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Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
WormClustClustering- and enrichment-based association of genes with the metabolic network

Instructions

The biomass composition of both the bacterial diet and the worm itself are variable. If you do not want to use the dafault values and have your own compositional parameters, you can adjust the bacterial degradation and worm biomass assembly reactions in the metabolic model in the following steps:
  1. Change the parameters in the tables below (click to display) when you have the necessary data (e.g., fatty acid composition).
  2. Click the submit button.
  3. Download the adjusted model following file links that will appear in the grey section below.
Note that energetic parameters such as maintenance costs are also adjustable and are included in the forms.
Worm biomass
► | Overall composition (click to view)▼ | Overall composition (click to hide)
► | Protein composition (click to view)▼ | Protein composition (click to hide)
► | Lipid composition (click to view)▼ | Lipid composition (click to hide)
Phospholipids composition (Overall) (?) Percentage (w/w basis) of different phospholipids in total. Hover help signs to see full name and formula of each entity. In the formulas "X" and "W" indicate the fatty acids. The composition of X is to be entered separately in the table below, while W is taken as 100% octadecanoate (n-C18:0) .

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.
back to default values
Fraction (% w/w)
pe (?) Name: Phosphatidylethanolamine
Formula : C5H12O4NPX2
pchol (?) Name: Phosphatidylcholine
Formula : C8H18O4NPX2
ps (?) Name: Phosphatidylserine
Formula : C6H11O6NPX2
pail (?) Name: Phosphatidylinositol
Formula : C9H16O9PX2
clpn (?) Name: Cardiolipin
Formula : C9H16O9P2X4
lpchol (?) Name: Lysophosphatidylcholine
Formula : C8H19O5NPX
sphmyln_ce (?) Name: Sphingomyelin
Formula : C24H50N2O4PX
akac2gpe (?) Name: 1-alkyl 2-acylglycerol 3-phosphoethanolamine
Formula : C5H12O5NPXW
alkenac2gpe (?) Name: 1-alkenyl 2-acylglycerol 3-phosphoethanolamine plasmalogen
Formula : C5H10O5NPXW
akac2gchol (?) Name: 1-alkyl 2-acylglycerol 3-phosphocholine
Formula : C8H18O5NPXW
Total
Phospholipids composition (X Fatty acids) (?) Percentage (w/w basis) of fatty cids in phospholipids. Hover help signs to see full name of each entity. These fatty acids make the pool indicated by "X" in the formula of phospholipids in the above table.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.
back to default values
Fraction (% w/w)
tdcoa (?) Name: Tetradecanoyl-CoA (n-C14:0CoA)
pmtcoa (?) Name: Palmitoyl-CoA (n-C16:0CoA)
stcoa (?) Name: Stearoyl-CoA (n-C18:0CoA)
fa16p1n7coa (?) Name: Palmitoleyl-coA
odecoa (?) Name: Octadecenoyl-CoA (n-C18:1CoA)
vacccoa (?) Name: Vaccenyl coenzyme A
lnlccoa (?) Name: linoleic coenzyme A
dlnlcgcoa (?) Name: dihomo-gamma-linolenyl coenzyme A
arachdcoa (?) Name: C20:4-CoA
eicostetcoa (?) Name: eicosatetranoyl coenzyme A
tmndnccoa (?) Name: timnodonyl coenzyme A
fa15p0isocoa (?) Name: Fatty acyl (C15:iso) coa
fa17p0isocoa (?) Name: Fatty acyl (C17:iso) coa
fa17c9coa (?) Name: cis-9,10-methylenehexadecanoyl coa
fa19c11coa (?) Name: cis-11,12-methyleneoctadecanoyl coa
lgnccoa (?) Name: lignocericyl coenzyme A
Total
TAG composition (Y Fatty acids) (?) Percentage (w/w basis) of fatty cids as triacylglycerides (TAG). Hover help signs to see full name of each entity. These fatty acids make the pool indicated by "Y" in the formula of TAG, which is C3H5Y3.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.
back to default values
Fraction (% w/w)
tdcoa (?) Name: Tetradecanoyl-CoA (n-C14:0CoA)
pmtcoa (?) Name: Palmitoyl-CoA (n-C16:0CoA)
stcoa (?) Name: Stearoyl-CoA (n-C18:0CoA)
fa16p1n7coa (?) Name: Palmitoleyl-coA
odecoa (?) Name: Octadecenoyl-CoA (n-C18:1CoA)
vacccoa (?) Name: Vaccenyl coenzyme A
lnlccoa (?) Name: linoleic coenzyme A
dlnlcgcoa (?) Name: dihomo-gamma-linolenyl coenzyme A
arachdcoa (?) Name: C20:4-CoA
eicostetcoa (?) Name: eicosatetranoyl coenzyme A
tmndnccoa (?) Name: timnodonyl coenzyme A
fa15p0isocoa (?) Name: Fatty acyl (C15:iso) coa
fa17p0isocoa (?) Name: Fatty acyl (C17:iso) coa
fa17c9coa (?) Name: cis-9,10-methylenehexadecanoyl coa
fa19c11coa (?) Name: cis-11,12-methyleneoctadecanoyl coa
lgnccoa (?) Name: lignocericyl coenzyme A
Total
► | Nucleic acid composition (click to view)▼ | Nucleic acid composition (click to hide)
DNA composition (?) Percentage (mol/mol basis) of nucleotides in DNA.
back to default values
Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total
RNA composition (?) Percentage (mol/mol basis) of nucleotides in RNA.
back to default values
Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total
► | Other (click to view)▼ | Other (click to hide)
Bacterial biomass
► | Overall composition (click to view)▼ | Overall composition (click to hide)
► | Protein composition (click to view)▼ | Protein composition (click to hide)
Amino acid composition (?) Percentage (mol/mol basis) of individual amino acids in bacterial protein.

If the total exceeds or remains below 100%, then the algorithm will normalize each value by the total, and a warning will be issued.
back to default values
Fraction (% mol/mol)
Ala
Arg
Asn
Asp
Cys
Glu
Gln
Gly
His
Ile
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
Total
► | Lipid composition (click to view)▼ | Lipid composition (click to hide)
► | Nucleic acid composition (click to view)▼ | Nucleic acid composition (click to hide)
DNA composition (?) Percentage (mol/mol basis) of nucleotides in DNA.
back to default values
Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total
RNA composition (?) Percentage (mol/mol basis) of nucleotides in RNA.
back to default values
Fraction (% mol/mol)
Adenine
Guanine
Cytosine
Thymine
Total
► | Other (click to view)▼ | Other (click to hide)
The information and tools provided in this website are to be used for academic purposes only.