virtualcell/vcell-7.5.0.58.zip
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virtualcell-vcell-614b353
.dockerignore
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.gitattributes
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.github
stale.yml
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workflows
CI-full.yml
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NightlyBMDB_CLI.yml
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biosimulations_cd.yml
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biosimulations_verify.yml
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ci_cd.yml
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codeql-analysis.yml
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create_bs_singularity.yml
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debug.yml
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nightly-model-testing.yml
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objective-c-xcode-debug.yml
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site_deploy.yml
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.gitignore
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.mailmap
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CODE_OF_CONDUCT.md
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CONTRIBUTING.md
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Dockerfile
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README.md
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README_BioSim.md
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README_Debugging.md
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README_certs.md
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README_flow_control.md
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README_git_trav_appv_dhub.md
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README_orphan.md
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auto.docker
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auto.vcellapps
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bionetgen
BNG2.pl
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CHANGES.txt
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CREDITS.txt
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LICENSE.txt
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Perl2
Aux2
MakeBin.pl
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bnglstat.pl
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count_blocks.pl
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count_lines.pl
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countdown.pl
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diff_cdat.pl
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express.pl
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express_main.pl
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group_size.pl
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runBNG.pl
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test.pl
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test_compartment.pl
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test_molorder.pl
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test_redirect.pl
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test_sub.pl
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BNGAction.pm
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BNGMessages.pm
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BNGModel.pm
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BNGOptions.pm
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BNGOutput.pm
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BNGUtils.pm
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Boolean2BNGL
ABC_example.txt
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Boolean2BNGL.pl
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Tcell_model_Nov2013_LAH.txt
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Tcell_model_Oct2013.txt
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Tcell_model_v16.txt
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Cache.pm
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CartesianProduct.pm
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Compartment.pm
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CompartmentList.pm
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Component.pm
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ComponentType.pm
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Console.pm
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EnergyPattern.pm
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Expression.pm
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Function.pm
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HNauty.pm
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MacroBNG2.pl
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MacroBNGModel.pm
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Map.pm
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ModelWrapper.pm
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Molecule.pm
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MoleculeType.pm
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MoleculeTypesList.pm
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Observable.pm
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Param.pm
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ParamList.pm
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Population.pm
