Flux Balance Analysis (FBA) Model

Upload FBA Model from a SBML formatted file

Flux Balance Analysis models can be uploaded into KBase as a Systems Biology Markup Language (SBML) file using the .sbml or .xml file extension. For this example, we will upload the file containing an FBA Model for Bacillus subtilis 168 that has been included in the supplementary materials for this publication:

Henry, C. S., Zinner, J. F., Cohoon, M. P., & Stevens, R. L. (2009). iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biology, 10(6), R69. doi:10.1186/gb-2009-10-6-r69

Go to the publication, find Additional file 4, right-click and select ‘Save Link As …’ to download and save FBA Model

Double-check that the Bacillus subtilis 168 FBA Model completely downloaded by opening the file in a text or code editor and ensuring that the file is 47527 lines long and ends with “</sbml>.” Otherwise, the data could be corrupted and will not import properly into KBase.

In order to successfully upload an FBA Model into your KBase workspace, you first need to add the Genome that corresponds to referenced in the FBA Model you wish to upload. For this example, we’ll add the Bacillus_subtilis_subsp._subtilis_str._168 Genome to our Narrative (from the Public tab of the Data Browser) before importing the FBA Model file.

To add the Genome to your Narrative, find the Data Panel along the left side of the screen and click the Add Data (or red “+”) button. This will open the Data Browser slideout. Select the Example tab at the top of the slideout, and search for “Bacillus subtillis subsp. Subtillis str. 168” genome. Mouse over the genome name and click the blue Add button.

Import FBA SBML

After you’ve added the Bacillus subtilis 168 genome to your Data Panel, open the new Import tab in the Data Slideout and drag the FBA Model file into your Staging area.

Drag & Drop Limitations

The drag & drop from your local computer works for many files, but there is a size limit that depends on your computer and browser. Some users have reported problems around 20 gigabases. For larger files, use the Globus Online transfer.

Now the FBA model is in your Staging area–it’s time to import it into your Narrative as a KBase FBA Model data object. Open the pulldown menu to the right of the filename in your Staging Area and select “FBA Model”:

Now click the import icon (up arrow) to the right of “FBA Model”. The data slideout will close and an app called “Import TSV/XLS/SBML File as an FBAModel from Staging Area” will be added to your Narrative.

Notice that the name of the Model file is already filled in, as is a suggested name for the FBA Model data object that will be created by the import (you can change that if you like). For this example, we will change it to Bacillus_subtilus_168.xml_model.

At this point, the corresponding Genome needs to be linked to the FBA Model. To add the name of the Genome, use the dropdown to select the GCF_000009045.1 genome (Bacillus_subtilis_subsp._subtilis_str._168) in the Data Panel. Note that although specifying the Genome is optional in the app, adding a Genome with gene IDs that match genes IDs in the model is required to import gene-protein-reactions (GPRs). GPRs are necessary to perform gene KO in the “Run Flux Balance Analysis” App.

Next, provide the name of the biomass reaction in the SBML file, in this case “bio00006”. NOTE: if the biomass reaction starts with “R_”, do NOT include the “R_” when entering the name in this field). Click the + to the right of Biomass and type in the name of the first biomass. If there are additional biomass values to enter, click the + to open another parameter field for another biomass.

Click “show advanced options” and select the Genome (in this example, the subtilis 168 genome) which contains features referenced in the FBAModel. Adjust any of the other advanced options if needed, then click the green Run button to start the import.

When the import is finished, your Data Panel will update to show the new FBA Model object, and a report will appear in the import app cell.

More Information

More SBML FBA Models for various organisms can be found here: http://systemsbiology.ucsd.edu/Downloads.
For a description of how to create a COBRA-compliant SBML file that can be imported as an FBA model into KBase, please see SBML Level Three Specifications.

Upload a FBA Model in Excel or TSV format

Flux Balance Analysis models can be uploaded into KBase as either an Excel file (.xls) or via a pair of Tab-Separated Values (.tsv) files containing the chemical compounds and reactions present in the FBA Model. In the Excel format, the tables containing the information about the chemical compounds and reactions in an FBA Model are stored in two separate tabs respectively titled “FBAModelCompounds” and “FBAModelReactions.” For the Tab-Separated Values file format, the chemical compounds and reactions tables are saved as two separate files named “FBAModelCompounds.tsv” and “FBAModelReactions.tsv” that will be transformed into the FBA Model data object within KBase.

