{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_C"},{"status":"SUCCEEDED","id":"data_set_CA_ER"},{"status":"SUCCEEDED","id":"data_set_C_T"},{"status":"SUCCEEDED","id":"data_set_H"}],"duration":0.103048,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"}],"tasks":[{"simulatorDetails":[{"value":"1000.0","key":"total"},{"value":"rungekutta","key":"meth"},{"value":"0.05","key":"dt"},{"value":"0.0","key":"t0"},{"value":"20","key":"njmp"}],"algorithm":"KISAO_0000032","duration":0.273533,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":0.480301,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 0 plots:\r\n  ca_bifurcation_xpp_TH.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 5 data sets\r\n\r\nExecuting SED-ML file 1: ca_bifurcation_xpp_TH.sedml ...\r\n  Found 1 tasks and 1 outputs:\r\n    Tasks:\r\n      `task`\r\n    Outputs:\r\n      `report`\r\n  Executing task 1: `task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 1 outputs ...\r\n      Generating output 1: `report` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"ca_bifurcation_xpp_TH.sedml"}],"duration":0.934517,"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   139  100   139    0     0    457      0 --:--:-- --:--:-- --:--:--   458\n\r100  256k  100  256k    0     0   609k      0 --:--:-- --:--:-- --:--:--  609k\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. Manifests should include their parent COMBINE/OMEX archives.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 1 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m====================================== Saving contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/ca_bifurcation_xpp_TH.ode  \n  inflating: contents/example_ca_sim_TH.m  \n  inflating: contents/autoRespTypeDetection_TH.m  \n  inflating: contents/README.txt     \n  inflating: contents/Histogram_Figures/low_ip3_panel2.fig  \n  inflating: contents/Histogram_Figures/all_ip3_panel3.fig  \n  inflating: contents/Histogram_Figures/all_ip3_panel1.fig  \n  inflating: contents/Histogram_Figures/all_ip3_panel2.fig  \n  inflating: contents/Histogram_Figures/low_ip3_panel3.fig  \n  inflating: contents/Histogram_Figures/low_ip3_panel1.fig  \n  inflating: contents/Supporting_Functions/RunParallelFunc_TH.m  \n  inflating: contents/Supporting_Functions/IP3Dyn_model_TH.m  \n  inflating: contents/Supporting_Functions/PeakLatency_TH.m  \n  inflating: contents/Supporting_Functions/plotCaAmountVsIP3Amount_TH.m  \n  inflating: contents/Supporting_Functions/PeaksAndTroughs_TH.m  \n  inflating: contents/Supporting_Functions/ip_function_TH.m  \n  inflating: contents/Supporting_Functions/CaRiseAndDecay_TH.m  \n  inflating: contents/Supporting_Functions/FourCaResponseTypes_TH.m  \n  inflating: contents/Supporting_Functions/plotCa_TH.m  \n  inflating: contents/Supporting_Functions/Official_Params_TH.m  \n  inflating: contents/Supporting_Functions/Paper_Ca_ODE_TH.m  \n  inflating: contents/Supporting_Functions/GenerateLegend_TH.m  \n  inflating: contents/ca_bifurcation_xpp_TH.sedml  \n  inflating: contents/metadata.rdf   \n  inflating: contents/manifest.xml   \nCompleted 43.8 KiB/~258.1 KiB (563.3 KiB/s) with ~13 file(s) remaining (calculating...)\rupload: contents/Histogram_Figures/all_ip3_panel1.fig to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Histogram_Figures/all_ip3_panel1.fig\nCompleted 43.8 KiB/~258.1 KiB (563.3 KiB/s) with ~12 file(s) remaining (calculating...)