Job Vacancy: PhD position Bioinformatics / Metabolomics

The Leibniz Institute of Plant Biochemistry (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 (PhD student Bioinformatics / Metabolomics).

in the context of the Leibniz project „DiSeMiNation“ on mangrove systems to contribute to global conservation. The focus of the position will be to analyse mass spectrometry data on the biotic composition of mangrove systems, adapt methods for creation of current and historic metabolite profiles from sediment samples and to adapt methods for metabolite annotation to Pyrolysis GC/MS data.

You should hold a 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 would be an advantage.

The position is limited to 3 years, and available from April 1st, 2017. Payment is according to local regulations TV-L. Further information is available from the IPB job opportunities page .

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

CASMI published first challenges

In the Critical Assessment of Small Molecule Identification (CASMI) contest we are publishing a set of LC/MS and GC/MS spectra on www.casmi-contest.org, and call the community to identify the underlying compounds. In different categories we ask for the molecular formula and/or for the molecular structure.

We now have deposited a first round of challenge spectra, and will add more over the course of the next weeks. If you are doing computational mass spectrometry, or you are an expert in spectral interpretation, or just started to learn mass spectrometry: these spectra help to "show off" your skills.

Early in 2013, we will reveal the compounds, evaluate the submissions and call for papers in a special issue of the journal Metabolites, where the participants describe their efforts.

If you have any questions, don't hesitate to contact us at casmi2012(at)ipb-halle.de, or join the mailing lists.

Post-doctoral Scientist

Within the EU Project COSMOS, 14 European project partners develop data standards and workflows for metabolomics, which are a requirement for efficient collaboration and data exchange. At the IPB we are leading the work package “Standards Development”.

You have a degree in Bioinformatics, Computer Science or a related discipline, and a PhD in Life Sciences, Data Standards, or e-Infrastructures. You are excited to work in the growing field of Open Data, and you want to specify the description of experimental (meta-)data with existing and new ontologies, and use semantic web technology to retrieve and analyse the data in the emerging e-Infrastructure for Metabolomics data.

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. For further details please check out our website.

Creating a table of molecules with R

We are using the excellent rCDK package by Rajarshi Guha,
to quickly summarize or work with chemical structures in R.

One thing that always irritated me was that the view.molecule.2d() function opened a separate Java window to display a table of molecule renderings. Because the Java window has no connection with R, this does not allow to use the rich functionality of the R graphics capabilities, while  view.image.2d() , which can return something I can use in conjunction with rasterImage(), handles only a single molecule but not lists.

library(rcdk)

# load demo data
data(bpdata)
mols <- parse.smiles(bpdata$SMILES)

# Set 10x10 molecules per page, and remove border area
par(mfrow=c(10,10))
par(mai=c(0,0,0,0)+0.1)

# Create and plot images
imgs <- lapply(mols, view.image.2d)
sapply (imgs, function(img) {plot.new(); rasterImage(img, 0,0,1,1)})

As a bonus, you can also output to a PDF or PNG file, and even set the page area for PDF to use a full print page.

Enjoy!

Workshop on Tools for Metabolomics Data Processing, Data Analysis and Pathway Analysis at metabolomics2012.org

The workshop will be held on June 25, the first day of the Metabolomics 2012 conference in Washington, D.C., and provides an opportunity to introduce and to present software and development frameworks for all steps in metabolomic data analysis. The workshop includes the option of live software demonstrations to academic and commercial participants.

The topics include, but are not limited to, data pre-processing of NMR and MS data, spectral alignment of multiple measurements, both library-based and de-novo metabolite identification, data normalization and statistical analysis, pathway mapping, pathway reconstruction and last but not least data integration between multiple studies or between data of multi-omics experiments.

Please submit your abstract through the “Abstract Submission” at www.metabolomics2012.org. Don’t forget to mention whether your presentation will include a live demonstration.

Open position at the IPB Halle in computational mass spectrometry

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 algorithms for the identification of metabolites from mass spectrometry data, together with colleagues from both bio- and chemoinformatics. The methods will be available as user-friendly web applications, but also as part of universal metabolomics workflows on the IPB compute cluster.

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 Java, the statistics framework R, and have worked with relational databases. Knowledge in metabolomics or biochemistry would be an advantage. The position is 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 http://www.ipb-halle.de/en/, for inquires please contact Dr. Steffen Neumann, Telephone: +49 345 5582-1470, e-Mail: sneumann@ipb-halle.de

Researcher Bioinformatics for Metabolomics @ PRI/Wageningen, The Netherlands

The Applied Bioinformatics group at Plant Research International is looking for a researcher bioinformatics for metabolomics:

Job description: A position for a researcher is available in the Bioinformatics group at Plant Research International (PRI) to participate as scientific programmer in the development of the BioAssist metabolomics support platform. Within PRI this development is central to various projects related to bioinformatics for metabolomics and the candidate is expected to take a proactive and coordinating role in this area. Specific tasks will include the implementation and further development of the data warehouse Metware and development of standards and webservices for existing metabolomics software tools and their implementation in the workflow management system Taverna.

Profile: We are looking for a communicative team player with:



• A recent PhD in chemoinformatics, chemometrics, bioinformatic or related area


• Advanced programming and database development skills (fluent in Java, SQL, and preferably in C++, Perl, or Python)


• Knowledge of BioMoby, tomcat, SQL, JSF, bioMART and semantic web (e.g. RDF, OWL)


• Basic knowledge of mass spectrometry and metabolomics technology is essential


• The drive, ambition and skills to acquire a leading role in the development of a metabolomics data analysis platform within PRI and to initiate new projects in this field

Further info can be found in here: 08.Biosc.04.