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PopulationList.pm
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RateLaw.pm
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RefineRule.pm
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Rxn.pm
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RxnList.pm
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RxnRule.pm
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Species.pm
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SpeciesGraph.pm
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SpeciesList.pm
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Visualization
ContactMap.pm
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GML.pm
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NetworkGraph.pm
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ProcessGraph.pm
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README
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RINF.pm
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StructureGraph.pm
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VisOptParse.pm
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Viz.pm
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analyze.pl
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readGML.pl
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visualize.pl
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XML
TreePP.pm
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XMLReader.pm
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auto_hpp.pl
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diff_net.pl
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scan_var.pl
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test_cartesianproduct.pl
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verify.pl
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README_FIRST.txt
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VERSION
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win32Standalone
BNG2_32bit.exe
8.2 MB
win64Standalone
BNG2.exe
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biosimulations_log4j2.xml
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biosimulators.json
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debug_log4j2.xml
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docker
.gitignore
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README.md
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README_Oracle.md
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README_admin.md
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README_serviceInfo.md
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build
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Dockerfile-api-dev
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Dockerfile-batch-dev
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Dockerfile-clientgen-dev
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Dockerfile-data-dev
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Dockerfile-db-dev
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Dockerfile-sched-dev
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Dockerfile-submit-dev
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Dockerfile-web-dev
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README.md
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README_Registry.md
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README_buildMachine.md
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admin
entrypoint.sh
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vcell-su.sh
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batch
JavaPostprocessor64
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JavaPreprocessor64
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JavaSimExe64
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README.md
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entrypoint.sh
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build.sh
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installers
.gitignore
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README.md
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VCell.install4j
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build_installers.sh
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icons
vcell.icns
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vcell_64x64.gif
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mongo
Dockerfile
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singularity-vm
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Vagrantfile
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run.sh
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singularity.sh
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vcell-admin.log4j.xml
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vcell-api.log4j.xml
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vcell-batch.log4j.xml
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vcell-data.log4j.xml
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vcell-db.log4j.xml
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vcell-opt.log4j.xml
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vcell-sched.log4j.xml
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vcell-submit.log4j.xml
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vcell-web.log4j.xml
