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GOSLIN 2.0

The next version of GOSLIN is there! Goslin is the first grammar-based computational library for the recognition/parsing and normalization of lipid names following the hierarchical lipid shorthand nomenclature. The new version Goslin 2.0 implements the latest nomenclature and adds an additional grammar to recognize systematic IUPAC-IUB fatty acyl names as stored, e.g., in the LIPID MAPS database and is perfectly suited to update lipid names in LIPID MAPS or HMDB databases to the latest nomenclature. Goslin 2.0 is available as a standalone web application with a REST API as well as C++, C#, Java, Python 3, and R libraries. Importantly, it can be easily included in lipidomics tools and scripts providing direct access to translation functions. All implementations are open source. https://pubs.acs.org/doi/10.1021/acs.analchem.1c05430

HFSP Award goes to our lab!

With great pleasure, I announce that we were awarded through the Human Frontier Science Program. We are eager to start the chapter of synaptoneurolipidomics, and we are thrilled to start this great project with labs around the globe:

Michael Kreutz:   http://www.kreutzlab.com/research.html

Steven Verhelst: https://www.verhelstlab.net/

Shane Ellis:          https://www.ihmri.org.au/researchers/dr-shane-ellis/

We Love Lipids

Twitter

We are delighted to contribute to the “We Love Lipids” Tutorial in 2022, introducing lipidomics and lipid sciences. Please save the dates and meet us again soon!

100 min with ILS

It is with great pleasure to announce the 2022 100 min with ILS podcast again. Stay tuned!  https://lipidomicssociety.org/2021/05/17/100-minutes-with-ils-podcast/

Signaling Lipidomics

Prof. Schebb

Prof. Dr. Nils Helge Schebb (Food Chemist and European Registered Toxicologist) is full professor for food chemistry at the University of Wuppertal, Germany. His group is developing instrumental analytical methods to investigate the biological activity of food ingredients.

The major focus of his research group in the last decade is set on targeted lipidomics of oxylipins. His lab developed one the most comprehensive internationally validated platforms for the analysis of oxylipins. Using this approach, the effect how n3-PUFA as well as polyphenols elicit their beneficial effects on human health, are analyzed. Dr. Schebb has published >100 peer reviewed publications of those > 50 about the analysis, formation and biology of oxylipins. Prof. Schebb gave a fantastic talk at the lipidomics seminar (24th of June 2021) on:

“Investigating the formation of eicosanoids and other oxylipins by means of LC-MS/MS (QqQ)”

We very much would like to thanks Prof. Schebb for his great and inspiring talk!

Prof. Thorsten Hornemann
Prof. Hornemann

It is for us a great pleasure to have Prof. Thorsten Hornemann as a guest speaker in our Department at the 24th of June 2021 on the topic of sphingolipid signaling. Th. Hornemann is professor for clinical chemistry and head of the lipidomics research facility at the Institute for Clinical Chemistry, University Zurich. His primary interest is the sphingolipid metabolism where he pioneered by identifying several new lipid metabolic pathways. He and his team developed several unique analytical methods and metabolic labelling techniques to investigate the structure, function and metabolism of sphingolipids with a particular focus on rare and atypical sphingolipid metabolites. He also established several lipid metabolites and lipid based metabolic signatures as diagnostic and prospective biomarkers for cardio-metabolic diseases including NAFLD, CVD, MetS and T2DM.

Thorsten many thanks for joining us it is always fantastic to listens to such great science!

Lipidomics.at turns virtual: ELM 2020 Bioinformatics for Lipidomics Symposium

Thanks to all attendees who helped to make this a great event! The ILS Applied Bioinformatics Interest Group invited to join the Bioinformatics for Lipidomics Symposium on October 2nd, 2020, as part of this year’s joint virtual European Lipidomics Meeting & Lipidomics Forum. With over 150 attendees discussing the challenges and future of lipidomics bioinformatics the event was a great success! We were very happy that this conference was supported by the ILS and the University of Vienna.

The schedule is available at ILS https://bit.ly/2IdlyJl

The symposium was divided into four major sessions:

Databases, Ontologies and Online Resources, Visualization and Exploration, Data Integration and Applications, Identification and Quantification Tools

The presentations of this symposium will be available soon via the ILS homepage!!

New Publication: Goslin

We introduce Goslin (August 2020), a polyglot grammar for common lipid shorthand nomenclatures based on the LipidMaps nomenclature and the shorthand nomenclature established by Liebisch et al. and used by LipidHome and SwissLipids. Goslin was designed to address the following pressing issues in the lipidomics field: 1) to simplify the implementation of lipid name handling for developers of mass spectrometry-based lipidomics tools; 2) to offer a tool that unifies and normalizes the main existing lipid name dialects enabling a lipidomics analysis in a high-throughput fashion. We provide implementations of Goslin in four major programming languages, namely C++, Java, Python 3, and R to kick-start adoption and integration. Further, we set up a web service for users to work with Goslin directly. All implementations are available free of charge under a permissive open source license. Here some links:

https://pubs.acs.org/doi/10.1021/acs.analchem.0c01690
https://bit.ly/30LuTOS
https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/ancham/2020/ancham.2020.92.issue-16/acs.analchem.0c01690/20200811/images/medium/ac0c01690_0002.gif

Lipidomics.at turns virtual: LipidCreator @ISMB

With great pleasure Lipidomics.at presented Lipid Creator on the annual meeting of the international Society for Computational Biology (ISCB) at the CompMS COSI track in Montreal (June 2020). Here comes the link: https://www.iscb.org/cms_addon/conferences/ismb2020/tracks/compmscosi

The lab also would like to thank all the people involved in the development of LIPIDCREATOR and the infrastructure around it and for their support! Also, thanks for the great questions and good suggestions during ISMB!

https://www.nature.com/articles/s41467-020-15960-z/metrics

Lipidomics.at turns virtual: Virtual Podium

Lipidomics.at@ Virtual Podium
https://virtualpodium2020.wixsite.com/scienceandchilll

Social distancing is a must, but should not block the science! Due to COVID-19, you have been impacted by the cancellation of conferences and are losing the chance to connect and to present your research. Therefore the lipidomics.at team is embracing the opportunity to present at virtual platforms. Updates where we go and present can be found here, please join to engage and discuss. We are also hosting regularly own seminars on Thursdays, please contact us for more information.