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Topics - michael.witting

1
Conferences and seminars / GENiE Workshop: Extending the consensus representation of C. elegans metabolism
Dear all,

from the 9.11. ot 10.11.2017 we will host a workshop at the Helmholtz Zentrum München to work on the consensus metabolic model for the nematode C. elegans. This workshop will include mainly hands-on group work on curating pathways, edit wrong annotations and add new ones.
This workshop could be interesting for all metabolomics scientist working with C. elegans.

More information and the registration page can be found here:

https://www.helmholtz-muenchen.de/genie-workshop-2018/index.html

Best regards,

Michael

GENiE Workshop:
Extending the consensus representation of C. elegans metabolism

Topic

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.

Goals

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 open to all researchers with an interest in C. elegans metabolomics and is not limited to GENiE consortium members. There are a limited number of places available, please register using the link on the left.
2
Courses and training / GENiE Workshop C. elegans Consensus Metabolic Reconstruction, Metabolism & Metab
Hi all,

this workshop might be interesting for people working with C. elegans.

Best regards,

Michael

GENiE Workshop C. elegans Consensus Metabolic Reconstruction, Metabolism & Metabolomics
 
April 19th-20th, 2017
Babraham Institute, Cambridge
 
Organizers: Olivia Casanueva, Janna Hastings, Christoph Kaleta, Michael Witting
 
Workshop website:
http://www.babraham.ac.uk/genie-workshop

Topic:
Five attributes define life: motility, growth, excitability, reproduction and metabolism, whereby metabolism is the most obligatory since it supplies energy and substances needed for all the others. Although studied for centuries, our picture of metabolism is still incomplete. A premier model organism for the study of metabolism is the small roundworm Caenorhabditis elegans, which enables to study the relation between nutrition, gene expression, metabolism and phenotypic traits. Recently the first two metabolic reconstruction of C. elegans were published.
These reconstructions serve as first blueprints of C. elegans metabolism and lay the foundation for further research in this direction. The first reconstruction, iCEL1273, 1985 metabolic reactions and 887 compounds, while ElegCyc contains 1914 reactions and 1640 compounds. So far it is not clear to which extend the two reconstructions overlap. Parallel to this two published version different other groups have been working on their own reconstructions.
The topic of this workshop is to determine the current state in C. elegans metabolism research and how different metabolic reconstructions, published and nonpublished, can be integrated in a community effort leading to a comprehensive consensus C. elegans Metabolic Reconstruction. Within the workshop people from wet and dry-lab will exchange on their experiences and expectations and how different type of knowledge as well as data can be integrated on basis of such reconstructions. Special attention will be drawn to integrate omics data, e.g. transcriptomics, proteomics and metabolomics to expand this reconstruction beyond gene annotations and integration with ChEBI or WormBase and other Alliance of Genomic Resources Databases.
In future it is planned to have jamboree sessions on specific topics identified during this workshop such as specific metabolic pathways that are of particular interest to the community to further improve the quality of the C. elegans Metabolic Reconstruction 2.0.
 
Call for scientific talks/topics:
During the first day we will have several scientific sessions in which several participants can present their current work on C. elegans metabolism, metabolic reconstruction or metabolomics. Talks will be 15-20 minutes plus 10 minutes of Q&A. The evening session will include a key note speaker (Reza Salek) and a discussion round on future collaborative efforts. The second day will include practical work on flux balance analysis, metabolic reconstruction and other hands on activities.
 
Preliminary schedule:
April 19th:
12:00 – 13:30:    arrival, registration and lunch
13:30 – 15:00:    Session 1
15:00 – 15:30:    Coffee Break
15:30 – 16:30:    Keynote speaker
16:30 – 17:00:    Break
17:30 - 18:30:     Session 2
From ~19:30 – 20:00: Dinner Downtown
 
April 20th:
8:30 – 10:00:      Practical session 1
10:00 – 10:30:    Coffee Break
10:30 – 11:30:    Practical Session 2
11:30-12:30:       Round table
12:30                     packed Lunch
 
 
Please contact one of the organizers if you have further ideas and suggestions for a scientific talk.
 
Contact:
Olivia Casanueva
Group Leader
Babraham Institute
Epigenetics ISPG
Olivia.Casanueva@babraham.ac.uk
 
Janna Hastings
Babraham Institute
Epigenetics ISPG
Janna.Hastings@babraham.ac.uk
 
Christoph Kaleta
Research Group Medical Systems Biology
Institute for Experimental Medicine
Christian-Albrechts-University Kiel (UKSH Campus)
c.kaleta@iem.uni-kiel.de
 
Michael Witting
Research Team Leader “C. elegans Metabolomics & Lipidomics”
Research Unit Analytical BioGeoChemistry
Helmholtz Zentrum München