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kubernetes
activemqint.yaml
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activemqsim.yaml
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api.yaml
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cluster.md
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data-claim0-persistentvolumeclaim.yaml
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data-claim1-persistentvolumeclaim.yaml
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data.yaml
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db.yaml
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mongodb.yaml
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sched.yaml
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simdata-persistentvolume.yaml
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submit-claim0-persistentvolumeclaim.yaml
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submit-claim1-persistentvolumeclaim.yaml
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submit.yaml
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vcelldb-uchc.yaml
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manual_orchestration
vcell.py
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mockslurm
fakejob.sh
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sacct
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sbatch_docker
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sbatch_singularity
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scancel
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squeue
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swarm
README.md
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README_DockerSwarmConfig.md
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README_ELK-old.md
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README_ElasticStack.md
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README_NodeAndSwarm.md
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README_RebuildSwarm.md
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README_admin.md
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README_localServicesDebug.md
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README_new_node_final_steps.md
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README_stack_on_mac.md
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deploy-action.sh
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deploy.sh
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dev_singularity_build.sh
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docker-compose-dev-msg.yml
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docker-compose.yml
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docker-stack-monitor.yml
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docker-stack-visualizer.yml
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generate_installers.sh
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link-installers.sh
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localconfig_mockslurm-not-used.sh
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localconfig_realslurm_oracle.sh
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localconfig_realslurm_postgres.sh
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sendMessage.sh
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serverconfig-uch.sh
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vcell-admin
README.md
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__init__.py
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poetry.lock
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pyproject.toml
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tests
__init__.py
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test_vcell_admin.py
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vcell_admin
__init__.py
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cli.py
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vcellNagios.sh
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docker_run.sh
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exampleModels
.gitignore
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Solver_Suite_6_2.xml
4.5 MB
jubula.vfrap
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optoPlexin_PRG_rule_based.xml
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git-build-deploy.txt
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license.txt
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localsolvers
README.md
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linux32
.gitignore
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linux64
.gitignore
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mac64
.gitignore
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win64
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nativelibs
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libhdf4.settings
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libhdf5.settings
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libjhdf.so
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libjhdf5.so
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linux64
libcombinej.so
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libhdf4.settings
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libhdf5.settings
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libjhdf.so
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libjhdf5.so
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mac64
