//===========================================================================
// Ecoli K-12: Palsson's Model
//
// Job Control Parameters, Biomass Composition, Loads and
// Boundary (Transport) Conditions
//===========================================================================
//
// Evgeni Nikolaev, 04-02-02
//
//===========================================================================
//===========================================================================
// Job Control Parameters
//===========================================================================
//
// Purpose / Description in Brief
// ------------------------------
//
// Job Control Parameters allow one to manage a modeling task, direct output of
// data from files or databases, assign general computational and modeling
// parameters etc
//
// ObjeType = 1 corresponds to the models loaded from files ecell_model_#.cpp
// ObjId = 1 corresponds to the simplest branching model
// ObjId = 2 corresponds to a simplified glycolytic pathway, Heinrich and Schuster book, p.93
ObjType = 0 // 0 - cell, 1 - test data, 100 - subsystem, 200 - pathway, etc.
ObjId = 0 // 0 - data loaded from files and id is set to default value 1
//---------------------------------------------------------------------------
// STOICHIOMETRIC MATRIX
//---------------------------------------------------------------------------
//not finished: JobId = 200 // a range of numerical ranks of the stoichiometric matrix
//not finished: JobId = 201 // singular values of the original and transposed stoichiometric matrices
//---------------------------------------------------------------------------
// BALANCING ANALYSIS
//---------------------------------------------------------------------------
//JobId = 300 // unbalanced substrates and products
//JobId = 301 // blocked reactions
//JobId = 302 // groups of identical reactions (isoenzymes)
//JobId = 303 // all active non-repetitive and non-blocked reactions with no boundary condition set
//JobId = 304 // the same as with JobId = 303 but with boundary conditions set
//---------------------------------------------------------------------------
// METABOLIC NETWORK CONNECTIVITY
//---------------------------------------------------------------------------
//JobId = 310 // a report on topological connectivity only
//not finished: JobId = 311 // a report on stoichiometric connectivity of a metabolic reaction network
//JobId = 350 // co-regulated enzyme subsets with biomass and free transport
// (a complex defined buffered medium)
//JobId = 351 // co-regulated enzyme subsets with biomass and directionally restricted transport
// (some transported substances are buffered and the others are blocked)
//JobId = 352 // co-regulated enzyme subsets without biomass and with free transport, see JobId = 350
// (cell free extracts in a complex buffered medium)
//JobId = 353 // co-regulated enzyme subsets without biomass and with directionally restricted transport, see JobId = 351
// (cell free extracts when some transported substances are buffered and the others are blocked)
//JobId = 360 // stoichiometric regulation reaction map for biomass and free transport
// (a complex defined buffered medium)
//JobId = 361 // stoichiometric regulation reaction map for biomass and directionally restricted transport
// (some transported substances are buffered and the others are blocked)
//JobId = 362 // stoichiometric regulation reaction map without biomass and with free transport, see JobId = 350
// (cell free extracts in a complex buffered medium)
//JobId = 363 // stoichiometric regulation reaction map without biomass and with directionally restricted transport, see JobId = 351
// (cell free extracts when some transported substances are buffered and the others are blocked)
//---------------------------------------------------------------------------
// CONSERVATION RELATIONSHIPS FOR METABOLITE POOLS
//---------------------------------------------------------------------------
JobId = 410 // the analysis of metabolites coupled in the pools which are conserved within the network with biomass
//JobId = 420 // the analysis of metabolites coupled in the pools which are conserved within the network without biomass
// FLUX OPTIMIZATION WITH LINDO
//JobId = 600 // optimization of fluxes with Lindo
//not finished: JobId = 601 // essential reactions
//JobId = 602 // Lindo parameters
//not finished: JobId = 603 // calculable fluxes under pre-computed optimized conditions
//not finished: JobId = 604 // demonstration of calculable fluxes with JobId = 603
//JobId = 605 // printing out a report on a detailed analysis of a Lindo optimized solution
// BIOINFORMATICS
//JobId = 700 // cell's model parameters and pathways names
//JobId = 710 // all cell's reactions
//JobId = 720 // all active unique cell's compounds
//JobId = 730 // all genes in an abc-order
Verb = 2 // 0 - no verbosity, 1 - intermediate and 2 - maximal
[Flux] = mmol/(gDW*h)
// GAMS FORMAT DATA
//JobId = 800 // generation of GAMS input file: rev.reactions are replaced by irr.reactions
//JobId = 801 // generation of GAMS input file: rev.reactions are replaced by irr.reactions + boundary conditions
//JobId = 802 // generation of GAMS input file: reactions - redundant reactions + boundary conditions
//===========================================================================
// Optimization Criteria
//===========================================================================
//
// Purpose / Description in Brief
// ------------------------------
//
// Optimization criteria allow one to choose between different strategies
// to optimise the cellular behaviour.
