diff --git a/modeldb/modeldb-run.yaml b/modeldb/modeldb-run.yaml index 89ca370..8b24843 100644 --- a/modeldb/modeldb-run.yaml +++ b/modeldb/modeldb-run.yaml @@ -465,10 +465,7 @@ - load_file("sample.hoc") - verify_graph_() script: - - sed 's,tstop *=,tstop = 100//, - - /whichAP/,$d - - ''' sample.hoc > temp.tmp' - - mv temp.tmp sample.hoc + - sed -i'.bak' -e 's/tstop *=/tstop = 100\/\//g;/whichAP/,$d' sample.hoc 76879: run: - tstop=20 @@ -503,10 +500,7 @@ 83590: run: [] script: - - sed 's/mustart = -0.400/mustart = 0.800/ - - ' s/sigmastart = 0.064/sigmastart = 0.128/' - - ''' mylibs/TFparams.hoc > temp.tmp' - - mv temp.tmp mylibs/TFparams.hoc + - sed -i'.bak' -e 's/mustart = -0.400/mustart = 0.800/g;s/sigmastart = 0.064/sigmastart = 0.128/g' mylibs/TFparams.hoc 84589: run: - //ignore sim in subdirectory @@ -673,9 +667,7 @@ - load_file("batch_.hoc") - verify_graph_() script: - - sed 's/batch_flag=0/batch_flag=1/ - - s/tstop = 1e3/tstop = 20/' batch_.hoc > temp.tmp - - mv temp.tmp batch_.hoc + - sed -i'.bak' -e 's/batch_flag=0/batch_flag=1/g;s/tstop = 1e3/tstop = 20/g' batch_.hoc 106551: run: - use_mcell_ran4(1) @@ -823,8 +815,7 @@ - //load_file("init.hoc") - //verify_graph_() script: - - sed 's/tstop = 100/tstop = 20/' init.hoc > temp.tmp - - mv temp.tmp init.hoc + - sed -i'.bak' -e 's/tstop = 100/tstop = 20/g' init.hoc 116835: run: - tstop=10 @@ -836,8 +827,7 @@ - run() - verify_graph_() script: - - sed 's/^showdemo=1/showdemo=0/' mosinit.hoc > temp.tmp - - mv temp.tmp mosinit.hoc + - sed -i'.bak' -e 's/^showdemo=1/showdemo=0/g' mosinit.hoc 116956: run: - run() @@ -962,16 +952,14 @@ - run() - verify_graph_() script: - - sed 's/tstop = 6500/tstop = 100/' session.ses > temp.tmp - - mv temp.tmp session.ses + - sed -i'.bak' -e 's/tstop = 6500/tstop = 100/g' session.ses 124291: run: - stim.amp = 0.1 - runa() - verify_graph_() script: # todo -> fix model for NEURON 8.0.0 and remove this script - - sed 's/return 0;//' MOPP_Fig_1B_left/ichan2.mod > temp.tmp - - mv temp.tmp MOPP_Fig_1B_left/ichan2.mod + - sed -i'.bak' -e 's/return 0;//g' MOPP_Fig_1B_left/ichan2.mod 138321: run: - run() @@ -1076,21 +1064,21 @@ - run() - verify_graph_() script: - - sed -i 's/tstop = /tstop = 50\/\//' Fig8_tuft_NMDA_spike.hoc - - sed -i 's/simul_iter=/simul_iter=2 \/\//' Fig8_tuft_NMDA_spike.hoc + - sed -i'.bak' -e 's/tstop = /tstop = 50\/\//' Fig8_tuft_NMDA_spike.hoc + - sed -i'.bak' -e 's/simul_iter=/simul_iter=2 \/\//' Fig8_tuft_NMDA_spike.hoc comment: usual simulation time is ~ 10 minutes (tstop = 120 and simul_iter=10) 206267: run: - run() - verify_graph_() script: - - sed -i 's/tstop=/tstop=100 \/\//' Start.hoc + - sed -i'.bak' -e 's/tstop=/tstop=100 \/\//' Start.hoc 157157: run: - run() - verify_graph_() script: - - sed -i 's/tstop = 5000/tstop = 250 \/\//g' PC.ses + - sed -i'.bak' -e 's/tstop = 5000/tstop = 250 \/\//g' PC.ses 244848: run: null comment: not straightforward to cut down simulation time, takes too long @@ -1105,15 +1093,15 @@ - run() - verify_graph_() script: - - sed -i 's/500/5/g' BPF.hoc - - sed -i 's/2\([0|1]\)000/2\1/g' BPF.hoc + - sed -i'.bak' -e 's/500/5/g' BPF.hoc + - sed -i'.bak' -e 's/2\([0|1]\)000/2\1/g' BPF.hoc comment: diving some numbers with 100 halvened the sim time 151126: run: - run() - verify_graph_() script: - - sed -i 's/tstop = 550/tstop = 100/' HAM_SR1.ses + - sed -i'.bak' -e 's/tstop = 550/tstop = 100/' HAM_SR1.ses # python models 189922: python: true @@ -1121,6 +1109,6 @@ - import os; os.system("python mosinit.py"); quit(); script: - 2to3 -w . - - sed -i 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close();quit()/' clay_mohit.py + - sed -i'.bak' -e 's/plt.show()/plt.show(block=False);plt.pause(1);plt.close();quit()/' clay_mohit.py