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.