waldeyr / insilicometabolicmodelingandengineering

In Silico Metabolic Modeling and Engineering

Journal: Processes

Special Issue: In Silico Metabolic Modeling and Engineering

Article: Exploring plant sesquiterpene diversity by generating chemical networks

Install Environment on Linux

Install Environment on Linux

Install Environment with Docker

Install Environment with Docker

Getting Started

After install the environment, test it with: $HOME/mod-v0.7.0/bin/mod

How to run the simulations?

Clone this repository: git clone https://github.com/waldeyr/InSilicoMetabolicModelingAndEngineering.git

Running the simulation 01

cd InSilicoMetabolicModelingAndEngineering/simulation_01

./runSimulation01

Running the simulation 02

cd InSilicoMetabolicModelingAndEngineering/simulation_02

./runSimulation02

Running the simulation 03

cd InSilicoMetabolicModelingAndEngineering/simulation_03

./runSimulation03

How to run the simulations on Docker environment?

cd InSilicoMetabolicModelingAndEngineering/simulation_store

Check if the database is running:

./neo4jStatus

If not, start it:

./neo4jStart

Enter on the simulation folder

./runSimulationStoringWithNeo4J

You can change the resulting network removing or adding rules to the simulation from the Processes_Store.py in the proper lines:

#!python
pushFilePrefix("../rules/")
opp_loss_for_fpp = ruleGML('opp_loss_for_fpp.gml')
fpp_1_10_cyc = ruleGML("fpp-1-10Cyc.gml")
fpp_1_11_cyc = ruleGML("fpp-1-11Cyc.gml")
ring_closure_c2_c10 = ruleGML("2-10Cyc.gml")
h_shift_c1_c2 = ruleGML("1-2Hshift.gml")
h_shift_c1_c3 = ruleGML("1-3Hshift.gml")
h_loss = ruleGML("h_loss.gml")
h2o_gain = ruleGML("h2o_gain.gml")
wagner_meerwein = ruleGML("WMshift.gml")
allyl_shift = ruleGML("allylshift.gml")
popFilePrefix()

You can change the initial set of molecules in the line:

#!python
eductMolecules = [fpp, H2O]

You can change the number of iterations in the line:

#!python
dg = hypergraph.getHyperGraph(eductMolecules, 4)