Our new overview article entitled “Current Challenges in Plant-Ecometabolomics” has just appeared in the International Journal of Molecular Sciences [tpcite key=”Peters:2018cv”]. As we explain in the abstract, “[t]he relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms.”
Postdoc: We are looking for a talented cheminformatician, bioinformatician or someone with comparable skills to work on the development cloud-based methods for computational metabolomics. The successful candidate will work closely with the H2020 e-infrastructure project PhenoMeNal, a European consortium of 14 partners. This position requires excellent skills in at least one modern, object-oriented programming language. A strong interest in metabolomics and cloud computing as well as the ability to work in a distributed team will be advantageous. The postdoc will also have the opportunity to participate in the day-to-day management of the group as well as in the organisation of seminars and practical courses for our students
The position requires a strong interest in metabolomics, molecular informatics and current IT technologies, programming skills a modern object oriented programming language and the ability to work in geographically distributed teams.
Please send applications in PDF format by email to christoph.steinbeck@uni-jena.de. We will accept applications until the position is filled.
Background information:
The Friedrich Schiller University Jena (FSU Jena), founded in 1558, is one of the oldest universities in Europe and a member in the COIMBRA group, a network of prestigious, traditional European universities. The University of Jena has a distinguished record of innovations and resulting educational strengths in  major fields such as optics, photonics and optical technologies, innovative materials and related technologies, dynamics of complex biological systems and humans in changing social environments. It has more than 18,000 students. The universityâs friendly and stimulating atmosphere and state-of-the-art facilities boost academic careers and enable excellence in learning, teaching and research. Assistance with proposing and inaugurating new research projects and with establishing public-private partnerships is considered a crucial point.
The Metabolomics Standards Initiative (MSI) guidelines were first published in 2007. These guidelines provided reporting standards for all stages of metabolomics analysis: experimental design, biological context, chemical analysis and data processing. Since 2012, a series of public metabolomics databases and repositories, which accept the deposition of metabolomic datasets, have arisen. In this study, the compliance of 399 public data sets, from four major metabolomics data repositories, to the biological context MSI reporting standards was evaluated. None of the reporting standards were complied with in every publicly available study, although adherence rates varied greatly, from 0 to 97%. The plant minimum reporting standards were the most complied with and the microbial and in vitro were the least. Our results indicate the need for reassessment and revision of the existing MSI reporting standards. Putty ISO download
Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the âFuture of metabolomics in ELIXIRâ was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community. The workshop established metabolite identification as the critical area, where a maximal impact of computational metabolomics and data management on other fields could be achieved. In particular, the existing four ELIXIR Use Cases, where the metabolomics community – both industry and academia – would benefit most, and which could be exhaustively mapped onto the current five ELIXIR Platforms were discussed. This opinion article is a call for support for a new ELIXIR metabolomics Use Case, which aligns with and complements the existing and planned ELIXIR Platforms and Use Cases.
PhD student Rachel Spicer, last woman standing in my research group in Cambridge, has just published her review on navigating freely-available software tools for metabolomics analysis. The review presents a comprehensive list of the most widely used freely available software and tools that are used primarily in metabolomics.
The Michael-Stifel Center in Jena promotes interdisciplinary research and teaching in the field of data-driven and simulation-based sciences.
For us, this is a great opportunity to interact with groups interested in all core areas in data-driven science, model-data-integration, simulation sciences and high-performance computing.
We have been co-organising the EMBO Course for Computational Metabolomics in Cambridge for the last four years. The next course has now been announced and is open for applications.
The course is usually heavily oversubscribed, but it is worth applying. One week of great fun with excellent teachers and students.
Date: Monday 5 - Friday 9 February 2018
Venue: European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom
Postdoc position and phd positions are available in our group at Jena University, Germany.
The successful candidates will work in an exciting network of local and international collaborations, such as the PhenoMeNal project funded by the European Commission in their Horizon2020 framework program.
Open Positions:
Postdoc: We are looking for a talented cheminformatician, bioinformatician or someone with comparable skills to work on the development cloud-based methods for computational metabolomics. The successful candidate will work closely with the H2020 e-infrastructure project PhenoMeNal, a European consortium of 14 partners. This position requires excellent skills in at least one modern, object-oriented programming language. A strong interest in metabolomics and cloud computing as well as the ability to work in a distributed team will be advantageous. The postdoc will also have the opportunity to participate in the day-to-day management of the group as well as in the organisation of seminars and practical courses for our students.
PhD student, biomedical information mining: In this phd project the candidate will combine methods of text mining, image mining and cheminformatics to extract information about metabolites and natural products from the published primary literature. This includes opportunities to work with the OpenMinTed consortium, where we have been leading the biomedical use case in the last 1.5 years, as well as with the ContentMine team.
PhD student, cheminformatic prediction of natural product structures:Â Depending on skills and interests of the successful candidate, this project can target the problem of structure prediction of natural products and metabolite from either the side of spectroscopic information which one might have about an unknown natural product or starting from the genome of a natural product producing organism. Two positions are available in this area.
All PhD positions require a strong interest in molecular informatics and current IT technologies, programming skills a modern object oriented programming language and the ability to work in geographically distributed teams.
Please send applications in PDF format by email to christoph.steinbeck@uni-jena.de. We will accept applications until the position is filled.
Background information:
The Friedrich Schiller University Jena (FSU Jena), founded in 1558, is one of the oldest universities in Europe and a member in the COIMBRA group, a network of prestigious, traditional European universities. The University of Jena has a distinguished record of innovations and resulting educational strengths in  major fields such as optics, photonics and optical technologies, innovative materials and related technologies, dynamics of complex biological systems and humans in changing social environments. It has more than 18,000 students. The universityâs friendly and stimulating atmosphere and state-of-the-art facilities boost academic careers and enable excellence in learning, teaching and research. Assistance with proposing and inaugurating new research projects and with establishing public-private partnerships is considered a crucial point.
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Rachel Spicer in my group in Cambridge has published an