I don't seem to find a way to specify how many experiments we want GNW to simulate. There's a default of 100 experiments and if I need more than this, I would have to go back and click the button again. Did I miss the feature somewhere? If it's not already there, would be very nice to have. :)

I commented out the outputDirectory option in the settings.txt, tried putting the -c settings.txt option both before and after --output-path some_path but neither works. Output is still generated in the current directory.

I am getting the error:

Error:(1016, 44) java: cannot find symbol
symbol: class PredictionTab
location: class ch.epfl.lis.gnwgui.Predictions

However, PredictionTab is defined in PredictionsPanel.java which is imported at the top of Predictions.java. I believe it can't see the protected inner class.

When I run Evaluation function on GNW I got above error. Please help me solve it.

Thank you so much,

If the option loadPerturbations is activated, GNW does not regard the order of species defined in the perturbation file. Instead, it assumes that the species are in the same order as in the corresponding gml or sbml file.

During the simulation, the perturbations file is overwritten by GNW to contain the perturbation that was performed (see
perturbations_after_execution.tsv.txt
)

Attached you may find an example, where the resulting timeseries contains a perturbation in the wrong species.

Remove tailing txt from tsv, xml and gml files and execute with:

java -jar gnw.jar -s -c ./settings.txt --input-net test_0-10.xml

settings.txt
test_0-10_dream4_timeseries_perturbations.tsv.txt
test_0-10.gml.txt
test_0-10.xml.txt

It would be nice if the binary of GNW would be updated on the webpage. The current binary has problems in parsing the parameters maxt and dt of the setting file and thus is not usable in a scripting setup.

Do you have an idea about GNW's scalability, like how long it would take to run ODE, Stochastic (DREAM4 settings) for a network of 10000-or-so genes?