KBase offers several options for loading media for analysis. Within the Narrative Interface, you can use the Create or Edit Media tool to build media based on the hundreds of media conditions available in KBase. You also can import your own custom media as a TSV or Excel file using the instructions below.

Formatting Media TSV or Excel files

If you choose to upload a custom media or use media from an external source, please ensure that it is formatted properly for use with KBase. Media can be uploaded as a TSV (tab-separated values) or Excel file with four columns:

  • Compound identifier (e.g., ModelSEED ID, KEGG ID, PubChem ID, or compound name such as “glucose”)
  • Concentration (concentration of compound in mol/L)
  • Min flux (minimum allowed uptake/excretion of compound)
  • Max flux (maximum allowed uptake/excretion of compound)

Currently, the concentration field is not used by any of the the metabolic modeling tools in KBase. However, it will be utilized in the future as these tools are continually developed. For now, it is best to account for these values accurately so that your media files will retain their utility pending future updates.

The “minflux” and “maxflux” columns connect media to a flux balance analysis (FBA) metabolic model. The values in these columns are absolute units representing the range of possible fluxes for reactions that transport the media compounds into and out of the cell. A negative flux value corresponds to excretion (transport out of the cell), and a positive flux value corresponds to uptake (transport into the cell). 

The combination of maximum and minimum flux will dictate whether uptake and/or excretion of a reagent is allowed. Assigning a positive number to “minflux” for a particular compound essentially forces uptake of that compound. Conversely, assigning a negative number to “maxflux” will force excretion of the compound.

Minimum and maximum flux are measured in mmol per gram cell dry weight per hour.

A list of all the biochemical compounds in KBase can be downloaded (as a 4.1 MB Excel file) here: ftp://ftp.kbase.us/assets/KBase_Reference_Data/Biochemistry. From this list you can find the IDs for compounds you wish to include in your custom media.

Note: When creating a media Excel file, the name of the worksheet that contains your media conditions must be named “MediaCompounds” or it will not upload. By default, the first sheet of any Excel file is called “Sheet1.” To rename it, find the worksheet tabs at the bottom left of the Excel file. Double-click on the default name and type in “MediaCompounds.”

Below is an example of a media file in TSV format. In this case, the compound IDs in the first column are from the KBase biochemistry database:

 

compounds concentration minflux maxflux
cpd00036 0.001 -100 5
cpd00048 0.001 -100 5
cpd00063 0.001 -100 100
cpd00011 0.001 -100 100
cpd10515 0.001 -100 100
cpd00104 0.001 -100 0.1

Upload Media from a TSV or Excel formatted file

  • Choose Media from the data type dropdown menu
  • Click the Next button
  • Select either the MEDIA FROM TSV FILE or the MEDIA FROM EXCEL FILE tab depending on your media format
  • Select the Media file from a directory on your computer
  • Provide a name for the Media data object Click the Import button
  • After the import process has completed, the Media data object will appear in your Data Panel

Import Media