BioLEGO - Supplementary materials

Supplementary Figures

• Supplementary Figure 1 - BioLego architecture schema
• Supplementary Figure 2 - All the charts resulted from reaction pairs knock-out analysis
• Supplementary Figure 3 - Results for GOrilla analysis of S. cerevisiae genes, identified in knock-out analysis

Supplementary Tables

• Supplementary Table 1 - Results for analysis of corn utilization

  Exploratory search for optimal biomass utilization for three different types of corn biomasses – corn cobs, corn fiber and corn stover.
  The exact biomass compositions for this experiment were derived from (Baldwin and Sniegowski, 1951; Mcaloon et al., 2000; Van Eylen et al., 2011).
  Five potential fermentation targets were evaluated: Ethanol, Acetone, 1-Butanol, (R)-Propane-1,2-diol and (S)-Propane-1,2-diol.
  For each tested biomass and fermentation target we performed simulations for both single-step and for two-step fermentations under either aerobic or anaerobic conditions for four organism models currently integrated in BioLego flow.
  In total, this experiment included 480 different simulations.

• Supplementary Table 2 - Sensitivity and gradient analyses for ethanol pro-duction using fermentation of Kappaphycus alvarezzi biomass

  We analyzed the possible effects of changes in composition of K. alvarezi algal biomass on the ethanol production yield in the anaerobic two-step process,
  in which first organism is S. cerevisiae and the second one is E. coli.
  Simulated K. alvarezi media is composed of 37 different compounds

• Supplementary Table 3 - Results for analysis of two-step fermentation (S. cerevisiae followed by E. coli) of Ulva sp. into Ethanol with knock-outs in each organism

  We analyzed the anaerobic two-step fermentation process of Ulva sp. into Ethanol,in which the first organism is S. cerevisiae and the second one is E. coli.
  We investigated the impact, on the estimated ethanol production yield, of knocking out single organism reactions either in one or in both organisms.
  The S. cerevisiae model is composed of 2,280 metabolic reactions and the E. coli model is composed of 2,914 metabolic reactions.
  In total, this leads to 6,649,115 possible single knock-out per organism scenarios.

  Includes:
  

  • Simulation results for all 6,649,115 knock-out scenarios)
  • Numbers for histograms (Supplementary Figure 2) summarizing the received results
  • List of reaction pairs most potentially promising for ethanol production
  • Per-organism (S. cerevisiae and E. coli) reactions identified as most potentially promising for increasing ethanol production
  • List of S. cerevisiae genes used as input for GOrilla analysis to construct Supplementary Figure 3
  • Perl scripts for parsing simulation results

• Supplementary Table 4 - Details of experimental validation of prediction quality

  We compared the experimentally measured ethanol fermentation efficiency with the efficiency predicted by BioLego system.
  Wet experiments measured ethanol production yield with presence of small initial amount of oxygen (0.5-2mmol*h^-1*gDW^-1) as a function of initial amount of U. lactuca sugars for 4 fermentation scenarios:

  • S. cerevisiae followed by E. coli
  • E. coli followed by S. cerevisiae
  • E. coli alone
  • S. cerevisiae alone

Latest stable release of BioLego platform

Includes:

• Installation instructions guide
• AzureCloud - Visual Studio Solution for the Azure Cloud side
• AzureStorage - Names and content of Azure Blobs to be created before system run
• LocalServer - Files for the Local Server side