How to Upload Data for Flux Analysis

This video shows users how to import data and use it for flux analysis through Flux Balance Analysis (FBA)

You can redo this tutorial yourself by using these input files:

- Experiment Description File

- HPLC data file

- OD data file

Here is the Jupyter notebook that uses the data from EDD to calculate fluxes:

(Flux Analysis, Notebook A)

Notes

The sample file for Experiment Description uses part IDs from the JBEI Public Registry. If the EDD instance is configured to use a different ICE repository, the strains will not be found. You may proceed with the tutorial by clicking the "Omit Strains" button on the warning message.

The sample file for HPLC data is updated to use the PubChem format to identify measured metabolites. This format uses a case-insensitive prefix of cid: followed by the numeric identifier of the chemical on PubChem (the "Compound CID" entry). The format can optionally be followed by a colon and a name to assist in reading files later. In the screencast below at about the 1:30 mark, instead of selecting the second row as "Measurement Type", instead select the entire row as "PubChem CIDs" to instruct EDD to interpret the labels of cid:5793:D-Glucose and cid:175:Acetate as PubChem references instead of forcing a search on types that already exist in EDD.

Screencast

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