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.