FBAModelCompounds

id name formula charge aliases
 cpd00113  Isopentenyldiphosphate  C5H10O7P2  -2
 cpd02590  all-trans-Heptaprenyl diphosphate  C35H58O7P2  -2
  • id: Compound identifier; see the KBase Biochemistry reference for a list of compounds [link]
  • name: Name of chemical compound
  • formula: Chemical formula using the Hill system
  • charge: Formal charge of the molecule
  • aliases: Alternative names for chemical compound

FBAModelReactions

id direction compartment gpr name enzyme pathway reference equation
rxn00001_c0 -> c0 fig|211586.9.peg.3751 Pyrophosphate phosphohydrolase_c0 (1) cpd00001[c0] + (1) cpd00012[c0] -> (2) cpd00067[c0] + (2) cpd00009[c0]
rxn00056_c0 <-> c0 fig|211586.9.peg.1038 Fe(II):oxygen oxidoreductase_c0 (4) cpd00067[c0] + (4) cpd10515[c0] + (1) cpd00007[c0] <-> (4) cpd10516[c0] + (2) cpd00001[c0]
  • id: Reaction identifier; see the KBase Biochemistry reference for a list of reactions
  • direction: Directionality of chemical reaction specified as forward (->), reversed (<-), or equilibrium (<->)
  • compartment: Cellular compartment that the reaction takes place in; see the Metabolic Modeling FAQ for more information
  • gpr: Gene-Protein Reaction in PATRIC identifier format
  • name: Protein associated with the reaction
  • enzyme: Optional, can be left empty
  • pathway: Optional, can be left empty
  • reference: Optional, can be left empty
  • equation: Chemical reaction equation specified with compound coefficients in parentheses, compound identifiers, and directional arrows

Importing an FBA Model into KBase requires you to specify reaction IDs for the biomass producing equations in the model. For a FBA Model of an individual organism, there will be a single biomass equation, while a community model may have multiple biomass producing equations. In the FBAModelReactions table, denote the biomass producing reaction of an individual organism, or the first in a community model, with an ID such as “bio1” so that this reaction is easily identifiable. For subsequent biomass producing reactions in a community model, it is recommended that you use “bio2” for the second biomass producing reaction, “bio3” for the third, and so on.

Upload FBA Model from an Excel formatted file

Importing using an Excel file is similar to importing SBML files. The most important requirement for the Excel file is naming the tabs “ModelCompounds” and “ModelReactions.”

In the Import app most of the options are the same as for SBML. Select a Genome from the dropdown, add a Biomass (remember, if the biomass reaction starts with “R_”, do NOT include the “R_” when entering the name in this field) and modify the FBA Model object name. The primary difference is that the default Model file type needs to be changed to “Excel”.

Upload FBA Model from a tab-delimited file

Importing a Tab-Separated file requires two files, one for reactions and one for compounds. In your Staging area (which you access from the Import tab in the Data slideout), go to the line with the name of the reactions file and select “FBA Model” from the dropdown.

Now click the import icon (up arrow) to the right of “FBA Model”. The data slideout will close and an app called “Import TSV/XLS/SBML File as an FBAModel from Staging Area” will be added to your Narrative.

There are two important differences between importing an FBA model from an SBML file vs. importing in tab-delimited format. First, in the import app, the default Model file type needs to be changed from SBML to Excel. Second, the app needs the name of the compounds file. In the line for “Compounds File Path”, type in the name of the compounds file. There is no pulldown or other help to get the name of the file right. Luckily, the name is usually a slight variation of the reactions file name.img src=”https://kbase.us/wp-content/uploads/2016/12/image12-1.png” alt=”” width=”637″ height=”630″ class=”screengrab alignnone size-full wp-image-13471″ />

Compressed/zipped files

In the example above, we used a Genome that was in the Example data. You can also import your own Genome data from a file (go here for more information).

The Genome import can handle gzipped (.gz) input files. However, .zip files require special handling and .Z files are not yet supported by the importers (we are working on adding that). You can upload a zip file to your Staging Area, but it is recommended that you use the “uncompress” button to its left (the one with the diagonal arrows) to unzip it before trying to import it.

Associating Model with Genome

For metabolic modeling apps, correctly associating a genome with the user uploaded models is necessary for ensuring fidelity between the genome annotations and gene-protein-reactions in the metabolic model. This means that the gene IDs between the model and genome need to match. Occasionally, researchers will use locus tags or gene IDs for constructing metabolic models that are different than those found commonly in reference genomes. If the gene IDs do not match, you will need to change either the model or the genome to ensure their gene IDs match. One way to accomplish this is to locate the genome used as the reference for building the model – based on shared gene IDs – and to upload this genome into KBase before uploading the model and associating it with the genome. If the user cannot locate the genome with the gene IDs used to build the model, the best option for reconciling the gene IDs is to edit the model file (as SBML or TSV) to change the gene IDs contained therein to match the gene IDs of the genome. See this public Help Board ticket for a detailed example of how to accomplish this.