The Leibniz Institute of Plant Biochemistry (IPB) is an international research institute located on the Weinberg-campus in Halle and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry.
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 (PhD student Bioinformatics / Metabolomics) in the context of the Leibniz project „DiSeMiNation“ on mangrove systems to contribute to global conservation. The focus of the position will be to analyse mass spectrometry data on the biotic composition of mangrove systems, adapt methods for creation of current and historic metabolite profiles from sediment samples and to adapt methods for metabolite annotation to Pyrolysis GC/MS data.
You should hold a degree in bioinformatics or computer science, with experience in algorithm and software engineering and statistics. You are able to program in the statistics framework R, and have worked in Java. Knowledge in metabolomics would be an advantage.
The position is limited to 3 years, and available from April 1st, 2017. Payment is according to local regulations TV-L. Further information is available from the IPB job opportunities page .
The Leibniz Institute of Plant Biochemistry (IPB) is an international research institute located on the Weinberg-campus in Halle and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry. 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 (Postdoc Bioinformatics / Metabolomics)
in the context of the German Network for Bioinformatics Infrastructure (de.NBI). The focus of the position will be to establish an infrastructure to support the experimental metabolomics community with efficient computational metabolomics services. The successful candidate will engage with users, provide support with metabolite annotation tools (MassBank, MetFrag) and standards-compliant data sharing.
You should hold a PhD in bioinformatics or computer science, with experience in algorithm and software engineering and statistics. You are able to program in the statistics framework R, and have worked in Java or C/C++. Knowledge in metabolomics or Grid-/Cloud computing would be an advantage. The position is limited to 3 years, and available from 01.11.2016. Payment is according to local regulations TV-L.
Please send your application (cover letter addressing your research interests, CV, transcripts, and names/contacts of two references) quoting reference number 7/2016 until July 31st, 2016 to:
Leibniz-Institut für Pflanzenbiochemie (IPB) Stiftung des öffentlichen Rechts AG Personalangelegenheiten Frau Kerstin Balkenhohl Weinberg 3 06120 Halle (Saale) or to bewerbungen@ipb-halle.de
we are calling for abstracts for the workshop “metaRbolomics: The R toolbox for Metabolomics”, held on Monday the 25th, 2016 as part of the annual meeting of the Metabolomics Society in Dublin (http://metabolomics2016.org/).
The workshop is aimed at Biologists, Bioinformaticians, and Chemists interested in high-throughput analysis. Contributions should highlight the tools available for metabolomics, how existing packages can be combined, and encourage participants to envision future developments and synergies. Speakers will be chosen based on the creativity of their approaches for metabolomics data processing and analysis in R, ideally with combinations of two or more R packages. Example data and R code should be available to the audience to explore for themselves the power of R.
Please enter your abstract in the form at http://goo.gl/forms/Lc9QLVRsKG. The deadline for submissions is Monday 7th of March 2016.
one of the big events this year will be the annual conference of the international Metabolomics society in Dublin (27.-30.6.2016, see http://metabolomics2016.org/), where around 1000 people can be expected to attend. Last year we coordinated several proposals for workshops and sessions, and we are delighted that ALL THREE proposed sessions got accepted! Among the other scientific topics like the session on “Advances in Statistical Tools”, we expect to have these sessions related to computational mass spectrometry and metabolomics:
New Approaches for Identification of Metabolites applying MS and NMR (Session team: Witting/Dunn)
Network and Pathway Analysis for Metabolomics (Session team: Willighagen/Jourdan)
Computational Mass Spectrometry (Session team: Neumann/Böcker)
There will also be these workshops :
Computational Workflows and Workflow Engines (Workshop lead: Christoph Steinbeck)
Workshop On Data Sharing and Standardisation (Workshop team: Reza Salek et al.)
metaRbolomics: The R toolbox for Metabolomics (Workshop team: Stanstrup/Neumann)
Of course, the official call for participation and papers by the conference organisers will follow in the next weeks, but you could already think about your contribution to make the workshops and sessions a whopping success!
Next year's Metabolomics 2016 conference had a call for sessions and proposals (see below).
It would be great if we could coordinate some of the CompMS related proposals beforehand to ensure a good coverage of the topics we're interested in. Please add your suggestions to the overview document at [1] and form small session organising teams.
Everyone with the link can view, but you'll need to request edit permissions in the google doc, but that is only because then it's simpler to send messages to everyone who is involved.
Once we converged towards a set of sessions, the session teams will have to send their detailed proposal to the Dublin organisers by October 30, 2015
URGENT: Open Call to Metabolomics Society Members for Scientific Sessions and Workshops?? We are in the process of planning workshops and scientific sessions and we welcome you to submit proposals for these important meetings. ??
