Additional data file 1:

Tables S1 and S2 contain all compound and reaction data associated with the model, respectively; Table S3 lists all of the open problem reactions in the model; Table S4 lists all of the essential genes that have nonessential homologs in the B. subtilis genome; Table S5 lists all of the changes made to the model during the model optimization process; Table S6 lists the reactions in the Oh et al. model that are not in the iBsu1103 model; Table S7 shows simulation results for all 1,500 experimental conditions; Table S8 provides the details on the media formulations used for each FBA simulation; and Tables S9, S10, and S11 show all data on the genes, functional roles, and subsystems in the B. subtilis SEED annotation.

Format: XLS Size: 3.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 2:

The text files may be copied into any spreadsheet program of choice to visualize the data for the iBsu1103 model.

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Additional data file 3:

These molfiles reflect the structure of the predominant ionic form of the compounds at neutral pH as predicted using the MarvinBeans software [28]. These structures were used with the group contribution method [40-42] to estimate the Δ_fG'° and Δ_rG'° for the compounds and reactions in the model.

Format: ZIP Size: 883KB Download file

Additional data file 4:

This may be used with the published COBRA toolbox [18] to run FBA on the model.

Format: XML Size: 1.9MB Download file