{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_CAI"},{"status":"SUCCEEDED","id":"data_set_H_IHVA"},{"status":"SUCCEEDED","id":"data_set_H_INA"},{"status":"SUCCEEDED","id":"data_set_H_INAD"},{"status":"SUCCEEDED","id":"data_set_INE"},{"status":"SUCCEEDED","id":"data_set_INI"},{"status":"SUCCEEDED","id":"data_set_INNE"},{"status":"SUCCEEDED","id":"data_set_INNI"},{"status":"SUCCEEDED","id":"data_set_M_IHVA"},{"status":"SUCCEEDED","id":"data_set_M_IKCA"},{"status":"SUCCEEDED","id":"data_set_M_IKM"},{"status":"SUCCEEDED","id":"data_set_M_IKV"},{"status":"SUCCEEDED","id":"data_set_M_INA"},{"status":"SUCCEEDED","id":"data_set_M_INAD"},{"status":"SUCCEEDED","id":"data_set_M_INAPD"},{"status":"SUCCEEDED","id":"data_set_VD"},{"status":"SUCCEEDED","id":"data_set_VS"}],"duration":0.165847,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"}],"duration":0.197448,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"1000.0","key":"total"},{"value":"euler","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"20","key":"njmp"}],"algorithm":"KISAO_0000030","duration":0.466553,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.948956,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml:\r\n Tasks (1):\r\n task\r\n Reports (1):\r\n report: 18 data sets\r\n Plots (1):\r\n plot: 1 curves\r\n\r\nExecuting SED-ML file 1: Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml ...\r\n Found 1 tasks and 2 outputs:\r\n Tasks:\r\n `task`\r\n Outputs:\r\n `plot`\r\n `report`\r\n Executing task 1: `task`\r\n Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n Generating 2 outputs ...\r\n Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n Generating output 2: `plot` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml"}],"duration":1.591051,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX archive =========================================\u001b[0m\n % Total % Received % Xferd Average Speed Time Time Time Current\n Dload Upload Total Spent Left Speed\n\r 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0\r100 138 100 138 0 0 475 0 --:--:-- --:--:-- --:--:-- 477\n\r 0 17.3M 0 67037 0 0 177k 0 0:01:39 --:--:-- 0:01:39 177k\r100 17.3M 100 17.3M 0 0 30.7M 0 --:--:-- --:--:-- --:--:-- 88.6M\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO: Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mCOMBINE/OMEX archive has warnings.\r\n - The manifest does not include its parent COMBINE/OMEX archive. 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path/Bazh_Ko_Cli_altKCC2_full_68.m\nCompleted 2.8 MiB/~16.9 MiB (7.5 MiB/s) with ~167 file(s) remaining (calculating...)\rCompleted 2.8 MiB/~16.9 MiB (7.5 MiB/s) with ~167 file(s) remaining (calculating...)\rupload: contents/Fig. 1/D/Data_fit/NKCC1(-).sfit to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 1/D/Data_fit/NKCC1(-).sfit\nCompleted 2.8 MiB/~16.9 MiB (7.5 MiB/s) with ~166 file(s) remaining (calculating...)\rCompleted 3.0 MiB/~16.9 MiB (7.8 MiB/s) with ~166 file(s) remaining (calculating...)\rupload: contents/Fig. 1/D/Data_fit/NKCC1_effect.jpg to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 1/D/Data_fit/NKCC1_effect.jpg\nCompleted 3.0 MiB/~16.9 MiB (7.8 MiB/s) with ~165 file(s) remaining (calculating...)\rCompleted 3.0 MiB/~16.9 MiB (7.8 MiB/s) with ~165 file(s) remaining (calculating...)\rupload: contents/Fig. 1/D/Data_fit/NKCC1_effect.png to 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2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.ode to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.ode\nCompleted 3.2 MiB/~17.3 MiB (7.7 MiB/s) with ~194 file(s) remaining (calculating...)\rCompleted 3.3 MiB/~17.3 MiB (7.6 MiB/s) with ~194 file(s) remaining (calculating...)\rupload: contents/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml\nCompleted 3.3 MiB/~17.3 MiB (7.6 MiB/s) with ~193 file(s) remaining (calculating...)\rCompleted 3.3 MiB/~17.3 MiB (7.6 MiB/s) with ~195 file(s) remaining (calculating...)\rupload: contents/Fig. 2/B/Bazh_Ko_Cli_altKCC2_path.m to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/B/Bazh_Ko_Cli_altKCC2_path.m\nCompleted 3.3 MiB/~17.3 MiB (7.6 MiB/s) with ~194 file(s) remaining 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Net/Net_bursters_no_connection_freq.m\nCompleted 4.3 MiB/~25.1 MiB (7.4 MiB/s) with ~265 file(s) remaining (calculating...)