• metaRbolomics: The R toolbox for Metabolomics (Workshop team: Stanstrup/Neumann)

Of course, the official call for participation and papers by the conference organisers will follow in the next weeks, but you could already think about your contribution to make the workshops and sessions a whopping success!


See you at #metabolomics2016,
Yours,
the session and workshop organisers !

Job Vacancy: Bioinformatician (Metabolomics) at the IPB Halle

The IPB is an international research institute located on the Weinberg-campus in Halle and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry.

The research group “Bioinformatics and Mass Spectrometry” in the department of Stress- and Developmental Biology at the Leibniz-Institute of Plant Biochemistry (IPB) is seeking applications by highly motivated candidates for a position as research assistant. In the context of the EU project  PhenoMeNal you will work on the integration of existing computational metabolomics methods into efficient and versatile workflows, and their execution on local and European grid infrastructures.

You should hold a diploma or masters degree in bioinformatics or computer science, with experience in algorithm and software engineering and statistics. You are able to program in the statistics framework R, and have worked in Java or C/C++. Knowledge in metabolomics or Grid-/Cloud computing would be an advantage. The position is limited to 3 years, and available from 01.10.2015.

Payment is according to local regulations TV-L.

Further information is available from the institute's homepage http://www.ipb-halle.de/en/, for inquires please contact Dr. Steffen Neumann, telephone: +49 345 5582-1470, e-Mail: sneumann@ipb-halle.de .

 

Please send your application (cover letter addressing your research interests, CV, transcripts, and names/contacts of two references) quoting reference number 20/2015 until September 15th, 2015 to:

     Leibniz-Institut für Pflanzenbiochemie (IPB)
     Stiftung des öffentlichen Rechts
     AG Personalangelegenheiten
     Frau Kerstin Balkenhohl
     Weinberg 3
     06120 Halle (Saale)

or to bewerbungen@ipb-halle.de 

Using mzCloud if your computer does not run Microsoft Windows

www.mzcloud.org is a mass spectral database that assists analysts in identifying compounds in fields such as metabolomics, toxicology and environmental sciences. It has a rich Web-based interface, which is based on Microsoft Silverlight.
For the majority of users on Windows the required  SIlverlight plugin is only a click away, but for Mac and Linux Microsoft points to the Open Source Mono plugin, which is deprecated and may or may not be fully compatible to work with mzCloud.

I recently solved a similar problem at home, where the consumption of Amazon Prime video streaming has very strict preconditions with regard to your operating system, which were not met by our home theatre PC under Ubuntu Linux, despite strong demands by some family members.

So check out the documentation around Pipelight, https://launchpad.net/pipelight and http://ubuntuhandbook.org /index.php/2013/12/pipelight-silverlight-in-linux-ubuntu-ppa/ . In essence, Pipelight executes the Silverlight runtime under the wine emulator inside a Firefox plugin.

This sounds scary, but it not only allows to watch Amazon videos, but also to connect to mzCloud and start the web GUI.

Job Vacancy: Bioinformatician (Metabolomics) at the IPB Halle

The IPB is an international research institute located on the Weinberg-campus of the Martin-Luther-University Halle-Wittenberg and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry.

The research group “Bioinformatics and Mass Spectrometry” in the department of Stress- and Developmental Biology at the Leibniz-Institute of Plant Biochemistry (IPB) is seeking applications by highly motivated candidates for a position as research assistant. You will work on methods for metabolomics data analyses and data fusion, to discover relationships between metabolites and their biomedical effects.

You should hold a diploma or masters degree in bioinformatics or computer science, with experience in algorithm- and software engineering and statistics. You are able to program in the statistics framework R, and have worked in Java. Knowledge in metabolomics or analytical biochemistry would be an advantage. The position is limited to 3 years, and available immediately. Payment is according to local regulations TV-L.

Further information is available from the institute's homepage http://www.ipb-halle.de/en/, for inquires please contact Dr. Steffen Neumann, telephone: +49 345 5582-1470, e-Mail: sneumann@ipb-halle.de .

Please send your application (cover letter addressing your research interests, CV, transcripts, and names/contacts of two references) quoting reference number 6/2015 until April 27th, 2015 to:

     Leibniz-Institut für Pflanzenbiochemie (IPB)
     Stiftung des öffentlichen Rechts
     AG Personalangelegenheiten
     Frau Kerstin Balkenhohl
     Weinberg 3
     06120 Halle (Saale)

or to bewerbungen@ipb-halle.de 

Job Vacancy: Bioinformatician (Metabolomics) at the IPB Halle

The research group “bioinformatics and mass spectrometry” in the department of Stress- and Developmental Biology at the Leibniz-Institute of Plant Biochemistry (IPB) is seeking applications by highly motivated candidates for a position as Bioinformatician (Metabolomics).

You will work on methods and algorithms for the analysis and interpretation of metabolomics data from state-of-the-art mass spectrometers. You should hold a diploma or masters degree in bioinformatics or computer science, with experience in algorithm- and software engineering and statistics. You are able to program in the statistics framework R, and have worked C/C++. Knowledge in metabolomics or analytical biochemistry would be an advantage.

The position is limited to 3 years and available immediately. Payment is according to local regulations TV-L.

The IPB is an international research institute located on the Weinberg-campus of the Martin-Luther-University Halle-Wittenberg and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry.

Further information is available from the institute's homepage and in particular http://www.ipb-halle.de/en/career/job-vacancies/joboffer-detail/bioinformatikerin-metabomolics/

CASMI 2012 finished -- and CASMI 2013 has started !

Hi, The CASMI 2012 special issue in Metabolites is finally finished! Emma Schymanski and I will continue to present the results of CASMI 2012 at different occasions, e.g. the ASMS conference in Minneapolis (June 2013) and the upcoming Water Forum in Langenau in November this year.

The organisation of the contest and special issue was a lot of work, but also a lot of fun. We'd like to thank all of our participants and our advisory board, but also everyone who expressed interest or engaged us in discussions at meetings.

And CASMI keeps going: CASMI 2013 is currently being organised by a team of Japanese mass spectrometry experts headed by Prof. Nishioka, and the challenge data has already been opened up.

In addition to the CASMI specific mailing lists, the Metabolomics' society is also hosting the Metabolite Identification Interest group.

The small molecule analytical chemistry and computational mass spectrometry world is quite small, we're looking forward to bumping into you at some time in the future!

Call for Papers: CASMI proceedings

The special issue will contain a summary where Emma and Steffen give details about the challenge compounds, the evaluation measures and comment on the submissions.

But the main content will be your articles about your participation: we are really interested in descriptions of how you actually tackled the challenges, which steps were automagic and, if necessary, where manual intervention was required.

If your approach was published previously, please focus on what is relevant for the CASMI challenges, and improvements that have been made since the last publication. All articles will be peer-reviewed by at least two reviewers from the community. There is no actual page limit, but the reviews will check that the length is adequate.

We ask you to send us your intent to submit an article to the special issue (including a preliminary title and author list), before heading into the holiday season.

Note that there is an Early-Bird-Bonus: MDPI will waive the article processing charges if you send us a reply with your submission intent by the end of this year! For articles announced after 01.01.2013 it will be the regular 300 CHF charge for the Metabolites journal.

For more details on the special issue see the journal's pages at MDPI. Please visit the Instructions for Authors before submitting a manuscript. Manuscripts should be submitted through the online manuscript submission and editorial system.

Important Dates for the proceedings:
31.03.2013    Submission deadline for full papers in the journal Metabolites.
31.12.2012    Last day of early-bird article pre-registration