SteinBlog

3D printer Wanhao Duplicator i3+ arrived

I had tremendous fun this weekend after my first 3D printer, a Wanhao Duplicator i3+ arrived.

The reason for getting a 3D printer was even more fun I am recently having with microcontrollers, especially the ESP8266, and I needed a way to printer perfectly fitting enclosures for my builds. Stay tuned for details.

My brand new WanHao i3+ 3D printer

Regarding the 3D printer, I originally wanted to go for an Anet A8 and then follow the upgrade instructions from Heise published in my favourite computer magazine more than a year ago, but then found the advice to circumvent all the hassle and buy the Wanhao or one of the many similar designs. The price is comparable to where you end up when you upgrade an A8. And I think the advice was correct. It took me 15 min to assemble the Wanhao i3+ and to get the first prints done. Within half a weekend, I had printed a filament guide, a case for the Raspberry Pi camera which mounts to the i3+ print bed and hooked the whole thing to a Raspberry Pi running the OctoPi operating system with OctoPrint. Of course, the Raspberry Pi will be in a printed case. As you can see from those links, none of the models that I printed this weekend were designed by myself. They are all downloaded from Thingiverse.com – an absolutely fantastic resource of 3D models, which were made available by makers around the planet.

Raspberry Pi case just printed on my new i3+

 

 


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