//
// Parameters:
// -----------
//
// Each parameters line should look like
//
// id direction goal
//
// id - compound's (string) name or reaction's (integer) id
//
// direction: input - a net uptake rate of the given compound
// output - a net secretion rate of the given compound
// fwd - a forward flux through the reaction with id
// bwd - a backward flux through the (reversible) reaction with id
//
// goal - min for minimization
// - max for maximization
//
// The id and direction of a reacton must be precomputed and known in advance.
// This can be done by running ezcell with special modeling task parameters.
//
//===========================================================================
biomass output max // specific growth rate for biomass formation
//===========================================================================
// Mass Doubling Time (min)
//===========================================================================
40 // specific growth rate should be around 1.04 g/(gDW*h)
//===========================================================================
// Biomass Composition Parameters
//===========================================================================
//
// Purpose / Description in Brief
// ------------------------------
//
// Biomass composition corresponds to drains related to biomass formation
//
// Parameters:
// -----------
//
// Each line should look like
//
// name D/P value
//
// name - compound's name
// D - Drain, mmol/(gDW*h)
// P - Production, mmol/(gDW*h), to balance some drains
// value - drain (different drains and productions for the same compound are accumulated)
//===========================================================================
//
//---------------------------------------------------------------------------
// Amino Acids (mmol/gDW)
//---------------------------------------------------------------------------
ALA D 0.488 // 1) alanine
ARG D 0.281 // 2) arginine
ASP D 0.229 // 3) aspartic acid
ASN D 0.229 // 4) asparagine !!!
CYS D 0.087 // 5) cysteine
GLU D 0.250 // 6) glutamic acide
GLN D 0.250 // 7) glutamine
GLY D 0.582 // 8) glycine
HIS D 0.090 // 9) histidine
ILE D 0.276 // 10) isoleucine
LEU D 0.428 // 11) leucine
LYS D 0.326 // 12) lysine
MET D 0.146 // 13) methionine
PHE D 0.176 // 14) phenylalanine
PRO D 0.210 // 15) proline
SER D 0.205 // 16) serine
THR D 0.241 // 17) threonine
TRP D 0.054 // 18) tryptophan
TYR D 0.131 // 19) tyrosine
VAL D 0.402 // 20) valine
//---------------------------------------------------------------------------
// Cell Wall (mmol/gDW)
//---------------------------------------------------------------------------
PEPTIDO D 0.02760 // Peptidoglycan
LPS D 0.00840 // Lippolysaccharide
PS D 0.00258 // Phosphatidyl serine
PE D 0.09675 // Phosphatidyl ethanolamine
CL D 0.00645 // Cardiolypin
PG D 0.02322 // Phosphatidyl glycerol
//---------------------------------------------------------------------------
// DNA nucleotides (mmol/gDW)
//---------------------------------------------------------------------------
DATP D 0.0247 // Deoxyadenosine triphosphate
DGTP D 0.0254 // Deoxyguanosine triphosphate
DCTP D 0.0254 // Deoxycytidine triphosphate
DTTP D 0.0247 // Thymidine triphosphate
//---------------------------------------------------------------------------
// RNA nucleotides (mmol/gDW)
//---------------------------------------------------------------------------
ATP D 0.165 // Adenosine triphosphate
GTP D 0.203 // Guanosine triphosphate
CTP D 0.126 // Cytidine triphosphate
UTP D 0.136 // Uridine triphosphate
//---------------------------------------------------------------------------
// Energy Storage (mmol/gDW)
//---------------------------------------------------------------------------
GLYCOGEN D 0.154 // Glycogen
//---------------------------------------------------------------------------
// Cofactors (mmol/gDW)
//---------------------------------------------------------------------------
MTHF D 0.050000 // 5-Methyl tetrahydrofolate
NAD D 0.002150 // Nicotinamide adenine dinucleotide
NADH D 0.000050 // Nicotinamide adenine dinucleotide reduce
NADP D 0.000130 // Nicotinamide adenine dinucleotide phosphate
NADPH D 0.000400 // Dihydronicotinamide adenine dinucleotide phosphate reduced