libcombinej.jnilib
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libhdf4.settings
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libhdf5.settings
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libjhdf.jnilib
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libjhdf5.jnilib
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win32
combinej.dll
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jhdf.dll
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jhdf5.dll
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msvcp100.dll
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msvcp100d.dll
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msvcr100.dll
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msvcr100d.dll
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zlib1.dll
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combinej.dll
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jhdf.dll
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jhdf5.dll
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msvcp100.dll
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msvcr100.dll
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non-maven-java-libs
non-maven-jar-libs.txt
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org
sbml
libcombine
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libCombineLinux64-0.2.7.jar.md5
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libCombineLinux64-0.2.7.jar.sha1
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libCombineLinux64-0.2.7.pom
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libCombineLinux64-0.2.7.pom.md5
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libCombineLinux64-0.2.7.pom.sha1
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maven-metadata.xml
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maven-metadata.xml.md5
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maven-metadata.xml.sha1
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libCombineOSX
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libCombineOSX-0.2.7.jar.md5
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libCombineOSX-0.2.7.jar.sha1
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libCombineOSX-0.2.7.pom
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libCombineOSX-0.2.7.pom.md5
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libCombineOSX-0.2.7.pom.sha1
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maven-metadata.xml
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maven-metadata.xml.md5
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maven-metadata.xml.sha1
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libCombineWin64
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libCombineWin64-0.2.7.jar
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libCombineWin64-0.2.7.jar.md5
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libCombineWin64-0.2.7.jar.sha1
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libCombineWin64-0.2.7.pom
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libCombineWin64-0.2.7.pom.md5
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libCombineWin64-0.2.7.pom.sha1
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maven-metadata.xml
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maven-metadata.xml.md5
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maven-metadata.xml.sha1
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pom.xml
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pythonProject
Dockerfile
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build.sh
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docker_run.sh
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run.sh
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vcell-opt
README.md
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mypy.ini
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paramest.ipynb
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poetry.lock
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pyproject.toml
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test_data
Biomodel_simple_parest.json
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Biomodel_simple_parest.vcml
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optproblem.json
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optproblem.vcml
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tests
__init__.py
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vcellopt_test.py
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vcell_opt
__init__.py
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data
__init__.py
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optService.py
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optUtils.py
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pythonScripts
VCell_API
testapi.py
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vcellapi.py
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VCell_ImageJ
__init__.py
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vcellij
SimulationService-remote
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SimulationService.py
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__init__.py
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constants.py
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ttypes.py
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VCell_Opt
__init__.py
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copasi.ipynb
