{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_T"},{"status":"SUCCEEDED","id":"data_set_DNK_B"},{"status":"SUCCEEDED","id":"data_set_DNK_G"},{"status":"SUCCEEDED","id":"data_set_H_HH"},{"status":"SUCCEEDED","id":"data_set_NCLI"},{"status":"SUCCEEDED","id":"data_set_NGL_C"},{"status":"SUCCEEDED","id":"data_set_NGL_C_E"},{"status":"SUCCEEDED","id":"data_set_NGL_C_G"},{"status":"SUCCEEDED","id":"data_set_NGL_C_I"},{"status":"SUCCEEDED","id":"data_set_NGL_E"},{"status":"SUCCEEDED","id":"data_set_NGL_E_G"},{"status":"SUCCEEDED","id":"data_set_NGL_E_I"},{"status":"SUCCEEDED","id":"data_set_NGL_REL"},{"status":"SUCCEEDED","id":"data_set_NKI"},{"status":"SUCCEEDED","id":"data_set_N_HH"},{"status":"SUCCEEDED","id":"data_set_R_AMPA"},{"status":"SUCCEEDED","id":"data_set_R_NMDA"},{"status":"SUCCEEDED","id":"data_set_V"},{"status":"SUCCEEDED","id":"data_set__CLE"},{"status":"SUCCEEDED","id":"data_set__CLI"},{"status":"SUCCEEDED","id":"data_set__ECL"},{"status":"SUCCEEDED","id":"data_set__EK"},{"status":"SUCCEEDED","id":"data_set__ENA"},{"status":"SUCCEEDED","id":"data_set__GL_C"},{"status":"SUCCEEDED","id":"data_set__GL_E"},{"status":"SUCCEEDED","id":"data_set__KE"},{"status":"SUCCEEDED","id":"data_set__KI"},{"status":"SUCCEEDED","id":"data_set__NAE"},{"status":"SUCCEEDED","id":"data_set__NAI"},{"status":"SUCCEEDED","id":"data_set__VL_E"},{"status":"SUCCEEDED","id":"data_set__VL_G"},{"status":"SUCCEEDED","id":"data_set__VL_I"}],"duration":0.297838,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_1"},{"status":"SUCCEEDED","id":"curve_2"},{"status":"SUCCEEDED","id":"curve_3"},{"status":"SUCCEEDED","id":"curve_4"},{"status":"SUCCEEDED","id":"curve_5"},{"status":"SUCCEEDED","id":"curve_6"},{"status":"SUCCEEDED","id":"curve_7"},{"status":"SUCCEEDED","id":"curve_8"}],"duration":0.360261,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a212b0> has a label of '_EK vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a21580> has a label of '_ENA vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a21850> has a label of '_ECL vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a21b20> has a label of '_VL_I vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5a21df0> has a label of '_VL_E vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5b05100> has a label of '_VL_G vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/viz/io.py:96: UserWarning: The handle <matplotlib.lines.Line2D object at 0x7fffe5b053d0> has a label of '_GL_C vs T' which cannot be automatically added to the legend.\r\n  axes.legend(curve_names)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"plot"}],"tasks":[{"simulatorDetails":[{"value":"stiff","key":"meth"},{"value":"400.0","key":"total"},{"value":"0.0","key":"t0"},{"value":"0.4","key":"dt"},{"value":"1","key":"njmp"}],"algorithm":"KISAO_0000668","duration":23.906032,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"task"}],"duration":24.739686,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  SD.sedml:\r\n    Tasks (1):\r\n      task\r\n    Reports (1):\r\n      report: 32 data sets\r\n    Plots (1):\r\n      plot: 8 curves\r\n\r\nExecuting SED-ML file 1: SD.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":"SD.sedml"}],"duration":25.293486,"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    448      0 --:--:-- --:--:-- --:--:--   449\n\r100  541k  100  541k    0     0  1245k      0 --:--:-- --:--:-- --:--:-- 1245k\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 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\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 (2):\n    Succeeded: 2\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/readme.html    \n  inflating: contents/SD.ode         \n  inflating: contents/SD.sedml       \n  inflating: contents/metadata.rdf   \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g001.