#2 simulation: either specify timeToConvergenceODE_ or maxtSDE

[James Jensen]

Hello!

I am using GeneNetWeaver from the command line (via a python script) to generate a large number of networks and associated datasets.

I first extract a subnetwork with

java -jar gnw3-standalone.jar --extract -c settings.txt --input-net ecoli_transcriptional_network_regulonDB_6_7.tsv --random-seed --greedy-selection --subnet-size=10 --num-subnets=1 --output-net-format=4 --output-path Ecoli/size_10/network_1

I then move into Ecoli/size_10/network_1/dataset_1 and attempt to generate a dataset with

java -jar /home/jamesdj/sandbox/gnw3-standalone.jar --simulate -c /home/jamesdj/sandbox/settings.txt --input-net ../ecoli_transcriptional_network_regulonDB_6_7-1.xml --output-path .

This is where the following error appears about half of the time:

[normal simulation output up to here]
Simulating steady-state "dualknockouts" using SDEs ...
SteadyStateExperiment::run(): For SDE steady-state simulation, either specify timeToConvergenceODE_ or maxtSDE_
java.lang.RuntimeException: For SDE steady-state simulation, either specify timeToConvergenceODE_ or maxtSDE_
at ch.epfl.lis.gnw.SteadyStateExperiment.run(SteadyStateExperiment.java:143)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.runSteadyStateExperiments(BenchmarkGeneratorDream4.java:313)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.runAll(BenchmarkGeneratorDream4.java:192)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.generateBenchmark(BenchmarkGeneratorDream4.java:115)
at ch.epfl.lis.gnwgui.Main.simulateNetwork(Main.java:608)
at ch.epfl.lis.gnwgui.Main.parseArguments(Main.java:784)
at ch.epfl.lis.gnwgui.Main.main(Main.java:70)
java.lang.RuntimeException: For SDE steady-state simulation, either specify timeToConvergenceODE_ or maxtSDE_
at ch.epfl.lis.gnw.SteadyStateExperiment.run(SteadyStateExperiment.java:143)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.runSteadyStateExperiments(BenchmarkGeneratorDream4.java:313)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.runAll(BenchmarkGeneratorDream4.java:192)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.generateBenchmark(BenchmarkGeneratorDream4.java:115)
at ch.epfl.lis.gnwgui.Main.simulateNetwork(Main.java:608)
at ch.epfl.lis.gnwgui.Main.parseArguments(Main.java:784)
at ch.epfl.lis.gnwgui.Main.main(Main.java:70)
Main::simulateNetwork(): null
java.lang.RuntimeException
at ch.epfl.lis.gnw.SteadyStateExperiment.run(SteadyStateExperiment.java:173)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.runSteadyStateExperiments(BenchmarkGeneratorDream4.java:313)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.runAll(BenchmarkGeneratorDream4.java:192)
at ch.epfl.lis.gnw.BenchmarkGeneratorDream4.generateBenchmark(BenchmarkGeneratorDream4.java:115)
at ch.epfl.lis.gnwgui.Main.simulateNetwork(Main.java:608)
at ch.epfl.lis.gnwgui.Main.parseArguments(Main.java:784)
at ch.epfl.lis.gnwgui.Main.main(Main.java:70)
ByeBye!

It appears to have something to do with the extracted network. If I can simulate datasets from a particular network once, I can simulate them every time; if simulation from a particular network fails the first time, it fails every time.

I'm puzzled by the error because 1) there is no command-line option to specify timeToConvergenceODE_ or maxtSDE_, and 2) it works half of the time without any such specification.