Metabolomics Society Forum

In my dataset I get features > 1000 with no problems. Are you sure your data contains data above 1000 Da?
If you are sure your data has peaks > 1000 Da your best bet is to post a reproducible example with code and sample data.

Hello, my name is Elisabeth Frankish and I am one of thousands of New Zealanders who are very concerned about our government's use of sodium fluoroacetate as a rodenticide, which is dropped by helicopter into New Zealand native bush including waterways. I'm not a trained scientist but am looking for an appropriate forum in which to ask questions about the metabolic pathway of sodium fluoroacetate and its metabolite fluorocitrate, and the implications of low-dose poisoning especially on the unborn, male fertility and neurotoxicity.
I have done some research and see that there are two other compounds which also metabolise to fluorocitrate, they are:
1. fluorouracil which is a chemotherapy drug, and,
2. fluoroquinolone which is an antibiotic.
Both of these drugs have multiple adverse effects which appear (to me) to be comparable to the adverse effects of sodium fluoroacetate, and I wonder if it is because we're really dealing with the adverse effects of FLUOROCITRATE, rather than the initial compunds. May I ask you all your thoughts?
If so,  would it be possible to borrow the research for fluorouracil and fluoroquinolone  and apply it to sodium fluoracetate? I have asked this question rhetorically on our Facebook page 1080 Eyewitness. https://m.facebook.com/groups/1399949210263741?multi_permalinks=1953946231530700¬if_t=like¬if_id=1502852914481434&ref=m_notif
I attach a diagram showing my question in concept. One of the reasons that our governments continues to drop it is that there is "no evidence" of the impacts, because the research "has not been done".
I am one of many thousands of New Zealanders who I greatly concerned by the implications of this poison and we would all be very grateful for your help, thank you.
Yours sincerely,
Elisabeth Frankish
Member of "1080 Eyewitness."

Yes, I have it installed on a Windows 64-bits machine! 

Hi,

Can it also be installed in a 64-bit Windows 10 machine? Thanks!

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.