I have a working GoLLM task for AMR enrichment. We need to integrate it with the rest of the task runner architecture @kbirk. Example outputs below.
{
"initials": {
"protein": {
"description": "Relative concentration of the effective protein, which is in the molecular state capable of inhibiting mRNA production.",
"unit": "dimensionless"
},
"mRNA": {
"description": "Relative concentration of mRNA, which is involved in the production of the effective protein.",
"unit": "dimensionless"
}
},
"parameters": {
"k": {
"description": "Scaling constant used in the nonlinear term of the mRNA production rate equation.",
"unit": "dimensionless"
},
"n": {
"description": "Hill coefficient representing the cooperativity in the negative feedback loop of protein on mRNA production.",
"unit": "dimensionless"
},
"rM": {
"description": "Scaled mRNA production rate constant.",
"unit": "hr^-1"
},
"m": {
"description": "Exponent representing the nonlinearity in the protein production cascade.",
"unit": "dimensionless"
},
"parameter_0000009": {
"description": "Not explicitly described in the provided text.",
"unit": "N/A"
},
"rP": {
"description": "Protein production rate constant.",
"unit": "hr^-1"
},
"qM": {
"description": "mRNA degradation rate constant.",
"unit": "hr^-1"
},
"qP": {
"description": "Protein degradation rate constant.",
"unit": "hr^-1"
},
"compartment_0000004": {
"description": "Not explicitly described in the provided text.",
"unit": "N/A"
}
}
}
{
"initials": {
"Ttum": {
"description": "Cell concentration of the original tumor",
"unit": "cells/ml"
},
"Tplas": {
"description": "Cancer cell concentration in the plasma",
"unit": "cells/ml"
},
"Tnew": {
"description": "Cell concentration of new and developing tumor",
"unit": "cells/ml"
}
},
"parameters": {
"b": {
"description": "Relative drug efficacy factor for specific growth rate",
"unit": "dimensionless"
},
"kf1": {
"description": "Rate constant for cell release from the original tumor to plasma",
"unit": "day^-1"
},
"kr1": {
"description": "Rate constant for cell attachment from plasma to the original tumor",
"unit": "day^-1"
},
"c": {
"description": "Rate constant for plasma clearance",
"unit": "day^-1"
},
"d": {
"description": "Relative drug efficacy factor for plasma clearance",
"unit": "dimensionless"
},
"kf2": {
"description": "Rate constant for cell release from plasma to new tumor",
"unit": "day^-1"
},
"kr2": {
"description": "Rate constant for cell attachment from new tumor to plasma",
"unit": "day^-1"
},
"T0": {
"description": "Equilibrium tumor cell concentration in the tumor",
"unit": "cells/ml"
},
"a": {
"description": "Relative drug efficacy factor for cell release rate",
"unit": "dimensionless"
},
"r": {
"description": "Specific growth rate of tumor cells",
"unit": "day^-1"
},
"n": {
"description": "Number of new tumors being developed simultaneously",
"unit": "dimensionless"
},
"Tumor": {
"description": "General term for tumor cell concentration",
"unit": "cells/ml"
}
}
}
{
"initials": {},
"parameters": {
"b_reac_r": {
"description": "Bio-reaction rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"AdoMet_r": {
"description": "Methionine adenosyl transfer rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"Methy_trans": {
"description": "Methyl transfer rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"SAM_Dec": {
"description": "SAM decarboxylation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"Spermi_uti": {
"description": "Spermidine utilization rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"MTR_e": {
"description": "MTR excretion rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"Polyamine_uti": {
"description": "Polyamine utilization rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"Pfs_prot_d": {
"description": "Pfs protein degradation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"pfs_transl": {
"description": "Pfs translation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"pfs_mRNA_d": {
"description": "Pfs mRNA degradation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"pfs_transc": {
"description": "Pfs transcription rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"Met_recov": {
"description": "Methionine recovery rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"DPD_deg_r": {
"description": "DPD degradation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"LuxS_prot_d": {
"description": "LuxS protein degradation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"LuxS_transl": {
"description": "LuxS translation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"LuxS_mRNA_d": {
"description": "LuxS mRNA degradation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"LuxS_transc": {
"description": "LuxS transcription rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"AI2_syn_r": {
"description": "AI-2 synthesis rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"AI2_excret_r": {
"description": "AI-2 excretion rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"AI2_trans_r": {
"description": "AI-2 transport rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"AI2_phos_r": {
"description": "AI-2 phosphorylation rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"MTR_syn_r": {
"description": "MTR synthesis rate constant",
"units": {
"expression": "1/min",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>min</ci></apply>"
}
},
"SAH_Hydro_r": {
"description": "SAH hydrolysis rate constant",
"units": {
"expression": "1/(M*min)",
"expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>M</ci><ci>min</ci></apply></apply>"
}
},
"SRH_cleav": {
"description": "SRH cleavage rate constant",
"units": {
"expression": "1/(M*min)",
"expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>M</ci><ci>min</ci></apply></apply>"
}
},
"SpeE_syn_r": {
"description": "Spermidine synthesis rate constant",
"units": {
"expression": "1/(M*min)",
"expression_mathml": "<apply><divide/><cn>1</cn><apply><times/><ci>M</ci><ci>min</ci></apply></apply>"
}
},
"compartment": {
"description": "Compartment for the reactions",
"units": {
"expression": "n/a",
"expression_mathml": "<ci>n/a</ci>"
}
}
}
}
{ "initials": {},
"parameters": {
"kb": {
"description": "Rate constant for the backward reaction in the model.",
"units": {
"expression": "1/s",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
}
},
"kf": {
"description": "Rate constant for the forward reaction in the model.",
"units": {
"expression": "1/s",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
}
},
"default_compartment": {
"description": "The default compartment where the reactions take place, typically representing the synaptic or cytosolic volume.",
"units": {
"expression": "fl",
"expression_mathml": "<ci>fl</ci>"
}
},
"geometry": {
"description": "The geometric configuration of the synaptic and cytosolic compartments, including their volumes.",
"units": {
"expression": "fl",
"expression_mathml": "<ci>fl</ci>"
}
},
"geometry_sbo_1_sbc_": {
"description": "Specific geometric parameter related to the synaptic and cytosolic compartments, possibly a scaling factor or specific volume.",
"units": {
"expression": "fl",
"expression_mathml": "<ci>fl</ci>"
}
},
"k1": {
"description": "Rate constant for a specific reaction involving AMPAR or CaMKII in the model.",
"units": {
"expression": "1/s",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
}
},
"k2": {
"description": "Rate constant for another specific reaction involving AMPAR or CaMKII in the model.",
"units": {
"expression": "1/s",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
}
},
"k3": {
"description": "Rate constant for yet another specific reaction involving AMPAR or CaMKII in the model.",
"units": {
"expression": "1/s",
"expression_mathml": "<apply><divide/><cn>1</cn><ci>s</ci></apply>"
}
}
}
}