InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/
OutFilePrefix /cse/faculty/karplus/dna/predict-2nd/testing/

ReadNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6.net
NameNet overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net

ReadParams params/2-feb-00-fast

# Note: the following includes read the training set(s),
# and, in doing so, reset the InFilePrefix

ReadToSet train
InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/training-data/
Include overrep-2260.t99-read

SetOverhang

ReportNetQualityForTrainTo quality-reports/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-t.quality
ReportNetQualityForCrossTrainTo quality-reports/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6.quality



unfreeze 0
freeze 1
freeze 2
freeze 3

TrainNet 100
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net


unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3

TrainNet 100
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net
TrainNet 100
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net

freeze 0
unfreeze 1
freeze 2
freeze 3
TrainNet 50
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net

freeze 0
freeze 1
unfreeze 2
freeze 3
TrainNet 50
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net

freeze 0
freeze 1
freeze 2
unfreeze 3
TrainNet 50
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net

unfreeze 0
unfreeze 1
unfreeze 2
unfreeze 3
TrainNet 100
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net
TrainNet 100
ReportNeuralNet networks/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.net


ReportTrainByChain quality-reports/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.by-chain

ReportQvsPhatTo quality-reports/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.q-vs-phat

ReportUnitUsageTo quality-reports/overrep-2260-IDaa13-5-8-7-10-5-9-11-ehl-seeded6-trained.unit-usage

TestNet