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The registry includes tools for a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and model formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). Many of the simulation tools provide Python packages, command-line programs, and Docker images with consistent interfaces. Together, BioSimulators makes it easier to run simulations. BioSimulators is powered by several "),o.TgZ(14,"a",7),o._uU(15,"conventions"),o.qZA(),o._uU(16," including SED-ML "),o.qZA(),o.BQk(),o.TgZ(17,"biosimulations-home-subsection",8),o._uU(18," BioSimulators makes it easy to find tools that can run specific simulations and download and run them. "),o.qZA(),o.TgZ(19,"biosimulations-home-subsection",9),o._uU(20," The tools in the BioSimulators registry can run a broad range of modeling frameworks, simulation algorithms, and model formats. "),o.qZA(),o.TgZ(21,"biosimulations-home-subsection",10),o._uU(22," BioSimulators makes it easier for developers to compare simulation tools. This can be used to identify the strengths of different approaches, find bugs, and drive standardization. "),o.qZA()(),o.TgZ(23,"div",11)(24,"mat-card",12)(25,"mat-card-header",13),o._uU(26," Quick Start "),o.qZA(),o.TgZ(27,"div",14)(28,"h2"),o._uU(29," Getting started with BioSimulators is easy! Explore "),o.TgZ(30,"a",15),o._uU(31," our documentation for a comprehensive guide and best practices. "),o.qZA()()(),o.TgZ(32,"mat-card-content")(33,"mat-tab-group")(34,"mat-tab"),o.YNc(35,_,2,0,"ng-template",16),o.TgZ(36,"div",17)(37,"span",18),o._uU(38,"You can easily run a BioSimulator from the command-line in as little as 3 simple steps:"),o.qZA(),o.TgZ(39,"p",19),o._uU(40," 1. Install the BioSimulator you want with pip. Here we will use "),o.TgZ(41,"code",20),o._uU(42,"biosimulators-tellurium"),o.qZA(),o._uU(43,". A full list of BioSimulators packages can be found "),o.TgZ(44,"a",6),o._uU(45,"here."),o.qZA()(),o.TgZ(46,"pre",21)(47,"code"),o._uU(48,"\n "),o.TgZ(49,"strong",22),o._uU(50,"%"),o.qZA(),o._uU(51," pip install biosimulators-tellurium\n "),o.qZA()(),o.TgZ(52,"p",23),o._uU(53," 2. Run the following from the command line, passing an OMEX filepath as -i and the output dir as -o "),o.qZA(),o.TgZ(54,"pre",24)(55,"code"),o._uU(56,"\n "),o.TgZ(57,"strong",22),o._uU(58,"%"),o.qZA(),o._uU(59," biosimulators-tellurium \\\n -i ~/experiments/my-file.omex \\\n -o ~/Desktop/results\n "),o.qZA()(),o.TgZ(60,"p",25),o._uU(61,"3. Go to the directory and view your results."),o.qZA(),o.TgZ(62,"pre",26)(63,"code"),o._uU(64,"\n "),o.TgZ(65,"strong",22),o._uU(66,"%"),o.qZA(),o._uU(67," cd ~/Desktop/results\n "),o.qZA()()()(),o.TgZ(68,"mat-tab"),o.YNc(69,v,2,0,"ng-template",16),o.TgZ(70,"div",27)(71,"span",28),o._uU(72,"You can easily run the same BioSimulator simulation with Docker:"),o.qZA(),o.TgZ(73,"pre")(74,"code"),o._uU(75,"\n "),o.TgZ(76,"strong",22),o._uU(77,"%"),o.qZA(),o._uU(78," docker pull \\\n ghcr.io/biosimulators/tellurium:2.2.8\n "),o.qZA()(),o.TgZ(79,"pre")(80,"code"),o._uU(81,"\n "),o.TgZ(82,"strong",22),o._uU(83,"%"),o.qZA(),o._uU(84," docker run \\\n ghcr.io/biosimulators/tellurium:2.2.8 \\\n -i /path/to/archive.omex \\\n -o /path/to/outputs\n "),o.qZA()()()(),o.TgZ(85,"mat-tab"),o.YNc(86,w,2,0,"ng-template",16),o.TgZ(87,"div",29)(88,"span",30),o._uU(89,"You can also easily run a BioSimulator programmatically with Python:"),o.qZA(),o.TgZ(90,"p",31),o._uU(91,"1. Import the desired