Job: Postdoctoral Researcher at EBI, Hinxton/UK

NatureJobs reports:

Research into and development of methods for computer-assisted structure elucidation of biological metabolites based on mass spectrometry and NMR data. For this position in the Steinbeck group, the postdoctoral researchers need to hold a PhD degree in chemistry, biology, bioinformatics, computer science or a related field. They have good knowledge of standard software development and the ability to use, modify and adapt others code if necessary. Applicants should have proven experience with programming in Java as well as chemoinformatics and bioinformatics software development. The successful applicant must work on their own initiative, but work as part of a wider team and collaborate with colleagues, internally and externally where required. The position is based in the Chemoinformatics and Metabolism (Steinbeck Research Group). It is initially termed for 12 months, extension may be possible.

Paper: Genetic algorithm based two-mode clustering of metabolomics data

Jos Hageman (UvA, now Biometris in Wageningen) published the paper Genetic algorithm based two-mode clustering of metabolomics data (DOI:10.1007/s11306-008-0105-7):

In this paper we introduce a two-mode clustering method based on a genetic algorithm that uses a criterion that searches for homogeneous clusters. Furthermore we introduce a cluster stability criterion to validate the clusters and we provide an extended knee plot to select the optimal number of clusters in both experimental and metabolite modes. The genetic algorithm-based two-mode clustering gave biological relevant results when it was applied to two real life metabolomics data sets.

If you are working in NL and you would like to see you paper listed in this blog too, please send me an email.

Paper: Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics

Velitchka Mihaleva et al. (Plant Research International/Wageningen University) just published a paper in Metabolomics: Accurate mass error correction in liquid chromatography time-of-flight mass spectrometry based metabolomics (doi:10.1007/s11306-008-0108-4):

Experimental LC/TOF-MS platforms equipped with a time-to-digital converter (TDC) give the best mass estimate for those mass signals with an intensity similar to that of the lock-mass used for internal calibration. However, they systematically underestimate the mass obtained at higher signal intensity and overestimate it at low signal intensities compared to that of the lock-mass. To compensate for these effects, specific tools are required for correction and automation of accurate mass calculations from LC/MS signals. Here, we present a computational procedure for the derivation of an intensity-dependent mass correction function.

If you are working in NL and you would like to see you paper listed in this blog too, please send me an email.

Sweden is looking for metabolomics post-docs too

It seems that NL is not the only country in need of qualified metabolomics post-docs. This position in Stockholm (found via NatureJobs) requires a bench analytical chemist :

You should have a Ph.D. in mass spectrometry and/or bioanalytical chemistry, with experience in small molecule mass spectrometry and biological sample preparation techniques. Prior experience in lipid analysis and bioinformatics is strongly preferred.

Post-doc and PhD vacancies in Netherlands Metabolomics Centre

A few new vacancies appeared on the Netherlands Metabolomics Centre website:

The mission of NMC is to take the lead in the creation of a world-class metabolomics knowledge infrastructure to improve personal health. The NMC has recently been founded by a subsidy from the Netherlands Genomics Initiative, and will have a budget of 50 M€ for the period from 2008-2012. The researchers will have a high degree of collaboration with each other, and will conduct their research at different places.

The NMC invites applications for the following positions:
• Post-doctoral Research Fellows
• PhD students

In particular, there seems to be a shortage on scientific programmers. Drop me line of you can program, and looking for a job in metabolomics.

Chemical Systems Biology Meeting, Philidelphia, August 17-21, 2008

Rajarshi Guha wrote on the Chemical Computation List:

Chemical Systems Biology: Integrating Chemistry and Biology for
Network Models
236th ACS National Meeting
Philadelphia, August 17-21, 2008
CINF Division
----------------------------------

Dear Colleagues,
Josef Scheiber and I are organizing a symposium focusing on the use of biological networks and their models for the purposes of drug discovery. Traditionally, such models have been applied to large scale biological systems such as protein-protein interaction networks. Recently, there has been increased interest in the study of these networks to gain a global understanding of biological systems and the impact of small molecules to them in the context of drug discovery. As a result, it has become important that such models integrate small molecules with the usual biological systems. By leveraging the power of established cheminformatics methods along with the network models we get closer to the goal of "chemical systems biology", the full integration of chemical and biological data in the development of better in silico-methods for drug discovery.

We invite you to submit contributions that address various computational aspects of this approach including, but not limited to: network construction, integration of multiple data sources in network models, drug repurposing, target identification, polypharmacology, incorporation of chemical structure/similarity into network models, bridging chemical structure and biological structure based network models. Case studies where computational network models have provided experimental insight are also welcome.

We would also like to point out that sponsorship opportunities are available.

Please use the on-line abstract submission system (OASYS) for submitting your abstract (http://oasys.acs.org/oasys.htm). OASYS will be accepting abstracts between 28th January and 24th March, 2008.

Please contact Josef or myself if you have any questions.

Thanks,

Josef Scheiber Rajarshi Guha
Novartis Indiana University

The CINF division of the American Chemical Society is oriented at chemical information (molecular really, so including metabolites) and includes chemoinformatics, and increasingly bioinformatics.