Additional details can be found by clicking on the links below. Do not delay – the proposals are due by October 30, 2015. ?
The IPB is an international research institute located on the Weinberg-campus in Halle and provides state-of-the-art facilities for research in bioinformatics, metabolomics and plant biochemistry.
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. In the context of the EU project PhenoMeNal you will work on the integration of existing computational metabolomics methods into efficient and versatile workflows, and their execution on local and European grid infrastructures.
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 the statistics framework R, and have worked in Java or C/C++. Knowledge in metabolomics or Grid-/Cloud computing would be an advantage. The position is limited to 3 years, and available from 01.10.2015.
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.
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 methods for metabolomics data analyses and data fusion, to discover relationships between metabolites and their biomedical effects.
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 the statistics framework R, and have worked in Java. Knowledge in metabolomics or analytical biochemistry would be an advantage. The position is limited to 3 years, and available immediately. Payment is according to local regulations TV-L.
The task group “Computational Mass Spectrometry” [1] represents the CompMS [2] initiative in the Metabolomics society. The CompMS initiative promotes the efficient, high quality analysis of mass spectrometry data with state-of-the art computational tools and algorithms through dissemination and training in existing, and coordination of new, innovative approaches. The CompMS initiative aims to exploit synergies between different application domains, in particular proteomics and metabolomics. The scientific remit of the group will include all aspects of computational method development from signal processing, feature alignment and grouping, to development of metabolite identification algorithms and metabolic network reconstruction.
The mission is to 1) build a community of scientists working in computational mass spectrometry, 2) integrate experimental and theoretical research, and 3) educate a new generation of computational scientists via training and dissemination of results. The CompMS is a joint initiative between the International Society for Computational Biology (ISCB CoSI CompMS), the Human Proteome Organization and its Computational Mass Spectrometry Initiative (HUPO CompMS), and the Metabolomics Society.
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 Bioinformatician (Metabolomics).
You will work on methods and algorithms for the analysis and interpretation of metabolomics data from state-of-the-art mass spectrometers. 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 the statistics framework R, and have worked C/C++. Knowledge in metabolomics or analytical biochemistry would be an advantage.
The position is limited to 3 years and 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.
The Critical Assessment of Small Molecule Identification CASMI 2012 special issue in Metabolites is finally finished! Emma Schymanski and I continue to present the results of CASMI 2012 at different occasions, e.g. the last ASMS conference in Minneapolis (June 2013) and the upcoming Water Forum in Langenau in November this year.
The organisation of the contest and special issue was a lot of work, but also a lot of fun. We'd like to thank all of our participants and our advisory board, but also everyone who expressed interest or engaged us in discussions at meetings.
And CASMI keeps going: CASMI 2013 is currently being organised by a team of Japanese mass spectrometry experts headed by Prof. Nishioka, and the challenge data has already been opened up. Make sure to send your submissions before the deadline in december 2013.
The small molecule analytical chemistry and computational mass spectrometry world is quite small, we're looking forward to bumping into you at some time in the future!
The full set of challenges in the CASMI contest (Critical Assessment of Small Molecule Identification, http://http://casmi-contest.org/) went online a few weeks ago. Now is the time to plan the special issue of the MDPI journal Metabolites, which will make up the proceedings of CASMI.
Please also note that we will send a mail to the casmi-announce mailing list shortly, with updates on the CASMI participation and evaluation details. Remember to sign up to the list(s) if you haven’t already.
Call for Papers: CASMI proceedings ===============================
The special issue will contain our summary articles, where we give details about the challenge compounds, solutions, evaluation measures and comment on the success of your 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 (casmi2012@ipb-halle.de) 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 the authors’ instructions and online article submission please see the details at http://http://www.mdpi.com/journal/metabolites/special_issues/CASMI .
We wish you a happy Christmas and a successful New Year 2013!
Yours sincerely, Emma Schymanski and Steffen Neumann
Important Dates: 31.03.2013 Submission deadline for full papers in the journal Metabolites (MDPI.com) 31.12.2012 Last day of early-bird article pre-registration
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.
I found a few cases so far where CAMERA was used in papers, but apparently the authors had difficulties finding the correct citation. In R in general you can use
Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann, S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)
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 http://www.metabolomics2012.org. Don’t forget to mention whether your presentation will include a live demonstration.
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://http://www.ipb-halle.de/en/, for inquires please contact Dr. Steffen Neumann, Telephone: +49 345 5582-1470, e-Mail: sneumann(at)IPB-Halle.DE
