virtualcell/vcell-7.5.0.153.zip
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virtualcell-vcell-cc40b37
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stale.yml
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workflows
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NightlyBMDB_CLI.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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CONTRIBUTING.md
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README.md
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auto.vcellapps
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CHANGES.txt
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CREDITS.txt
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LICENSE.txt
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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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BNGOutput.pm
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Boolean2BNGL.pl
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Tcell_model_Oct2013.txt
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Tcell_model_v16.txt
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Map.pm
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README
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VERSION
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AccessTokenRepresentation.md
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AdminResourceApi.md
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BioModel.md
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BioModelResourceApi.md
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BiomodelRef.md
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HelloWorldApi.md
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HelloWorldMessage.md
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Identity.md
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IdentityProvider.md
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KeyValue.md
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MapUser.md
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Publication.md
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PublicationResourceApi.md
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Simulation.md
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User.md
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User1.md
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UserIdentity.md
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mypy.ini
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vcell_pipeline
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citation.py
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datamodels.py
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openapi.yaml
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vcell-admin
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src
main
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cbit
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MatlabFunctionResults.java
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MatlabServices.java
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MatlabServicesTest.java
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vcell
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MathGenerationDebugger.java
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ServerConfiguration.java
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VCellHost.java
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org
sbpax
test
TestJPAX.java
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vcell
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ListservMail.java
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VCComprehensiveStatistics.java
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VCStatistics.java
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cli
AdminCLI.java
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CLIDatabaseService.java
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DatabaseCreateScriptCommand.java
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DatabaseDestroyAndRecreateCommand.java
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mathverifier
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ModeldbMathGenTestCommand.java
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models
ModelCommands.java
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ModelListCommand.java
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ModelPermissionCommand.java
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sim
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JobInfoCommand.java
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ResultSetCrawler.java
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ResultSetCrawlerCommand.java
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SimDataVerifier.java
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SimDataVerifierCommand.java
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VCellSimStatus_NOT_USED.java
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stochtest
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StochtestCompare.java
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StochtestCompareService.java
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StochtestDbUtils.java
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StochtestFileUtils.java
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StochtestMathType.java
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StochtestRun.java
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StochtestRunService.java
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play.jpage
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stochtestcompare.sql
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stochtestrun.sql
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java
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RuleBasedTest.java
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TimeSeriesMultitrialData.java
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TestMissingSimData.java
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org
vcell
LoadAll.java
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sbml
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UserDbDriverExtended.java
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stochtest.sql
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vcell-api
