WOLFRAM SYSTEM MODELER

Cytosol

Cytosolic compartment

Diagram

Wolfram Language

In[1]:=
SystemModel["IndustryExamples.LifeSciences.Glycolysis.Cytosol"]
Out[1]:=

Information

Library Dependency

This model requires the BioChem library.

  • The free BioChem library is an extendable, general purpose Modelica library for modeling, simulation and visualization of biological and biochemical systems. The library is designed to be used together with Wolfram System Modeler, which enables several extra features such as Systems Biology Markup Language (SBML) import and export. BioChem can, for instance, be used for selecting drug targets with PK/PD modeling or searching for novel drug targets with mechanistic modeling of the reactions in a cell or organism.

Model of the cytosolic glycolysis compartment used in the main glycolysis model.

Parameters (1)

mainCompartment

Value: false

Type: Boolean

Description: Specifies whether the compartment is a main (top-level) compartment. Used in SBML import/export.

Connectors (5)

Glc_node

Type: SubstanceConnector

Description: Connector between substances and reactions

G6P_node

Type: SubstanceConnector

Description: Connector between substances and reactions

EtOH_node

Type: SubstanceConnector

Description: Connector between substances and reactions

Glyc_node

Type: SubstanceConnector

Description: Connector between substances and reactions

ACA_node

Type: SubstanceConnector

Description: Connector between substances and reactions

Components (31)

Glc

Type: Glc_

Description: Cytosolic glucose

ATP

Type: ATP_

Description: ATP

G6P

Type: G6P_

Description: Glucose-6-Phosphate

ADP

Type: ADP_

Description: ADP

F6P

Type: F6P_

Description: Fructose-6-Phosphate

FBP

Type: FBP_

Description: Fructose 1,6-bisphosphate

GAP

Type: GAP_

Description: Glyceraldehyde 3-phosphate

DHAP

Type: DHAP_

Description: Dihydroxyacetone phosphate

NAD

Type: NAD_

Description: NAD

BPG

Type: BPG_

Description: 1,3-Bisphosphoglycerate

NADH

Type: NADH_

Description: NADH

PEP

Type: PEP_

Description: Phosphoenolpyruvate

Pyr

Type: Pyr_

Description: Pyruvate

ACA

Type: ACA_

Description: Acetaldehyde

EtOH

Type: EtOH_

Glyc

Type: Glyc_

Description: Glycerol

AMP

Type: AMP_

Description: AMP

vHK

Type: vHK_

Description: Hexokinase

vPGI

Type: vPGI_

Description: Phosphoglucoisomerase

vPFK

Type: vPFK_

Description: Phosphofructokinase

vALD

Type: vALD_

Description: Aldolase

vTIM

Type: vTIM_

Description: Triosephosphate isomerase

vGAPDH

Type: vGAPDH_

Description: Glyceraldehyde 3-phosphate dehydrogenase

vlpPEP

Type: vlpPEP_

Description: Phosphoenolpyruvate synthesis

vPK

Type: vPK_

Description: Pyruvate kinase

vPDC

Type: vPDC_

Description: Pyruvate decarboxylase

vADH

Type: vADH_

Description: Alcohol dehydrogenase

vlpGlyc

Type: vlpGlyc_

Description: Glycerol synthesis

vstorage

Type: vstorage_

Description: Storage

vconsum

Type: vconsum_

Description: ATP consumption

vAK

Type: vAK_

Description: Adenylate kinase

Used in Examples (1)

GlycolysisModel

IndustryExamples.LifeSciences.Glycolysis

Main model - Extracellular compartment