BioSimulator."),o.qZA(),o.TgZ(92,"pre")(93,"code"),o._uU(94,"\n import biosimulators_tellurium as bt\n "),o.qZA()(),o.TgZ(95,"p",32),o._uU(96,"2. Define the paths to both your OMEX file and desired output destination:"),o.qZA(),o.TgZ(97,"pre")(98,"code"),o._uU(99,"\n omex = 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'\n "),o.qZA()(),o.TgZ(100,"pre")(101,"code"),o._uU(102,"\n results_dir = '/content/my_results'\n "),o.qZA()(),o.TgZ(103,"p",33),o._uU(104,"3. Run the simulation and get the results and log. Print the results:"),o.qZA(),o.TgZ(105,"pre")(106,"code"),o._uU(107,"\n results, log = bt.exec_sedml_docs_in_combine_archive(\n omex,\n results_dir,\n config\n )\n\n print(results)\n print(log)\n "),o.qZA()(),o.TgZ(108,"p",34),o._uU(109,"This is the full implementation:"),o.qZA(),o.TgZ(110,"pre")(111,"code"),o._uU(112,"\n import biosimulators_tellurium as bt\n\n omex = 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex'\n results_dir = '/content/my_results'\n results, log = bt.exec_sedml_docs_in_combine_archive(\n omex,\n results_dir,\n config\n )\n\n print(results)\n print(log)\n "),o.qZA()()()(),o.TgZ(113,"mat-tab"),o.YNc(114,M,2,0,"ng-template",16),o.TgZ(115,"div",35),o._uU(116," A fully interactive Binder tutorial is available "),o.TgZ(117,"a",36),o._uU(118," here. "),o.qZA()()()()()()()()(),o.TgZ(119,"div",37)(120,"biosimulations-home-section",4),o.ynx(121,5),o._uU(122," Consistent access to "),o.TgZ(123,"span",38)(124,"a",39),o._uU(125," multiple modeling frameworks, algorithms, formats & tools "),o.qZA()(),o.BQk(),o.TgZ(126,"biosimulations-home-subsection",40),o._UZ(127,"biosimulations-home-logo",41)(128,"biosimulations-home-logo",42)(129,"biosimulations-home-logo",43)(130,"biosimulations-home-logo",44)(131,"biosimulations-home-logo",45)(132,"biosimulations-home-logo",46)(133,"biosimulations-home-logo",47)(134,"biosimulations-home-logo",48),o.qZA(),o.TgZ(135,"biosimulations-home-subsection",49),o._UZ(136,"biosimulations-home-logo",50),o.qZA(),o.TgZ(137,"biosimulations-home-subsection",51),o._UZ(138,"biosimulations-home-logo",52)(139,"biosimulations-home-logo",53)(140,"biosimulations-home-logo",54),o.qZA()()(),o.TgZ(141,"mat-card",55)(142,"biosimulations-home-section",4),o.ynx(143,5),o._uU(144," About "),o.TgZ(145,"strong"),o._uU(146,"BioSimulators"),o.qZA(),o.BQk(),o.ynx(147,56),o.TgZ(148,"div",57)(149,"div",58)(150,"p"),o._uU(151," BioSimulators was developed by the Center for Reproducible Biomedical Modeling "),o.TgZ(152,"a",59),o._UZ(153,"biosimulations-icon",60),o.qZA(),o._uU(154,", the Karr Lab at the Icahn School of Medicine at Mount Sinai "),o.TgZ(155,"a",61),o._UZ(156,"biosimulations-icon",60),o.qZA(),o._uU(157,", and the Center for Cell Analysis & Modeling at the University of Connecticut Health Center "),o.TgZ(158,"a",62),o._UZ(159,"biosimulations-icon",60),o.qZA(),o._uU(160," with support from the National Institutes of Health and the National Science Foundation. "),o.qZA(),o.TgZ(161,"p"),o._uU(162," BioSimulators is implemented using several open-source tools and cloud platforms. The simulators are available under the licenses specified for each simulator. The BioSimulators code is openly available under the MIT license "),o.TgZ(163,"a",63),o._UZ(164,"biosimulations-icon",60),o.qZA(),o._uU(165,". "),o.qZA(),o.TgZ(166,"p"),o._uU(167," Please see the "),o.TgZ(168,"a",64),o._uU(169,"documentation"),o.qZA(),o._uU(170," for more information. 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