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g002.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g003.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g004.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g005.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g006.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g007.jpg  \n  inflating: contents/article-figures/PMC5655358/pcbi.1005804.g008.jpg  \n  inflating: contents/screenshot.png  \n  inflating: contents/manifest.xml   \nCompleted 17.0 KiB/736.1 KiB (161.5 KiB/s) with 14 file(s) remaining\rupload: contents/SD.ode to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/SD.ode\nCompleted 17.0 KiB/736.1 KiB (161.5 KiB/s) with 13 file(s) remaining\rCompleted 33.6 KiB/736.1 KiB (288.7 KiB/s) with 13 file(s) remaining\rupload: contents/SD.sedml to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/SD.sedml\nCompleted 33.6 KiB/736.1 KiB (288.7 KiB/s) with 12 file(s) remaining\rCompleted 143.5 KiB/736.1 KiB (1.0 MiB/s) with 12 file(s) remaining \rupload: contents/article-figures/PMC5655358/pcbi.1005804.g001.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g001.jpg\nCompleted 143.5 KiB/736.1 KiB (1.0 MiB/s) with 11 file(s) remaining\rCompleted 240.7 KiB/736.1 KiB (1.6 MiB/s) with 11 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g002.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g002.jpg\nCompleted 240.7 KiB/736.1 KiB (1.6 MiB/s) with 10 file(s) remaining\rCompleted 302.9 KiB/736.1 KiB (1.9 MiB/s) with 10 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g007.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g007.jpg\nCompleted 302.9 KiB/736.1 KiB (1.9 MiB/s) with 9 file(s) remaining\rCompleted 304.6 KiB/736.1 KiB (1.9 MiB/s) with 9 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/manifest.xml\nCompleted 304.6 KiB/736.1 KiB (1.9 MiB/s) with 8 file(s) remaining\rCompleted 378.6 KiB/736.1 KiB (2.3 MiB/s) with 8 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g008.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g008.jpg\nCompleted 378.6 KiB/736.1 KiB (2.3 MiB/s) with 7 file(s) remaining\rCompleted 439.8 KiB/736.1 KiB (2.5 MiB/s) with 7 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g005.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g005.jpg\nCompleted 439.8 KiB/736.1 KiB (2.5 MiB/s) with 6 file(s) remaining\rCompleted 502.0 KiB/736.1 KiB (2.7 MiB/s) with 6 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g006.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g006.jpg\nCompleted 502.0 KiB/736.1 KiB (2.7 MiB/s) with 5 file(s) remaining\rCompleted 502.9 KiB/736.1 KiB (2.7 MiB/s) with 5 file(s) remaining\rupload: contents/readme.html to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/readme.html\nCompleted 502.9 KiB/736.1 KiB (2.7 MiB/s) with 4 file(s) remaining\rCompleted 591.6 KiB/736.1 KiB (2.9 MiB/s) with 4 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g003.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g003.jpg\nCompleted 591.6 KiB/736.1 KiB (2.9 MiB/s) with 3 file(s) remaining\rCompleted 675.5 KiB/736.1 KiB (3.2 MiB/s) with 3 file(s) remaining\rupload: contents/article-figures/PMC5655358/pcbi.1005804.g004.jpg to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/article-figures/PMC5655358/pcbi.1005804.g004.jpg\nCompleted 675.5 KiB/736.1 KiB (3.2 MiB/s) with 2 file(s) remaining\rCompleted 694.4 KiB/736.1 KiB (3.3 MiB/s) with 2 file(s) remaining\rupload: contents/screenshot.png to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/screenshot.png\nCompleted 694.4 KiB/736.1 KiB (3.3 