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optService.py
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optprob.bin
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vcellopt
__init__.py
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constants.py
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ttypes.py
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VCell_VTK
__init__.py
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makeLittleVtk.py
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pyvcell
VCellProxy-remote
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VCellProxy.py
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__init__.py
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constants.py
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ttypes.py
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vcellvismesh
__init__.py
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constants.py
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ttypes.py
70.5 kB
vtkAddData_not_used.py
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vtkService.py
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requirements.txt
174 Bytes
results
.gitkeep
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sample_model
model.xml
29.4 kB
sample.sedml
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sample_omex_files
CSHL_2012_Exercise_7___OMEX_test.omex
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Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
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Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
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Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.omex
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Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex
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Parmar-BMC-Syst-Biol-2017-iron-distribution.omex
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Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex
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Tomida-EMBO-J-2003-NFAT-translocation.omex
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Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex
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Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
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Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
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Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex
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Vilar-PNAS-2002-minimal-circardian-clock.omex
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_00_omex_test_cvode.vcml
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_00_omex_test_cvode.xml
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_00_omex_test_cvode_single_task.vcml
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__bm35_test_deterministic.vcml
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__bm35_test_deterministic_multi.vcml
43.2 kB
ortega_single_sim.omex
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vcell_cli_test.omex
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tagLatest.py
388 Bytes
thriftBuild
ImageDataset.thrift
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VCellImageJ.thrift
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VisMesh.thrift
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codegen-jtd.sh
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genVCThriftClasses.bat
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genVCellThriftClasses.sh
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pyVCell.thrift
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vcellopt.jtd.json
2.6 kB
vcell-admin
.gitignore
23 Bytes
pom.xml
4.7 kB
src
main
java
cbit
matlab
MatlabException.java
727 Bytes
MatlabFunctionResults.java
2.7 kB
MatlabServices.java
10.5 kB
MatlabServicesTest.java
2.0 kB
vcell
math
validation
gui
MathGenerationDebugger.java
8.7 kB
server
manage
ServerConfiguration.java
4.4 kB
VCellHost.java
3.6 kB
org
sbpax
test
TestJPAX.java
1.5 kB
vcell
admin
ListservMail.java
14.3 kB
VCComprehensiveStatistics.java
26.3 kB
VCStatistics.java
13.3 kB
cli
AdminCLI.java
2.6 kB
CLIDatabaseService.java
7.0 kB
db
DatabaseCompareSchemaCommand.java
1.9 kB
DatabaseDestroyAndRecreateCommand.java
2.6 kB
mathverifier
ModeldbLoadTestCommand.java
3.3 kB
ModeldbMathGenTestCommand.java
3.2 kB
sim
JobAdmin.java
5.0 kB
JobInfoCommand.java
3.5 kB
ResultSetCrawler.java
10.3 kB
ResultSetCrawlerCommand.java
3.2 kB
SimDataVerifier.java
13.1 kB
SimDataVerifierCommand.java
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tools
UsageCommand.java
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stochtest
Stochtest.java
308 Bytes
StochtestCompare.java
458 Bytes
StochtestCompareService.java
5.9 kB
StochtestDbUtils.java
19.0 kB
StochtestFileUtils.java
4.3 kB
StochtestMathType.java
605 Bytes
StochtestRun.java
501 Bytes
StochtestRunService.java
13.5 kB
TimeSeriesMultitrialData.java
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play.jpage
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stochtest.sql
6.8 kB
stochtestcompare.sql
5.1 kB
stochtestrun.sql
13.3 kB
test
java
cbit
vcell
client
ClientFactory.java
3.3 kB
ClientTaskDispatcherTest.java
2.2 kB
RuleBasedTest.java
15.5 kB
StandaloneRuleBasedTest.java
12.8 kB
TimeSeriesMultitrialData.java
6.8 kB