\rCompleted 87.5 KiB/300.8 KiB (737.3 KiB/s) with 24 file(s) remaining                   \rupload: contents/Histogram_Figures/low_ip3_panel1.fig to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Histogram_Figures/low_ip3_panel1.fig\nCompleted 87.5 KiB/300.8 KiB (737.3 KiB/s) with 23 file(s) remaining\rCompleted 124.4 KiB/300.8 KiB (921.2 KiB/s) with 23 file(s) remaining\rupload: contents/Histogram_Figures/all_ip3_panel3.fig to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Histogram_Figures/all_ip3_panel3.fig\nCompleted 124.4 KiB/300.8 KiB (921.2 KiB/s) with 22 file(s) remaining\rCompleted 126.3 KiB/300.8 KiB (895.3 KiB/s) with 22 file(s) remaining\rupload: contents/Supporting_Functions/Paper_Ca_ODE_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/Paper_Ca_ODE_TH.m\nCompleted 126.3 KiB/300.8 KiB (895.3 KiB/s) with 21 file(s) remaining\rCompleted 127.8 KiB/300.8 KiB (785.6 KiB/s) with 21 file(s) remaining\rupload: contents/Supporting_Functions/GenerateLegend_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/GenerateLegend_TH.m\nCompleted 127.8 KiB/300.8 KiB (785.6 KiB/s) with 20 file(s) remaining\rCompleted 134.7 KiB/300.8 KiB (801.8 KiB/s) with 20 file(s) remaining\rupload: contents/Supporting_Functions/RunParallelFunc_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/RunParallelFunc_TH.m\nCompleted 134.7 KiB/300.8 KiB (801.8 KiB/s) with 19 file(s) remaining\rCompleted 171.6 KiB/300.8 KiB (999.3 KiB/s) with 19 file(s) remaining\rupload: contents/Histogram_Figures/all_ip3_panel2.fig to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Histogram_Figures/all_ip3_panel2.fig\nCompleted 171.6 KiB/300.8 KiB (999.3 KiB/s) with 18 file(s) remaining\rCompleted 172.8 KiB/300.8 KiB (948.4 KiB/s) with 18 file(s) remaining\rupload: contents/Supporting_Functions/Official_Params_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/Official_Params_TH.m\nCompleted 172.8 KiB/300.8 KiB (948.4 KiB/s) with 17 file(s) remaining\rCompleted 174.3 KiB/300.8 KiB (929.3 KiB/s) with 17 file(s) remaining\rupload: contents/Supporting_Functions/IP3Dyn_model_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/IP3Dyn_model_TH.m\nCompleted 174.3 KiB/300.8 KiB (929.3 KiB/s) with 16 file(s) remaining\rCompleted 211.0 KiB/300.8 KiB (1.0 MiB/s) with 16 file(s) remaining  \rupload: contents/Histogram_Figures/low_ip3_panel2.fig to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Histogram_Figures/low_ip3_panel2.fig\nCompleted 211.0 KiB/300.8 KiB (1.0 MiB/s) with 15 file(s) remaining\rCompleted 211.9 KiB/300.8 KiB (1.0 MiB/s) with 15 file(s) remaining\rupload: contents/Supporting_Functions/PeakLatency_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/PeakLatency_TH.m\nCompleted 211.9 KiB/300.8 KiB (1.0 MiB/s) with 14 file(s) remaining\rCompleted 213.5 KiB/300.8 KiB (997.2 KiB/s) with 14 file(s) remaining\rupload: contents/Supporting_Functions/ip_function_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/ip_function_TH.m\nCompleted 213.5 KiB/300.8 KiB (997.2 KiB/s) with 13 file(s) remaining\rCompleted 214.8 KiB/300.8 KiB (963.6 KiB/s) with 13 file(s) remaining\rupload: contents/Supporting_Functions/plotCa_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/plotCa_TH.m\nCompleted 214.8 KiB/300.8 KiB (963.6 KiB/s) with 12 file(s) remaining\rCompleted 216.4 KiB/300.8 KiB (950.6 KiB/s) with 12 file(s) remaining\rupload: contents/Supporting_Functions/PeaksAndTroughs_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/PeaksAndTroughs_TH.m\nCompleted 216.4 KiB/300.8 KiB (950.6 KiB/s) with 11 file(s) remaining\rCompleted 217.7 KiB/300.8 KiB (915.6 KiB/s) with 11 file(s) remaining\rupload: contents/ca_bifurcation_xpp_TH.ode to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/ca_bifurcation_xpp_TH.ode\nCompleted 217.7 KiB/300.8 KiB (915.6 KiB/s) with 10 file(s) remaining\rCompleted 224.0 KiB/300.8 KiB (910.9 KiB/s) with 10 file(s) remaining\rupload: contents/autoRespTypeDetection_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/autoRespTypeDetection_TH.m\nCompleted 224.0 KiB/300.8 KiB (910.9 KiB/s) with 9 file(s) remaining\rCompleted 225.3 KiB/300.8 KiB (910.7 KiB/s) with 9 file(s) remaining\rupload: contents/Supporting_Functions/plotCaAmountVsIP3Amount_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/plotCaAmountVsIP3Amount_TH.m\nCompleted 225.3 KiB/300.8 KiB (910.7 KiB/s) with 8 file(s) remaining\rCompleted 228.3 KiB/300.8 KiB (918.4 KiB/s) with 8 file(s) remaining\rupload: contents/example_ca_sim_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/example_ca_sim_TH.m\nCompleted 228.3 KiB/300.8 KiB (918.4 KiB/s) with 7 file(s) remaining\rCompleted 231.5 KiB/300.8 KiB (921.5 KiB/s) with 7 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/manifest.xml\nCompleted 231.5 KiB/300.8 KiB (921.5 KiB/s) with 6 file(s) remaining\rCompleted 235.7 KiB/300.8 KiB (931.9 KiB/s) with 6 file(s) remaining\rupload: contents/ca_bifurcation_xpp_TH.sedml to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/ca_bifurcation_xpp_TH.sedml\nCompleted 235.7 KiB/300.8 KiB (931.9 KiB/s) with 5 file(s) remaining\rCompleted 236.7 KiB/300.8 KiB (844.6 KiB/s) with 5 file(s) remaining\rupload: contents/README.txt to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/README.txt\nCompleted 236.7 KiB/300.8 KiB (844.6 KiB/s) with 4 file(s) remaining\rCompleted 238.3 KiB/300.8 KiB (822.9 KiB/s) with 4 file(s) remaining\rupload: contents/Supporting_Functions/CaRiseAndDecay_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/CaRiseAndDecay_TH.m\nCompleted 238.3 KiB/300.8 KiB (822.9 KiB/s) with 3 file(s) remaining\rCompleted 253.0 KiB/300.8 KiB (864.4 KiB/s) with 3 file(s) remaining\rupload: contents/Supporting_Functions/FourCaResponseTypes_TH.m to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Supporting_Functions/FourCaResponseTypes_TH.m\nCompleted 253.0 KiB/300.8 KiB (864.4 KiB/s) with 2 file(s) remaining\rCompleted 289.7 KiB/300.8 KiB (861.3 KiB/s) with 2 file(s) remaining\rupload: contents/Histogram_Figures/low_ip3_panel3.fig to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/Histogram_Figures/low_ip3_panel3.fig\nCompleted 289.7 KiB/300.8 KiB (861.3 KiB/s) with 1 file(s) remaining\rCompleted 300.8 KiB/300.8 KiB (863.0 KiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/contents/metadata.rdf\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /ca_bifurcation_xpp_TH.sedml\ncreating dataset /ca_bifurcation_xpp_TH.sedml/report, shape: (5, 1001), type: float64\ndataset created, uuid: d-f2a3855f-2ac6a331-6b8a-91fcfb-21a0cf, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /ca_bifurcation_xpp_TH.sedml\ncreating attribute uri in /ca_bifurcation_xpp_TH.sedml\ncreating attribute _type in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlDataSetDataTypes in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlDataSetIds in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlDataSetLabels in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlDataSetNames in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlDataSetShapes in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlId in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute sedmlName in /ca_bifurcation_xpp_TH.sedml/report\ncreating attribute uri in /ca_bifurcation_xpp_TH.sedml/report\ncreate_links: /\ngot link: ca_bifurcation_xpp_TH.sedml\ncreate_links: /ca_bifurcation_xpp_TH.sedml\ngot link: report\nwrite_dataset src: /ca_bifurcation_xpp_TH.sedml/report to tgt: /ca_bifurcation_xpp_TH.sedml/report, shape: (5, 1001), type: float64\niterating over chunks for /ca_bifurcation_xpp_TH.sedml/report\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /ca_bifurcation_xpp_TH.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42b687550e369891bb60\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 62%)\n  adding: outputs/reports.h5 (deflated 86%)\n  adding: rawLog.txt (deflated 83%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 5.4 KiB/18.0 KiB (62.4 KiB/s) with 2 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/output.zip\nCompleted 5.4 KiB/18.0 KiB (62.4 KiB/s) with 1 file(s) remaining\rCompleted 18.0 KiB/18.0 KiB (173.3 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/rawLog.txt\nCompleted 14.7 KiB/14.7 KiB (222.8 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/outputs/reports.h5\nCompleted 1.9 KiB/1.9 KiB (28.3 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42b687550e369891bb60/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nProcess the metadata in the COMBINE archive ... succeeded.\nPost the metadata to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}