UDPG D 0.003000 // UDP Glucose
COA D 0.000006 // Coenzyme A
SUCCOA D 0.000003 // Succinate CoA
ACCOA D 0.000050 // Acetyl-CoA
FAD D 0.000010 // Flavin adenine dinucleotide
//---------------------------------------------------------------------------
// Polyamines (mmol/gDW)
//---------------------------------------------------------------------------
SPMD D 0.007 // Spermidine
PTRC D 0.035 // Putrescine
//---------------------------------------------------------------------------
// Growth Associated Maintenance Requirements (mmol/gDW)
//---------------------------------------------------------------------------
ATP D 23.200 // Adenosine triphosphate
ADP P 23.200 // Adenosine diphosphate
PI P 23.200 // Phosphate (inorganic)
//===========================================================================
// Net drains
//===========================================================================
//
// Purpose / Description in Brief
//
// Net drains correspond to different kinds of expences for maintenance, which
// does not directly relate to the biomass formation
//
// Parameters:
// -----------
//
// Each line should look like
//
// name drain
//
// name - compound's name
// drain - drain value (different drains for the same compound are accumulated)
//
//===========================================================================
// Flux Boundary Conditions (mmol/(gDW*h))
//===========================================================================
//
// Purpose / Description in Brief
// ------------------------------
//
// flux boundary conditions are lower and upper bounds for net fluxes of
// substances of external pools, which may be transported to or from the cell;
//
// Parameters
// ----------
//
// Each parameters line should look like
//
// name dir min max
//
// name - the name of a transported substance
// dir - transport direction on the cell's membrane
// input - uptake
// output - secretion
// exchange - both uptake and secretion are possible
//
// min and max are positive real numbers
//
// Interpretation of data for input and output (irreversible) transport:
// min - minimal allowable net uptake/secretion rate
// max - maximal allowable net uptake/secretion rate
//
// Interpretation of data for exchange (reversible) transport:
// min - maximal allowable net uptake rate
// max - maximal allowable net secretion rate
//
// Special notation:
// inf - unconstrained (unbounded) flux value corresponding the case when flux
// has no lower or/and upper bounds, for example "H2O exchange inf inf"
// means that there is no restriction for boundary fluxes of H2O
//===========================================================================
// OUTPUT MIN-OUT MAX-OUT
//---------------------------------------------------------------------------
biomass output 0.0 inf
//---------------------------------------------------------------------------
// INPUT MIN-IN MAX-IN
//---------------------------------------------------------------------------
GLC input 0.0 10.0 // 10.0 alpha-D-Glucose, mmol/(gDW*h)
SLF input 0.0 inf // sulfate
//---------------------------------------------------------------------------
// EXCHANGE MAX-IN MAX-OUT
//---------------------------------------------------------------------------
NH3 exchange inf inf // default inf inf
O2 exchange inf 0.0 // last time 15.0 0.0
CO2 exchange inf inf // inf inf
PI exchange inf inf // inorganic phosphate
H exchange 0.0 0.0 // 0.0 0.0
K exchange inf inf // potassium
NA exchange inf inf // sodium
//---------------------------------------------------------------------------
// List of metabolites consumed by the cell
//---------------------------------------------------------------------------
// INPUT MIN MAX (allowable consumption range)
//---------------------------------------------------------------------------
ADN input 0.0 0.0 // Adenosine
AD input 0.0 0.0 // Adenine
ALA input 0.0 0.0 // Alanine
ARG input 0.0 0.0 // Arginine
C140 input 0.0 0.0 // Myristic acid
C160 input 0.0 0.0 // Palmitic acid
C180 input 0.0 0.0 // Stearic acid
CYS input 0.0 0.0 // Cysteine
CYTD input 0.0 0.0 // Cytidine
CYTS input 0.0 0.0 // Cytosine
DA input 0.0 0.0 // Deoxyadenosine
DC input 0.0 0.0 // Deoxycytidine
DG input 0.0 0.0 // Deoxyguanosine
DHA input 0.0 0.0 // ???