test
ClientTester.java
4.8 kB
message
server
dispatcher
SimulationDatabaseDirectTest.java
2.3 kB
numericstest
MathTestingReportGenerator.java
2.2 kB
util
AmplistorUtilsTest.java
10.9 kB
TestMissingSimData.java
54.5 kB
org
vcell
LoadAll.java
2.6 kB
sbml
CurrentWorkingAsInstall.java
653 Bytes
SBMLSolver.java
656 Bytes
support
ChangeEmail.java
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EmailList.java
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UserDbDriverExtended.java
1.3 kB
stochtest.sql
17.6 kB
vcell-api
.gitignore
23 Bytes
MobileAppRequirements.txt
933 Bytes
README.TXT
1.3 kB
UseCases.txt
153 Bytes
WebAPIDoc.rtf
35.6 kB
WebApiRequirements.txt
1.2 kB
docroot
dygraph-combined.js
136.1 kB
jquery_1_3_2.min.js
57.3 kB
keystore_macbook.jks
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localMac.jks
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localMac_pswd.txt
9 Bytes
pom.xml
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self-signed-keytool-instructions.txt
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src
main
java
org
vcell
rest
UserService.java
5.4 kB
VCellApiApplication.java
19.4 kB
VCellApiMain.java
11.7 kB
VCellCookieAuthenticator.java
4.3 kB
VCellStatusService.java
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admin
AdminJobsRestlet.java
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AdminService.java
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AdminStatsRestlet.java
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auth
AuthenticationTokenRestlet.java
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BearerTokenVerifier.java
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CookieVerifier.java
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CustomAuthHelper.java
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client
Client.java
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common
AccessTokenRepresentation.java
987 Bytes
ApplicationRepresentation.java
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BiomodelBNGLResource.java
553 Bytes
BiomodelDiagramResource.java
319 Bytes
BiomodelOMEXResource.java
580 Bytes
BiomodelReferenceRepresentation.java
1.0 kB
BiomodelRepresentation.java
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BiomodelResource.java
350 Bytes
BiomodelSBMLResource.java
574 Bytes
BiomodelSimulationSaveResource.java
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BiomodelSimulationStartResource.java
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BiomodelSimulationStopResource.java
292 Bytes
BiomodelVCMLResource.java
573 Bytes
BiomodelsResource.java
353 Bytes
MathmodelReferenceRepresentation.java
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OptimizationResource.java
294 Bytes
OptimizationRunResource.java
490 Bytes
OverrideRepresentation.java
5.1 kB
ParameterRepresentation.java
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PublicationRepresentation.java
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PublicationResource.java
356 Bytes
PublicationsResource.java
359 Bytes
SimDataRepresentation.java
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SimDataResource.java
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SimDataValuesRepresentation.java
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SimDataValuesResource.java
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SimDataVariableRepresentation.java
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SimDataVariableValuesRepresentation.java
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SimulationRepresentation.java
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SimulationResource.java
354 Bytes
SimulationStatusRepresentation.java
2.3 kB
SimulationStatusResource.java
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SimulationStatusesResource.java
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SimulationTaskRepresentation.java
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SimulationTaskResource.java
176 Bytes
SimulationTasksResource.java
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events
EventsRestlet.java
2.4 kB
RestEventService.java
7.0 kB
health
HealthRestlet.java
4.7 kB
HealthService.java
16.4 kB
rpc
AbstractRpcServerProxy.java
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RpcDataServerProxy.java
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RpcDbServerProxy.java
16.0 kB
RpcRestlet.java
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RpcService.java
1.4 kB
RpcSimServerProxy.java
4.0 kB
server
AbstractServerResource.java
1.2 kB
BiomodelBNGLServerResource.java
5.1 kB
BiomodelDiagramServerResource.java
4.8 kB
BiomodelOMEXServerResource.java
4.0 kB
BiomodelSBMLServerResource.java
5.3 kB
BiomodelServerResource.java
5.8 kB
BiomodelSimulationSaveServerResource.java
5.7 kB
BiomodelSimulationServerResource.java
6.2 kB
BiomodelSimulationStartServerResource.java
4.6 kB
BiomodelSimulationStopServerResource.java
4.6 kB
BiomodelVCMLModelInfoResource.java
11.8 kB
BiomodelVCMLServerResource.java
4.4 kB
BiomodelsServerResource.java
9.3 kB
ClientTopicMessageCollector.java
8.9 kB
OptimizationRunServerResource.java
13.3 kB
PublicationServerResource.java
13.0 kB
PublicationsServerResource.java
5.9 kB
RestDatabaseService.java
43.3 kB
SimDataServerResource.java
6.5 kB
SimDataValuesServerResource.java
7.8 kB
SimulationStatusServerResource.java
9.7 kB
SimulationTaskServerResource.java
2.7 kB
SimulationTasksServerResource.java
11.8 kB
TestRestServerBlinov.java
12.7 kB
users
ContactUsRestlet.java