MiB/s) with 1 file(s) remaining\rCompleted 736.1 KiB/736.1 KiB (3.2 MiB/s) with 1 file(s) remaining\rupload: contents/metadata.rdf to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/contents/metadata.rdf\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /SD.sedml\ncreating dataset /SD.sedml/plot, shape: (9, 1001), type: float64\ndataset created, uuid: d-42aff6f4-6d032ab6-8828-0b4440-5701fa, chunk_size: (9, 1001)\ncreating dataset /SD.sedml/report, shape: (32, 1001), type: float64\ndataset created, uuid: d-42aff6f4-6d032ab6-d895-debb4a-89219a, chunk_size: (32, 1001)\ncreating attribute combineArchiveLocation in /SD.sedml\ncreating attribute uri in /SD.sedml\ncreating attribute _type in /SD.sedml/plot\ncreating attribute sedmlDataSetDataTypes in /SD.sedml/plot\ncreating attribute sedmlDataSetIds in /SD.sedml/plot\ncreating attribute sedmlDataSetLabels in /SD.sedml/plot\ncreating attribute sedmlDataSetNames in /SD.sedml/plot\ncreating attribute sedmlDataSetShapes in /SD.sedml/plot\ncreating attribute sedmlId in /SD.sedml/plot\ncreating attribute uri in /SD.sedml/plot\ncreating attribute _type in /SD.sedml/report\ncreating attribute sedmlDataSetDataTypes in /SD.sedml/report\ncreating attribute sedmlDataSetIds in /SD.sedml/report\ncreating attribute sedmlDataSetLabels in /SD.sedml/report\ncreating attribute sedmlDataSetNames in /SD.sedml/report\ncreating attribute sedmlDataSetShapes in /SD.sedml/report\ncreating attribute sedmlId in /SD.sedml/report\ncreating attribute sedmlName in /SD.sedml/report\ncreating attribute uri in /SD.sedml/report\ncreate_links: /\ngot link: SD.sedml\ncreate_links: /SD.sedml\ngot link: plot\ngot link: report\nwrite_dataset src: /SD.sedml/plot to tgt: /SD.sedml/plot, shape: (9, 1001), type: float64\niterating over chunks for /SD.sedml/plot\nwriting dataset data for slice: (slice(0, 9, 1), slice(0, 1001, 1))\ndone with dataload for /SD.sedml/plot\nwrite_dataset src: /SD.sedml/report to tgt: /SD.sedml/report, shape: (32, 1001), type: float64\niterating over chunks for /SD.sedml/report\nwriting dataset data for slice: (slice(0, 32, 1), slice(0, 1001, 1))\ndone with dataload for /SD.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/621d42bdd8a14a834cbf3f0f\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 80%)\n  adding: outputs/SD.sedml/ (stored 0%)\n  adding: outputs/SD.sedml/plot.pdf (deflated 18%)\n  adding: outputs/reports.h5 (deflated 10%)\n  adding: rawLog.txt (deflated 82%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 253.7 KiB/288.8 KiB (2.7 MiB/s) with 4 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/output.zip\nCompleted 253.7 KiB/288.8 KiB (2.7 MiB/s) with 3 file(s) remaining\rCompleted 265.3 KiB/288.8 KiB (2.7 MiB/s) with 3 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/outputs/plots.zip\nCompleted 265.3 KiB/288.8 KiB (2.7 MiB/s) with 2 file(s) remaining\rCompleted 274.4 KiB/288.8 KiB (2.7 MiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/rawLog.txt\nCompleted 274.4 KiB/288.8 KiB (2.7 MiB/s) with 1 file(s) remaining\rCompleted 288.8 KiB/288.8 KiB (2.0 MiB/s) with 1 file(s) remaining\rupload: outputs/SD.sedml/plot.pdf to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/outputs/SD.sedml/plot.pdf\nCompleted 256.0 KiB/265.1 KiB (6.5 MiB/s) with 1 file(s) remaining\rCompleted 265.1 KiB/265.1 KiB (1.4 MiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/outputs/reports.h5\nCompleted 5.9 KiB/5.9 KiB (101.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/621d42bdd8a14a834cbf3f0f/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 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.\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.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}