Introduction to Metabolic Modeling in KBase Webinar - 1 April 2020

Interested in constructing metabolic models from your genomics data? This webinar will introduce participants to the basics of metabolic modeling in KBase. Learn how to annotate genomes, reconstruct metabolic models, and perform flux balance analysis to better understand the metabolic capacity of your organism.
Presented by José Faria of Argonne National Laboratory on 1 April 2020.
View related resources and Q&A here: docs.google.com/document/d/17...

[@user-km4iv8zz3h]

Thank you for the webinar! I'm just starting to learn kbase tools and I have a question that I can't seem to find an answer to, so I want to ask here: during the metabolic model building stage, you chose glucose to fill in the gaps in the annotation, however, what if I want my metabolic model to the model “could grow” on a medium containing glucose and arabinose. In the "Media" field it is possible to add only one of the substances, so I don't understand if this is possible?

[@rupreti123]

Very helpful. Thank you very much

[@marie57153]

Thank you for the video, could you explain the unit of the objective value in the output from run flux balance analysis? You said it's in g/mol/mL of dry weight but I don't understand where the volume comes from.

[@DOEKBase]

Hi Marie, thanks for reporting this. The correct unit should be mmol per gram cell dry weight, as seen here: docs.kbase.us/workflows/metabolic-models/faq-metabolic-modeling#how-are-units-of-flux-measured-within-the-media

[@chrissyveldhuizen3384]

Thank you so much for this helpful webinar! I hope you can help me with the following: What is the best approach in setting up a metabolic model using the Build Metabolic Model app to determine which medium or what ingredients for a medium are good for optimal biomass production or for sporulation of a bacterial strain? Thank you

[@DOEKBase]

Hi Chrissy, you might want to check out our documentation on metabolic modeling: docs.kbase.us/workflows/metabolic-models or some of the other metabolic modeling webinars and tutorials on the channel

[@teresagarcia-ybarra6143]

Great video. Is it possible to have the link of the slides and narrative? Thank you

[@DOEKBase]

Hi Teresa, I just added a link to the Q&A doc from this webinar in the description. It has links to the slides and Narrative as well as some other resources.

[@arpitsrivastava54]

Thank you so much for this kind of tutorial, I have run it from the first step... But it is not Showing the OUTPUT FILE (Nothing is present in that Cell) The file runs successful, Also got Summary... But below that there is option of OUTPUT FROM ANNOTATE.... That is Empty, need help... Thanks

[@arpitsrivastava54]

Mycobacterium tuberculosis TKK-01-0051, this was the input file

[@DOEKBase]

Hi @@arpitsrivastava54, thanks for your interest. We can help you with that error on the help board if you create a ticket so we can direct it to the appropriate person to address it. You can see instructions for that here: www.kbase.us/support/