2.9 kB
EmailTokenVerifyRestlet.java
3.4 kB
LoginFormRestlet.java
1.7 kB
LoginRestlet.java
1.1 kB
LostPasswordRestlet.java
2.3 kB
NewUserRestlet.java
11.0 kB
RegistrationFormRestlet.java
3.4 kB
SWVersionRestlet.java
578 Bytes
UnverifiedUser.java
642 Bytes
resources
TestTemplate.vcml
38.4 kB
biomodel.ftl
2.3 kB
biomodels.ftl
4.6 kB
logging.properties
144 Bytes
newpublication.ftl
2.3 kB
optimization.ftl
531 Bytes
publication.ftl
2.9 kB
publications.ftl
3.0 kB
simdata.ftl
1.1 kB
simdatavalues.ftl
1.8 kB
simulation.ftl
13.0 kB
simulationStatus.ftl
4.5 kB
simulationTasks.ftl
5.2 kB
vcellapi.yaml
16.9 kB
webapp
angular.min.js
106.9 kB
app.js
1.4 kB
auth
auth-directives.js
884 Bytes
auth-module.js
3.4 kB
login-form.html
383 Bytes
vcell-loginbar.html
271 Bytes
bootstrap.min.css
106.0 kB
diagram_icon.gif
890 Bytes
index.html
1.8 kB
models
models-controllers.js
1.5 kB
models-directives.js
216 Bytes
models-module.js
73 Bytes
vcell-biomodel.html
1.5 kB
run2_16x16.gif
173 Bytes
sims
sims-controllers.js
1.6 kB
sims-directives.js
236 Bytes
sims-module.js
71 Bytes
vcell-jobs.html
570 Bytes
wordpress
vcell-shortcode.php
17.3 kB
vcell-apiclient
.gitignore
23 Bytes
pom.xml
3.8 kB
src
main
java
org
vcell
api
client
VCellApiClient.java
34.5 kB
VCellApiInvocationTargetException.java
206 Bytes
VCellApiRpcRequest.java
1.6 kB
VCellOptClient.java
8.1 kB
examples
VCSchedulerPanel.java
15.6 kB
VCellApiClientTest.java
5.9 kB
query
BioModelsQuerySpec.java
649 Bytes
SimTasksQuerySpec.java
1.3 kB
common
AccessTokenRepresentation.java
590 Bytes
ApplicationRepresentation.java
764 Bytes
BioModelLink.java
2.0 kB
BiomodelRepresentation.java
1.2 kB
MathModelLink.java
1.1 kB
SimDataRepresentation.java
357 Bytes
SimDataValuesRepresentation.java
298 Bytes
SimDataVariableRepresentation.java
230 Bytes
SimDataVariableValuesRepresentation.java
379 Bytes
SimpleJobStatusRepresentation.java
4.3 kB
SimulationRepresentation.java
2.5 kB
SimulationTaskRepresentation.java
1.6 kB
UserInfo.java
1.5 kB
events
BroadcastEventRepresentation.java
211 Bytes
DataJobEventRepresentation.java
771 Bytes
EventWrapper.java
542 Bytes
ExportEventRepresentation.java
1.1 kB
ExportTimeSpecs.java
435 Bytes
ExportVariableSpecs.java
283 Bytes
SimulationJobStatusEventRepresentation.java
693 Bytes
SimulationJobStatusRepresentation.java
4.4 kB
test
java
org
vcell
api
client
VCellApiClientTest.java
331 Bytes
vcell-cli
.gitignore
23 Bytes
pom.xml
9.1 kB
src
main
java
org
vcell
cli
CLIPythonManager.java
15.2 kB
CLIRecordable.java
638 Bytes
CLIRecorder.java
8.1 kB
CLIStandalone.java
3.0 kB
CLIUtils.java
3.0 kB
PythonStreamException.java
491 Bytes
VersionCommand.java
1.7 kB
biosimulation
BiosimulationsCommand.java
5.3 kB
exceptions
ExecutionException.java
541 Bytes
run
ExecuteCommand.java
5.9 kB
ExecuteImpl.java
11.1 kB
ExecutionJob.java
9.2 kB
OmexHandler.java
6.6 kB
PythonCalls.java
9.3 kB
RunUtils.java
33.1 kB
SedmlJob.java
24.1 kB
SedmlStatistics.java
4.4 kB
SolverHandler.java
38.6 kB
Status.java
389 Bytes
TaskJob.java
797 Bytes
hdf5
Hdf5DataContainer.java
685 Bytes
Hdf5DataExtractor.java
3.8 kB
Hdf5DataPreparer.java
8.4 kB
Hdf5DataSourceSpatialVarDataItem.java
4.9 kB
Hdf5File.java
18.2 kB
Hdf5SedmlMetadata.java
948 Bytes
Hdf5SedmlResultData.java
205 Bytes
Hdf5SedmlResults.java
245 Bytes
Hdf5SedmlResultsNonspatial.java
501 Bytes
Hdf5SedmlResultsSpatial.java
301 Bytes
Hdf5Writer.java
6.4 kB
NonspatialResultsConverter.java
15.3 kB
SimpleDataGenCalculator.java
3.1 kB
SpatialResultsConverter.java
11.7 kB
sbml
MemoryLogger.java
1.2 kB
ModelCommand.java
3.4 kB
vcml
DatabaseCommand.java
5.4 kB
ExportOmexBatchCommand.java
4.6 kB
ExportOmexCommand.java
2.7 kB
ImportOmexBatchCommand.java
2.6 kB
ImportOmexCommand.java
2.6 kB
VCMLHandler.java
5.5 kB
ValidateBatchCommand.java
3.4 kB
VcmlOmexConverter.java
17.4 kB
VcmlValidator.java
6.6 kB
resources
log4j2.xml
905 Bytes
test
java
org
vcell
cli
run
BSTSBasedOmexExecTest.java
9.6 kB
BSTSBasedTestSuiteFiles.java
8.0 kB
BiosimulationsExecTest.java
8.5 kB
BiosimulationsFiles.java
2.1 kB
ExecuteImplTest.java
2.2 kB
SpatialArchiveFiles.java
1.9 kB
SpatialExecTest.java
8.7 kB
hdf5
Hdf5WriterTest.java
7.0 kB
resources
BioModel1.omex
5.9 kB
BiosimulationsOmexWithResults
BIOMD0000000003_tellurium_A_minimal_cascade_model_for_th.h5
135.2 kB
BIOMD0000000003_tellurium_A_minimal_cascade_model_for_th.spec.omex
214.4 kB
BIOMD0000000006_tellurium_Modeling_the_cell_division_cyc.h5
94.0 kB
BIOMD0000000006_tellurium_Modeling_the_cell_division_cyc.spec.omex
188.2 kB
BIOMD0000000036_tellurium_A_simple_model_of_circadian_rh.h5
100.3 kB
BIOMD0000000036_tellurium_A_simple_model_of_circadian_rh.spec.omex
179.2 kB
bsts-omex
misc-projects
BIOMD0000000005.omex
245.8 kB
sbml-core
Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
303.5 kB
Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex
152.9 kB
Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
152.9 kB
Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex
188.7 kB
Elowitz-Nature-2000-Repressilator.omex
92.2 kB
Parmar-BMC-Syst-Biol-2017-iron-distribution.omex
110.3 kB
Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex
343.2 kB
Tomida-EMBO-J-2003-NFAT-translocation.omex
78.4 kB
Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML.omex
213.1 kB
Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
120.9 kB
Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
46.1 kB
Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA.omex
45.8 kB
Vilar-PNAS-2002-minimal-circardian-clock.omex
280.1 kB
synths
combine_archive
CombineArchiveHasSedDocumentsInNestedDirectories