\rCompleted 4.3 MiB/~25.1 MiB (7.4 MiB/s) with ~265 file(s) remaining (calculating...)\rupload: contents/Fig. 2/B/Ko_Cli.mat to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/B/Ko_Cli.mat\nCompleted 4.3 MiB/~25.1 MiB (7.4 MiB/s) with ~264 file(s) remaining (calculating...)\rCompleted 4.4 MiB/25.1 MiB (7.3 MiB/s) with 264 file(s) remaining \rupload: contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.fig to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.fig\nCompleted 4.4 MiB/25.1 MiB (7.3 MiB/s) with 263 file(s) remaining\rCompleted 4.4 MiB/25.1 MiB (7.3 MiB/s) with 263 file(s) remaining\rupload: contents/Fig. 2/C/One neuron and Net/M_diff.m to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/One neuron and Net/M_diff.m\nCompleted 4.4 MiB/25.1 MiB (7.3 MiB/s) with 262 file(s) remaining\rCompleted 4.5 MiB/25.1 MiB (7.4 MiB/s) with 262 file(s) remaining\rupload: contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.jpg to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.jpg\nCompleted 4.5 MiB/25.1 MiB (7.4 MiB/s) with 261 file(s) remaining\rCompleted 4.5 MiB/25.1 MiB (7.3 MiB/s) with 261 file(s) remaining\rupload: contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.sfit to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.sfit\nCompleted 4.5 MiB/25.1 MiB (7.3 MiB/s) with 260 file(s) remaining\rCompleted 4.5 MiB/25.1 MiB (7.3 MiB/s) with 260 file(s) remaining\rupload: contents/Fig. 2/C/One neuron and Net/Net_bursters_no_connection.m to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/One neuron and Net/Net_bursters_no_connection.m\nCompleted 4.5 MiB/25.1 MiB (7.3 MiB/s) with 259 file(s) remaining\rCompleted 4.6 MiB/25.1 MiB (7.4 MiB/s) with 259 file(s) remaining\rupload: contents/Fig. 2/C/5Hz/NORM_KCC2(+)_5Hz.jpg to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/5Hz/NORM_KCC2(+)_5Hz.jpg\nCompleted 4.6 MiB/25.1 MiB (7.4 MiB/s) with 258 file(s) remaining\rCompleted 4.6 MiB/25.1 MiB (7.3 MiB/s) with 258 file(s) remaining\rupload: contents/Fig. 2/C/One neuron and Net/Stimulation frequencies/KCC2(+)/Bazh_Ko_Cli_diff_net_NORM.m to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 2/C/One neuron and Net/Stimulation frequencies/KCC2(+)/Bazh_Ko_Cli_diff_net_NORM.m\nCompleted 4.6 MiB/25.1 MiB (7.3 MiB/s) with 257 file(s) remaining\rCompleted 4.6 MiB/25.1 MiB (7.3 MiB/s) with 257 file(s) remaining\rupload: contents/Fig. 2/C/One neuron and Net/SN_fit/SN_fit.mat to 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8/Simulations/spect_peak.m to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 8/Simulations/spect_peak.m\nCompleted 24.9 MiB/25.1 MiB (9.7 MiB/s) with 5 file(s) remaining\rupload: contents/Fig. 8/Simulations/spect_shift.m to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 8/Simulations/spect_shift.m\nCompleted 24.9 MiB/25.1 MiB (9.7 MiB/s) with 4 file(s) remaining\rCompleted 24.9 MiB/25.1 MiB (9.7 MiB/s) with 4 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/manifest.xml\nCompleted 24.9 MiB/25.1 MiB (9.7 MiB/s) with 3 file(s) remaining\rCompleted 25.0 MiB/25.1 MiB (9.7 MiB/s) with 3 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/metadata.rdf\nCompleted 25.0 MiB/25.1 MiB (9.7 MiB/s) with 2 file(s) remaining\rCompleted 25.0 MiB/25.1 MiB (9.7 MiB/s) with 2 file(s) remaining\rupload: contents/Fig. 8/Simulations/raster_40-50.jpg to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 8/Simulations/raster_40-50.jpg\nCompleted 25.0 MiB/25.1 MiB (9.7 MiB/s) with 1 file(s) remaining\rCompleted 25.1 MiB/25.1 MiB (9.4 MiB/s) with 1 file(s) remaining\rupload: contents/Fig. 8/Simulations/raster_0-10.jpg to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/contents/Fig. 8/Simulations/raster_0-10.jpg\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /Fig. 2\ncreating group /Fig. 2/B\ncreating group /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml\ncreating dataset /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot, shape: (2, 1001), type: float64\ndataset created, uuid: d-eaee5e3c-03f5bc03-4dda-541529-124175, chunk_size: (2, 1001)\ncreating dataset /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report, shape: (18, 1001), type: float64\ndataset created, uuid: d-eaee5e3c-03f5bc03-a328-e7d07d-0817ba, chunk_size: (18, 1001)\ncreating attribute combineArchiveLocation in /Fig. 2\ncreating