{"label":"Obtain genome annotation","group":"Data Collection"}
{"label":"Identify candidate metabolic functions","group":"Data Collection"}
{"label":"Identify candidate metabolic reactions","group":"Data Collection"}
{"label":"Assemble draft reconstruction","group":"Draft Reconstruction"}
{"label":"Use the phylogenetically close organisms","group":"Reconstruction Refinement"}
{"label":"Collect the experimental data","group":"Reconstruction Refinement"}
{"label":"Determine the substrates and cofactors for usage","group":"Information Analysis"}
{"label":"Obtain the neutral molecular formula","group":"Data Collection"}
{"label":"Determine the charged molecular formula","group":"Data Collection"}
{"label":"Calculate the reaction stoichiometry","group":"Data Quality Control"}
{"label":"Determine reaction directionality","group":"Data Collection"}
{"label":"Add the cellular compartments information","group":"Data Collection"}
{"label":"Add the subsystem information","group":"Data Collection"}
{"label":"Verify gene-protein-reaction associations","group":"Reconstruction Refinement"}
{"label":"Add metabolite identifiers","group":"Data Collection"}
{"label":"Unify metabolite/reaction identifiers","group":"Information Analysis"}
{"label":"Determine and add the confidence score","group":"Reconstruction Refinement"}
{"label":"Add reaction information sources","group":"Reconstruction Refinement"}
{"label":"Add notes based on experiments","group":"Reconstruction Refinement"}
{"label":"Initial ireration","group":"Reconstruction Refinement"}
{"label":"Add spontaneous reactions","group":"Data Curation"}
{"label":"Add exracellular transport and periplasmic transport reactions","group":"Data Curation"}
{"label":"Add exchange reactions","group":"Data Curation"}
{"label":"Add intracellular transport reactions","group":"Data Curation"}
{"label":"Draw the metabolic map","group":"Reconstruction Refinement"}
{"label":"Determine cytochemical compositions","group":"Reconstruction Refinement"}
{"label":"Estimate amino acid contents","group":"Reconstruction Refinement"}
{"label":"Determine amino acid coefficients","group":"Information Analysis"}
{"label":"Estimate nucleotide contents","group":"Reconstruction Refinement"}
{"label":"Determine nucleotide coefficients","group":"Information Analysis"}
{"label":"Estimate lipid contents","group":"Reconstruction Refinement"}
{"label":"Estimate cofactor contents","group":"Reconstruction Refinement"}
{"label":"Estimate ion contents","group":"Reconstruction Refinement"}
{"label":"Determine growth-associated ATP maintenance reactions","group":"Reconstruction Refinement"}
{"label":"Add biomass reactions","group":"Data Curation"}
{"label":"Add no growth-associated ATP maintenance reactions","group":"Data Curation"}
{"label":"Add demand reactions","group":"Data Curation"}
{"label":"Add sink reactions","group":"Data Curation"}
{"label":"Determine growth medium requiremnets","group":"Reconstruction Refinement"}
{"label":"Use COBRA","group":"Reconstruction Refinement"}
{"label":"Load reconstructions into Matlab","group":"Reconstruction Refinement"}
{"label":"Verify matrix","group":"Data Quality Control"}
{"label":"Set objective functions","group":"Data Curation"}
{"label":"Set simulaton constraints","group":"Data Curation"}
{"label":"Check for stoichiometrically unbalanced reactions","group":"Data Quality Control"}
{"label":"Evaluate stoichiometrically unbalanced reactions","group":"Data Quality Control"}
{"label":"Identify terminal metabolites","group":"Information Analysis"}
{"label":"Identify candidate reactions to fill gaps","group":"Data Curation"}
{"label":"Add gap reactions to fill gaps","group":"Data Curation"}
{"label":"Add notes and references to terminal metabolites","group":"Reconstruction Refinement"}
{"label":"Add missing exchange reactions","group":"Data Curation"}
{"label":"Set missing exchange constraints for a simulation condition","group":"Data Curation"}
{"label":"Test for Type III pathways","group":"Data Quality Control"}
{"label":"Discover Type III pathways","group":"Information Analysis"}
{"label":"Identify Type III pathways","group":"Information Analysis"}
{"label":"Analyze reactions direactionality in Type III","group":"Information Analysis"}
{"label":"Recompute networks gaps","group":"Data Quality Control"}
{"label":"Obtain biomass reaction metabolites","group":"Information Analysis"}
{"label":"Add demand reactions for biomass reaction","group":"Model Evaluation"}
{"label":"Set objective functions of biomass reactions","group":"Model Evaluation"}
{"label":"Maximize objective functions","group":"Model Evaluation"}
{"label":"Identify the main reactions","group":"Model Evaluation"}
{"label":"Sitimulate the multi-growth media","group":"Model Evaluation"}
{"label":"Collect secretions and growth conditions","group":"Reconstruction Refinement"}
{"label":"Set the simulation constraints for the single secretion","group":"Model Evaluation"}
{"label":"Set the objective functions of the single secretion","group":"Model Evaluation"}
{"label":"Maximize the objective functions of the single secretion","group":"Model Evaluation"}
{"label":"Set the constraints of multiple secretions","group":"Model Evaluation"}
{"label":"Validate the model","group":"Model Evaluation"}
{"label":"Add secretion reactions","group":"Data Curation"}
{"label":"Set the objective functions of multiple secretions","group":"Model Evaluation"}
{"label":"Maximize the objective reactions of multiple secreations","group":"Model Evaluation"}
{"label":"Simulate rich media","group":"Model Evaluation"}
{"label":"Check for blocked reactions","group":"Information Analysis"}
{"label":"Fill gaps by blocked reactions","group":"Data Curation"}
{"label":"Simulate the single-gene deletion","group":"Model Evaluation"}
{"label":"Validate the single-gene deletion model","group":"Reconstruction Refinement"}
{"label":"Set the simulation conditions","group":"Reconstruction Refinement"}
{"label":"Simulate the single-reaction deletion","group":"Model Evaluation"}
{"label":"Validate the single-reaction deletion model","group":"Model Evaluation"}
{"label":"Validate the multi-media model (fast enough)","group":"Model Evaluation"}
{"label":"Determine model quality","group":"Model Evaluation"}
{"label":"Maximize the objective multiple media","group":"Model Evaluation"}
{"label":"Determine the reduced cost associated with network reactions when optimizing for objective function.","group":"Model Evaluation"}
{"label":"Validate multiple-media model (too fast)","group":"Model Evaluation"}
{"label":"Use single-reaction deletion to identify single reactions that may enable the model to grow too fast","group":"Reconstruction Refinement"}
{"label":"Validate the integrity of bimass metabolites","group":"Reconstruction Refinement"}
{"label":"Identify shuttling reactions","group":"Reconstruction Refinement"}
{"label":"Last iteration","group":"Data Curation"}
{"label":"Identify excessive growth","group":"Model Evaluation"}
{"label":"Use reduced cost analysis to identify those reactions that can reduce the growth rate","group":"Information Analysis"}
{"label":"Output files","group":"Reconstruction Output"}
{"label":"Annote gap reactions","group":"Reconstruction Output"}