The best person I know who perform extensive C. elegans + metabolomics" research are Professor Arthur Edison, who was at University of Florida, and now UGA, : http://edison.ccrc.uga.edu/?page_id=356 , and his colleagues Fatma Kaplan: https://biology.ufl.edu/fkaplan/ and Greg Stupp/ Dr. Chris Beecher et al. who published: Isotopic Ratio Outlier Analysis Global Metabolomics of Caenorhabditis elegans : http://pubs.acs.org/doi/abs/10.1021/ac4025413 . But all this NMR-metabolomics.
They would be the best to consult anything on worm metabolomics!
I want to run a commercial mass-spectrometry software (from GC-MS, LC-MS instrument vendors) on a cluster and also integrate into our existing Galaxy server! Computational load wise the server is huge and have sufficient capabilities. We have personnel who can do it but need to suggest them/ provide instructions.
Questions are:
How to get the commercial tool(s) integrated into Galaxy workflow? What do we need from the commercial software provider? How to automate or semi-automate the entire process, like file upload, batch processing, obtaining results so that the outputs are human readable (say a .csv outputs etc.)! What expertise/ softtools does one need to have access to be able to furnish this work?
1. Compulsory Data Archiving (MetaboLights, MetabolomicsWorkbench- MetabolomeExchnage) and Accession ID before/ during peer-review/ post-publication. Published literature and submissions at these databases do not match. 2. No features list published without validations/ identifications/ assignments. 3. Open Access or not, but fees needs to be minimum and realistic. 4. Sections on animal, plant, microbial, tools, databases, applications, interdisciplinary clearly specified so that readers find them easily. 5. Section on announcements of opportunities (jobs/ positions), conferences/ symposium/ workshops and online resources. 6. Yes, all R and Python scripts, Matlab tools available. 7. Faster turn around times for peer review, and more inclusive peer reviewers with ECRs. 8. Reviewer MUST sign for identity at the end of peer review process. 9. Perks for peer reviewers with discounted offers, honorarium etc. 10. Videos for implementation of workflows (bioinfo, stats, computational, mass spec runs) and them being mirrored from Youtube or MetSoc Journal websites. This would be informative and enriching for wider readership interests/ experience.
However, this is poorly narrated, organized, content are out dated, not growing/ enriched with latest discoveries/ inventions/ tools/ workflows, no attractive pictures and so on. For instance better definitions are available than the existing : "metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind"". Also, at present the information are heavily tilted to few popular tools, and scientific groups only- the vast majority are still missing.
Of course other platforms exist for such information, however, Wiki is Wiki, and first hit is important for out reach. Entire community efforts, MetSoc members, EMN/ ECRs should take a lead to do so.
As a MetSoc community, EMN, ECRs it is vital for us to make/ edit the page to inform public and interested researchers on the actual potential of metabolomics, which is currently lacking. We should start EDITING on a regular basis with "pictures, tools, links, references, real (updated) definitions, platforms, applications and so on. This is of importance as far as I am concerned.
Just a suggestion- such community efforts and outreach is an important avenue to be not overlooked for a sustainable future with and around Metabolomics.
I have run the 37 FAME Mix from Supelco on a Thermo GC-MS, using Rtx5-sil column, and wish to generate/ assign the Retention Indices to the FAMES using AMDIS or so ? How is it done to generate the .CAL file (from the .netCDF/ .raw files from Thermo with me!) so that I can compare and identify all my compounds run using same conditions (full-scan mode!).
Do I have to (a) search NIST first to assign RIs to these compounds based on their known RIs from similar columns such as DB5, HP5 etc, or (b) I have to calculate them de novo to be able to identity and assign their RI, and use these values for "other compound" identifications ?, or, (c) should I use the Hydrocarbon RI .CAL File inbuilt in AMDIS-NIST Library to first generate the RI for these FAMES, first ? But that is not comparable, right ?