attribute uri in /Fig. 2\ncreating attribute combineArchiveLocation in /Fig. 2/B\ncreating attribute uri in /Fig. 2/B\ncreating attribute combineArchiveLocation in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml\ncreating attribute uri in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml\ncreating attribute _type in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute sedmlDataSetIds in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute sedmlDataSetLabels in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute sedmlDataSetNames in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute sedmlDataSetShapes in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute sedmlId in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute uri in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\ncreating attribute _type in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlDataSetDataTypes in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlDataSetIds in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlDataSetLabels in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlDataSetNames in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlDataSetShapes in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlId in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute sedmlName in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreating attribute uri in /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\ncreate_links: /\ngot link: Fig. 2\ncreate_links: /Fig. 2\ngot link: B\ncreate_links: /Fig. 2/B\ngot link: Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml\ncreate_links: /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot to tgt: /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot, shape: (2, 1001), type: float64\niterating over chunks for /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\nwriting dataset data for slice: (slice(0, 2, 1), slice(0, 1001, 1))\ndone with dataload for /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot\nwrite_dataset src: /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report to tgt: /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report, shape: (18, 1001), type: float64\niterating over chunks for /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\nwriting dataset data for slice: (slice(0, 18, 1), slice(0, 1001, 1))\ndone with dataload for /Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42b9b50991044c79ae18\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n adding: outputs/ (stored 0%)\n adding: outputs/log.yml (deflated 70%)\n adding: outputs/Fig. 2/ (stored 0%)\n adding: outputs/Fig. 2/B/ (stored 0%)\n adding: outputs/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/ (stored 0%)\n adding: outputs/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot.pdf (deflated 33%)\n adding: outputs/reports.h5 (deflated 26%)\n adding: rawLog.txt (deflated 92%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 5.4 KiB/227.0 KiB (58.4 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/outputs/plots.zip\nCompleted 5.4 KiB/227.0 KiB (58.4 KiB/s) with 3 file(s) remaining\rCompleted 83.2 KiB/227.0 KiB (852.5 KiB/s) with 3 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/output.zip\nCompleted 83.2 KiB/227.0 KiB (852.5 KiB/s) with 2 file(s) remaining\rCompleted 218.8 KiB/227.0 KiB (1.8 MiB/s) with 2 file(s) remaining \rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/rawLog.txt\nCompleted 218.8 KiB/227.0 KiB (1.8 MiB/s) with 1 file(s) remaining\rCompleted 227.0 KiB/227.0 KiB (1.8 MiB/s) with 1 file(s) remaining\rupload: outputs/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/outputs/Fig. 2/B/Bazh_PY_altKCC2_Ko_Cli_min_burst_Ko_Cli_fix_NEW.sedml/plot.pdf\nCompleted 80.5 KiB/80.5 KiB (1.1 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/outputs/reports.h5\nCompleted 2.9 KiB/2.9 KiB (41.6 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42b9b50991044c79ae18/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[1;33mCreate thumbnails from the images specified in the manifest ... failed:\nThere was an error creating thumbnails for the project. Please ensure that the images specified in the manifest are valid. A validation tool is available at https://run.biosimulations.org/utils/validate-project.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}