SteinBlog

Proud members of Microverse Cluster of Excellence

We are thrilled to announce that the proposal “Balance of the Microverse” has been selected as a cluster of excellence by the Excellence Commission, consisting of the members of the international Committee of Experts and the research ministers of the federal and state governments of Germany. Group leader Prof. Christoph Steinbeck is one of the principle investigators of the proposal. The cluster will be funded with 50 mio Euros over 7 years. The mission of the Balance of the Microverse Cluster is to understand microbial balance from the molecular to the ecosystem level and to develop detection and manipulation technologies to create beneficial impact.

 


Slides of my talk on NMR data sharing at ACS Boston, August 2018

The slides of my talk on NMR data sharing at ACS Boston, August 2018, can be found at https://doi.org/10.6084/m9.figshare.6984314

The submitted abstract was:

NMR spectroscopic data is a cornerstone in the structure elucidation and identification of organic molecules. In publications on newly synthesised compounds and their intermediates as well as in the characterisation of novel natural products, NMR data are indispensable components of experimental sections, albeit typically reported in ways which destroy information. This talk reports on two current community efforts to a) create an open, distributed and internationally adopted repository for raw NMR data (McAlpine2018) and b) the new NMReData format, a lightweight description of curated NMR data and their assignment to chemical structures (Pupier2018).

Raw NMR data only reaches its maximum potential usefulness if it is universally accessible. While molecular biology has paved the way through the establishment of open data repositories in many of its subfields, developments in areas overlapping with chemistry, such as metabolomics, have shown that the technology for a repository for open raw NMR data is at our fingertips and we will discuss aspects leading towards the creation of such an archive. Furthermore, here is no standard file for the NMR data relevant to structure elucidation. With NMReData, a file format is introduced and presented here, to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds with the assigned chemical structure. NMReDATA descriptions include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times and diffusion rates. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, automating the verification of published result, and for assisting the constitution of open-access structural databases.

We believe that the combination of these two grassroots movements as well as a requirement from publishers to deposit the raw NMR data in open access repositories, as is customary and well accepted in genetics, crystallography and other fields, will have a substantial impact on the reproducibility of chemistry studies and aid the development of new and better tools for dereplication and structure verification.

References:

[tpsingle key=”Pupier:2018jo” link=true]

[tpsingle key=”McAlpine:2018ee” link=true]

 


Steinbeck group joins ChemBioSys to lead INF project

With effect from 1 July 2018, we are proud members of the collaborative research center ChemBioSys to lead the informatics project. ChemBioSys, composed of 18+ research groups and PIs at the University of Jena, the Leibniz Institute for Natural Product Research and Infection Biology and the Max-Planck-Institute for Chemical Ecology,  investigates the regulation, activity and function of natural products in complex communities.


Current Challenges in Plant-Ecometabolomics

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.”

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Postdoc Position in Cheminformatics and Computational Metabolomics

A postdoc position is available in my research group at Friedrich-Schiller-University Jena, Germany.

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

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 university’s 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.

About Christoph Steinbeck

 


Compliance with minimum information guidelines in public metabolomics repositories

Rachel Spicer in my group in Cambridge has published an article in Nature Scientific Data on the compliance with minimum information guidelines in public metabolomics repositories. 

The abstract:

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.


Opinion Piece on the Future of Metabolomics in ELIXIR

Leading metabolomics researchers across Europe have co-authored an opinion piece in F1000 Research about “The Future of Metabolomics in ELIXIR”.

ABSTRACT:

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 “Future of metabolomics in ELIXIR” 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.