readmodel

Synopsis: Read a model file and print out its details after processing into model objects.

Usage: python astools.py readmodel [option]

where [option] can be

• modelfile: Relative path to the model specification file.
• mtype: Type of model specification file. Allowable types are 'ASM' (AdvanceSyn Model Specification), 'MO' (AdvanceSyn Model Objects). Default = 'ASM'.

For example:

python astools.py readmodel --mtype=ASM --modelfile=models/asm/glycolysis.modelspec

Working example:

D:\Dropbox\MyProjects\astoolkit>python astools.py readmodel --mtype=ASM --modelfile=models/asm/glycolysis.modelspec
-------- Model Identifiers --------
name: glycolysis

author: Maurice Ling

-------- Model Objects --------
Name: glucose
Description: D-glucose
Initial: 1e-5
Influx:
{}
Outflux:
{'r1': '(1e-6 * hk * glucose)/(1e-6 + (hk * glucose))'}

Name: atp
Description: adenosine-triphosphate
Initial: 1e-5
Influx:
{'r10': '(1e-6 * pk * pep)/(1e-6 + (pk * pep))',
 'r7': '(1e-6 * pkg * bpg13)/(1e-6 + (pkg * bpg13))'}
Outflux:
{'r1': '(1e-6 * hk * glucose)/(1e-6 + (hk * glucose))',
 'r3': '(1e-6 * pfk * f6p)/(1e-6 + (pfk * f6p))'}

Name: adp
Description: adenosine-diphosphate
Initial: 1e-5
Influx:
{'r1': '(1e-6 * hk * glucose)/(1e-6 + (hk * glucose))',
 'r3': '(1e-6 * pfk * f6p)/(1e-6 + (pfk * f6p))'}
Outflux:
{'r10': '(1e-6 * pk * pep)/(1e-6 + (pk * pep))',
 'r7': '(1e-6 * pkg * bpg13)/(1e-6 + (pkg * bpg13))'}

Name: proton
Description: proton
Initial: 1e-5
Influx:
{'r1': '(1e-6 * hk * glucose)/(1e-6 + (hk * glucose))',
 'r3': '(1e-6 * pfk * f6p)/(1e-6 + (pfk * f6p))',
 'r6': '(1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))'}
Outflux:
{'r10': '(1e-6 * pk * pep)/(1e-6 + (pk * pep))'}

Name: nad
Description: NAD
Initial: 1e-5
Influx:
{}
Outflux:
{'r6': '(1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))'}

Name: pi
Description: phosphate
Initial: 1e-5
Influx:
{}
Outflux:
{'r6': '(1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))'}

Name: nadh
Description: NADH
Initial: 1e-5
Influx:
{'r6': '(1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))'}
Outflux:
{}

Name: water
Description: water
Initial: 1e-5
Influx:
{'r9': '(1e-6 * eno * pg2)/(1e-6 + (eno * pg2))'}
Outflux:
{}

Name: g6p
Description: a-D-Glucose-6-phosphate
Initial: 1e-9
Influx:
{'r1': '(1e-6 * hk * glucose)/(1e-6 + (hk * glucose))'}
Outflux:
{'r2': '(1e-6 * pgi * g6p)/(1e-6 + (pgi * g6p))'}

Name: f6p
Description: b-D-Fructose-6-phosphate
Initial: 1e-9
Influx:
{'r2': '(1e-6 * pgi * g6p)/(1e-6 + (pgi * g6p))'}
Outflux:
{'r3': '(1e-6 * pfk * f6p)/(1e-6 + (pfk * f6p))'}

Name: f16p
Description: b-D-Fructose-1,6-phosphate
Initial: 1e-9
Influx:
{'r3': '(1e-6 * pfk * f6p)/(1e-6 + (pfk * f6p))'}
Outflux:
{'r4': '(1e-6 * aldo * f16p)/(1e-6 + (aldo * f16p))'}

Name: gadp
Description: D-glyceraldehyde 3-phosphate
Initial: 1e-9
Influx:
{'r4': '(1e-6 * aldo * f16p)/(1e-6 + (aldo * f16p))',
 'r5': '(1e-6 * tpi * dhap)/(1e-6 + (tpi * dhap))'}
Outflux:
{'r6': '(1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))'}

Name: dhap
Description: Dihydroxyacetone phosphate
Initial: 1e-9
Influx:
{'r4': '(1e-6 * aldo * f16p)/(1e-6 + (aldo * f16p))'}
Outflux:
{'r5': '(1e-6 * tpi * dhap)/(1e-6 + (tpi * dhap))'}

Name: bpg13
Description: D-1,3-bisphosphoglycerate
Initial: 1e-9
Influx:
{'r6': '(1e-6 * gapdh * gadp)/(1e-6 + (gapdh * gadp))'}
Outflux:
{'r7': '(1e-6 * pkg * bpg13)/(1e-6 + (pkg * bpg13))'}

Name: pg3
Description: 3-phosphoglycerate
Initial: 1e-9
Influx:
{'r7': '(1e-6 * pkg * bpg13)/(1e-6 + (pkg * bpg13))'}
Outflux:
{'r8': '(1e-6 * pgm * pg3)/(1e-6 + (pgm * pg3))'}

Name: pg2
Description: 2-phosphoglycerate
Initial: 1e-9
Influx:
{'r8': '(1e-6 * pgm * pg3)/(1e-6 + (pgm * pg3))'}
Outflux:
{'r9': '(1e-6 * eno * pg2)/(1e-6 + (eno * pg2))'}

Name: pep
Description: phosphoenolpyruvate
Initial: 1e-9
Influx:
{'r9': '(1e-6 * eno * pg2)/(1e-6 + (eno * pg2))'}
Outflux:
{'r10': '(1e-6 * pk * pep)/(1e-6 + (pk * pep))'}

Name: pyr
Description: pyruvate
Initial: 1e-9
Influx:
{'r10': '(1e-6 * pk * pep)/(1e-6 + (pk * pep))'}
Outflux:
{}

Name: hk.rna
Description: hexokinase
Initial: 0
Influx:
{'e1.rna': '1e-7'}
Outflux:
{}

Name: hk
Description: hexokinase
Initial: 0
Influx:
{'e1': '1e-5 * hk.rna'}
Outflux:
{}

Name: pgi
Description: Phosphoglucose isomerase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: pfk
Description: phosphofructokinase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: aldo
Description: fructose-bisphosphate aldolase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: tpi
Description: triosephosphate isomerase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: gapdh
Description: glyceraldehyde phosphate dehydrogenase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: pkg
Description: phosphoglycerate kinase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: pgm
Description: phosphoglycerate mutase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: eno
Description: enolase
Initial: 1e-6
Influx:
{}
Outflux:
{}

Name: pk
Description: pyruvate kinase
Initial: 1e-6
Influx:
{}
Outflux:
{}