1.execution-should-succeed.omex
304.7 kB
CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
1.execution-should-succeed.omex
606.2 kB
WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
1.execution-should-succeed.omex
304.6 kB
WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
1.execution-should-succeed.omex
304.6 kB
docker_image
SingularityImageExecutesSimulationsSuccessfully
1.execution-should-succeed.omex
303.2 kB
log
SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
1.execution-should-succeed.omex
303.2 kB
SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
1.execution-should-succeed.omex
303.2 kB
SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
1.execution-should-succeed.omex
303.2 kB
SimulatorReportsTheStatusOfTheExecutionOfSedTasks
1.execution-should-succeed.omex
303.2 kB
results_report
SimulatorGeneratesReportsOfSimulationResults
1.execution-should-succeed.omex
303.2 kB
sedml
SimulatorCanResolveModelSourcesDefinedByUriFragments
1.execution-should-succeed.omex
303.2 kB
SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
1.execution-should-succeed.omex
303.3 kB
SimulatorProducesLinear2DPlots
1.execution-should-succeed.omex
303.2 kB
2.execution-should-succeed.omex
303.3 kB
SimulatorProducesLogarithmic2DPlots
1.execution-should-succeed.omex
303.2 kB
2.execution-should-succeed.omex
303.3 kB
SimulatorProducesMultiplePlots
1.execution-should-succeed.omex
303.2 kB
2.execution-should-succeed.omex
303.3 kB
SimulatorSupportsAddReplaceRemoveModelElementChanges
1.execute-should-fail.omex
303.2 kB
2.execution-should-succeed.omex
306.5 kB
3.execute-should-fail.omex
303.3 kB
SimulatorSupportsAlgorithmParameters
1.execution-should-succeed.omex
303.2 kB
SimulatorSupportsComputeModelChanges
1.execute-should-fail.omex
304.2 kB
2.execution-should-succeed.omex
304.5 kB
SimulatorSupportsDataGeneratorsWithDifferentShapes
1.execution-should-succeed.omex
303.3 kB
SimulatorSupportsDataSetsWithDifferentShapes
1.execution-should-succeed.omex
303.3 kB
SimulatorSupportsModelAttributeChanges
1.execute-should-fail.omex
304.6 kB
2.execution-should-succeed.omex
306.3 kB
SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
1.execution-should-succeed.omex
303.2 kB
SimulatorSupportsMultipleReportsPerSedDocument
1.execution-should-succeed.omex
303.2 kB
SimulatorSupportsMultipleTasksPerSedDocument
1.execution-should-succeed.omex
303.3 kB
SimulatorSupportsRepeatedTasksWithChanges
1.execute-should-fail.omex
304.8 kB
2.execution-should-succeed.omex
305.3 kB
SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
1.execute-should-fail.omex
304.9 kB
2.execution-should-succeed.omex
305.4 kB
SimulatorSupportsRepeatedTasksWithFunctionalRanges
1.execution-should-succeed.omex
303.5 kB
SimulatorSupportsRepeatedTasksWithLinearUniformRanges
1.execution-should-succeed.omex
303.4 kB
SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
1.execution-should-succeed.omex
303.4 kB
SimulatorSupportsRepeatedTasksWithMultipleSubTasks
1.execution-should-succeed.omex
303.4 kB
SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
1.execution-should-succeed.omex
303.5 kB
SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
1.execution-should-succeed.omex
303.4 kB
SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
1.execution-should-succeed.omex
303.4 kB
2.execution-should-succeed.omex
303.4 kB
SimulatorSupportsRepeatedTasksWithVectorRanges
1.execution-should-succeed.omex
303.4 kB
SimulatorSupportsSubstitutingAlgorithms
1.execute-should-fail.omex
303.2 kB
2.execution-should-succeed.omex
303.2 kB
3.execute-should-fail.omex
303.2 kB
4.execution-should-succeed.omex
303.2 kB
SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
1.execution-should-succeed.omex
303.2 kB
SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
1.execution-should-succeed.omex
303.2 kB
vcml
Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength.omex
100.2 kB
spatial
SimpleSpatialModel.omex
10.4 kB
TinySpatialProject.omex
6.8 kB
vcell-cli-utils
.gitignore
1.4 kB
CHANGELOG.md
528 Bytes
License
1.1 kB
README.md
1.8 kB
biosimulations_pipeline
README.md
3.6 kB
__init__.py
0 Bytes
biosim_api.py
4.8 kB
cli.py
8.2 kB
data_manager.py
4.3 kB
datamodels.py
744 Bytes
hdf5_compare.py
2.2 kB
mypy.ini
193 Bytes
omex
output
biosimulations_comparisons.ndjson
13.3 kB
biosimulations_projects.ndjson
595 Bytes
biosimulations_runs.ndjson
7.6 kB
poetry.lock
211.2 kB
pyproject.toml
1.4 kB
setup.cfg
117 Bytes
tests
citation_test.py
684 Bytes
cli_test.py
1.2 kB
fixtures
Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
10.3 kB
reports.h5
353.5 kB
simulation_1.sedml
Figure_3a.csv
85.2 kB
Figure_3b.csv
85.2 kB
Figure_3c.csv
85.2 kB
Figure_3d.csv
85.2 kB
report.csv
84.2 kB
validation
Aavani2019_BIOMD0000000876_vcell_7.5.0.27.omex
11.7 kB
Aavani2019_BIOMD0000000876_vcell_7.5.0.27.report.json
3.2 kB
VerySimple_vcell_7.5.0.27.omex
5.4 kB
VerySimple_vcell_7.5.0.27.report.json
1.8 kB
eungdamrong_and_Iyengar_BiophysJ_vcell_7.5.0.30.omex
74.7 kB
eungdamrong_and_Iyengar_BiophysJ_vcell_7.5.0.30.report.json
382.2 kB
hdf5_test.py
1.2 kB
vcell_datamodels_test.py
1.9 kB
vcell_cli_utils
__init__.py
0 Bytes
cli.py
16.5 kB
status.py
14.0 kB
wrapper.py
3.0 kB
vcell_common
__init__.py
0 Bytes
api_utils.py
781 Bytes
vcell_pipeline
__init__.py
0 Bytes
citation.py
3.2 kB
download_biosim_projects.py
2.1 kB
download_vcell_omex.py
2.8 kB
vcell_datamodels.py
633 Bytes
vcell-client
.gitignore
23 Bytes
UserDocumentation
originalXML
01User guide mapping.doc
41.0 kB
HelpSet.hs
824 Bytes
TOC.xml
11.0 kB
pageTemplate.txt
1.5 kB