Funded by the Horizon 2020 Framework Programme
of the European Union

Extending the consensus representation of C. elegans metabolism

GENiE workshop

Nov. 9 – 10, 2017

Helmholtz Zentrum München

Organizer: Michael Witting


C. elegans has recently been advanced as a premier model organism for the study of metabolism, with the publication of two whole-genome metabolic models. Using those models together with transcriptomics, metabolomics and proteomics data allows the relationship between gene expression, nutrition, metabolism, and phenotype to be explored in-depth in data-driven systems-level in silico simulations. In a GENiE workshop held April 19-20 2017 at the Babraham Institute, Cambridge, UK, the relationships between the two existing metabolic models have been explored with the objective of generating a consensus model that builds on the strengths of each separate model. This consensus model will be directly usable by a wide range of C. elegans researchers. However, the two published models are still incomplete, and certain important pathways and areas of metabolism are currently under-annotated, e.g. lipid metabolism and many metabolites that are specific to nematodes. During the April 2017 workshop, specific such areas of incompleteness have been discussed together with the community in order to prioritize “key” missing annotation pathways of importance for current GENiE community objectives in C. elegans metabolic research. A number of such pathways will be selected for this follow-up “annotation jamboree” workshop.

One of the strengths of our first workshop and that we intend to also bring to the second workshop, was that it brings together GENIE members with the larger C. elegans community as well as with a wider community of computer scientists with expertise in Metabolic Reconstruction and with experts in Metabolomics from a wide variety of fields. Therefore our workshops will bring a wide range of new skills and knowledge to the worm community.


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The aim of the second workshop is to fill such gaps and annotate missing pathways. It will thus constitute a natural follow-on from the success of the first workshop. Scientists using metabolomics to study C. elegans metabolism will be asked to participate in this workshop to add their knowledge on newly identified molecules. This workshop will be more hands-on and practical compared to the first one. We will only have a few tutorials and a keynote talk on important aspects of metabolic pathway curation and/or C. elegans metabolism. Different pathways and gaps will be annotated in group work.

Specific overall goals of the workshop are:

  • Gap filling of metabolic pathways
  • Curation of new pathways, especially secondary metabolism and lipid metabolism
  • Annotation of new enzymes
  • Planning of validation experiments
  • Bring new cutting edge methods and technology to Worm Recon 2.
  • Expose C. elegans researchers to gold standards in metabolomics and Flux balance analysis practices.
  • Align European standards with WormBase and the wider Metabolic reconstruction community.
  • Gear towards a publication of a merged open source model, available to the C. elegans community at large.

This workshop is supported by COST action BM1408

Please contact Michael Witting for all inquiries.