DIN input 0.0 0.0 // Deoxyinosine
DIPEP input 0.0 0.0 // Dipeptide
DT input 0.0 0.0 // Thymidine
DU input 0.0 0.0 // Deoxyuridine
FRU input 0.0 0.0 // Fructose
GABA input 0.0 0.0 // 4-Aminobutanoate
GL3P input 0.0 0.0 // Glycerol 3-phosphate
GLAC input 0.0 0.0 // Galactose
GLCN input 0.0 0.0 // Gluconate
GLN input 0.0 0.0 // Glutamine
GLTL input 0.0 0.0 // ???
GLT input 0.0 0.0 // ???
GSN input 0.0 0.0 // Guanosine
HIS input 0.0 0.0 // Histidine
ILE input 0.0 0.0 // Isoleucine
INS input 0.0 0.0 // Inosine
LEU input 0.0 0.0 // Leucine
MAN input 0.0 0.0 // ???
MDAP input 0.0 0.0 // Meso-diaminopimelat
MELI input 0.0 0.0 // Melibiose
MET input 0.0 0.0 // Methionine
MLT input 0.0 0.0 // ???
MNT input 0.0 0.0 // ???
NAC input 0.0 0.0 // Nicotinate
NAD input 0.0 0.0 // Nicotinamide adenine dinucleotide
OPEP input 0.0 0.0 // Oligopeptide
ORN input 0.0 0.0 // Ornithine
PEPT input 0.0 0.0 // Peptide
PTRC input 0.0 0.0 // Putrescine
RIB input 0.0 0.0 // Ribose
RMN input 0.0 0.0 // Rhamnose
SLA input 0.0 0.0 // Sialic acid
SPMD input 0.0 0.0 // Spermidine
SUC input 0.0 0.0 // ???
TRE input 0.0 0.0 // ???
URA input 0.0 0.0 // Uracil
URI input 0.0 0.0 // Uridine
VAL input 0.0 0.0 // Valine
XYL input 0.0 0.0 // D-Xylose
//---------------------------------------------------------------------------
// List of metabolites secreted by the cell
//---------------------------------------------------------------------------
// OUTPUT MIN MAX (allowable secretion range)
//---------------------------------------------------------------------------
AMP output 0.0 inf // Adenosine monophosphate
//---------------------------------------------------------------------------
// List of metabolites which can leave and re-entere the cell
//---------------------------------------------------------------------------
// DIRECTION IN OUT (maximal allowable values)
//---------------------------------------------------------------------------
ACAL exchange 0.0 inf // Acetaldehyde
AC exchange 0.0 inf // Acetate
AKG exchange 0.0 inf // a-Ketoglutarate
ARAB exchange 0.0 inf // Arabinose
ASN exchange 0.0 inf // Asparagine
ASP exchange 0.0 inf // Aspartate
BCAA exchange 0.0 inf // Branched chain amino acid
DALA exchange 0.0 inf // D-Alanine
DSER exchange 0.0 inf // D-Serine
ETH exchange 0.0 inf // Ethanol
FOR exchange 0.0 inf // Formate
FUC exchange 0.0 inf // Fucose
FUM exchange 0.0 inf // Fumarate
GLAL exchange 0.0 inf // D-Glyceraldehyde
GLU exchange 0.0 inf // Glutamate
GLY exchange 0.0 inf // Glycine
GL exchange 0.0 inf // Glycerol
GN exchange 0.0 inf // Guanine
HYXN exchange 0.0 inf // Hypoxanthine
LAC exchange 0.0 inf // D-Lactate
LCTS exchange 0.0 inf // Lactose
LYS exchange 0.0 inf // L-Lysine
MAL exchange 0.0 inf // Malate
NMN exchange 0.0 inf // Nicotinamide mononucleotide
PHE exchange 0.0 inf // Phenylalanine
PNTO exchange 0.0 inf // Pantothenate
PRO exchange 0.0 inf // Proline
PYR exchange 0.0 inf // Pyruvate
SER exchange 0.0 inf // Serine
SUCC exchange 0.0 inf // Succinate
THR exchange 0.0 inf // Threonine
TRP exchange 0.0 inf // Tryptophan
TYR exchange 0.0 inf // Tyrosine
UREA exchange 0.0 inf // Urea
XAN exchange 0.0 inf // Xanthine
XTSN exchange 0.0 inf // Xanthosine
//===========================================================================
// Simple Constraints for Reactions Fluxes
//===========================================================================
//
// Purpose / Description in Brief
// ------------------------------
//
// The constraints are a sort of thermodynamical lower and upper bounds allowable
// for fluxes through intracellular and transport reactions
//===========================================================================