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MobileAppRequirements.txt
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README.TXT
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UseCases.txt
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WebAPIDoc.rtf
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WebApiRequirements.txt
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dygraph-combined.js
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jquery_1_3_2.min.js
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localMac.jks
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localMac_pswd.txt
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pom.xml
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self-signed-keytool-instructions.txt
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src
main
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org
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UserService.java
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VCellApiApplication.java
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VCellApiMain.java
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VCellCookieAuthenticator.java
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VCellStatusService.java
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admin
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AdminService.java
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AdminStatsRestlet.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
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ApplicationRepresentation.java
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BiomodelBNGLResource.java
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BiomodelDiagramResource.java
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BiomodelOMEXResource.java
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BiomodelReferenceRepresentation.java
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BiomodelRepresentation.java
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BiomodelResource.java
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BiomodelSBMLResource.java
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BiomodelSimulationSaveResource.java
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BiomodelSimulationStartResource.java
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BiomodelSimulationStopResource.java
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BiomodelVCMLResource.java
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BiomodelsResource.java
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MathmodelReferenceRepresentation.java
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OptimizationResource.java
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OptimizationRunResource.java
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OverrideRepresentation.java
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ParameterRepresentation.java
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PublicationRepresentation.java
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PublicationResource.java
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PublicationsResource.java
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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
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SimulationStatusRepresentation.java
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SimulationStatusResource.java
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SimulationStatusesResource.java
1.7 kB
SimulationTaskRepresentation.java
5.1 kB
SimulationTaskResource.java
176 Bytes
SimulationTasksResource.java
2.0 kB
events
EventsRestlet.java
2.4 kB
RestEventService.java
7.0 kB
health
HealthRestlet.java
4.7 kB
HealthService.java
16.5 kB
n5data
N5ExportRestlet.java
3.8 kB
N5GetInfoRestlet.java
2.3 kB
N5Service.java
1.6 kB
rpc
AbstractRpcServerProxy.java
2.7 kB
RpcDataServerProxy.java
8.5 kB
RpcDbServerProxy.java
16.0 kB
RpcRestlet.java
9.3 kB
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
6.0 kB
BiomodelSimulationSaveServerResource.java
5.7 kB
BiomodelSimulationServerResource.java
6.4 kB
BiomodelSimulationStartServerResource.java
4.6 kB
BiomodelSimulationStopServerResource.java
4.6 kB
BiomodelVCMLModelInfoResource.java
11.8 kB
BiomodelVCMLServerResource.java
4.4 kB
BiomodelsServerResource.java
9.5 kB
ClientTopicMessageCollector.java
8.6 kB
OptimizationRunServerResource.java
13.3 kB
PublicationServerResource.java
13.3 kB
PublicationsServerResource.java
6.1 kB
RestDatabaseService.java
43.2 kB
SimDataServerResource.java
6.7 kB
SimDataValuesServerResource.java
8.0 kB
SimulationStatusServerResource.java
9.9 kB
SimulationTaskServerResource.java
2.7 kB
SimulationTasksServerResource.java
12.0 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
10.8 kB
RegistrationFormRestlet.java
3.4 kB
SWVersionRestlet.java
578 Bytes
UnverifiedUser.java
642 Bytes
resources
TestTemplate.vcml
38.4 kB
biomodel.ftl
2.4 kB
biomodels.ftl
4.7 kB
logging.properties
144 Bytes
newpublication.ftl
2.3 kB
optimization.ftl
557 Bytes
publication.ftl
3.0 kB
publications.ftl
3.0 kB
simdata.ftl
1.1 kB
simdatavalues.ftl
1.9 kB
simulation.ftl
13.2 kB
simulationStatus.ftl
4.6 kB
simulationTasks.ftl
5.3 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
4.2 kB
src
main
java
org
vcell
api
client
VCellApiClient.java
35.2 kB
VCellApiInvocationTargetException.java
206 Bytes
VCellApiRpcRequest.java
1.6 kB
VCellOptClient.java
8.1 kB
examples
VCellApiClientTest.java
5.9 kB
query
BioModelsQuerySpec.java
649 Bytes
SimTasksQuerySpec.java
1.3 kB
common
AccessTokenRepresentation.java
629 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
1.3 kB
ExportHumanReadableDataSpec.java
1.2 kB
ExportTimeSpecs.java
435 Bytes
ExportVariableSpecs.java
283 Bytes
SimulationJobStatusEventRepresentation.java
693 Bytes
SimulationJobStatusRepresentation.java
4.4 kB
vcell-cli
.gitignore
23 Bytes
pom.xml
5.3 kB
src
main
java
org
vcell
cli
CLIPythonManager.java
15.2 kB
CLIRecordable.java
638 Bytes
CLIRecorder.java
8.1 kB
CLIStandalone.java
2.9 kB
CLIUtils.java
3.0 kB
PythonStreamException.java
491 Bytes
VersionCommand.java
1.7 kB
biosimulation
BiosimulationsCommand.java
5.5 kB
exceptions
ExecutionException.java
541 Bytes
run
ExecuteCommand.java
6.1 kB
ExecuteImpl.java
13.1 kB
ExecutionJob.java
9.4 kB
OmexHandler.java
8.0 kB
PythonCalls.java
9.3 kB
RunUtils.java
31.1 kB
SedmlJob.java
25.5 kB
SedmlStatistics.java
4.4 kB
SolverHandler.java
34.3 kB
Status.java
389 Bytes
TaskJob.java
797 Bytes
hdf5
BiosimulationsHdf5File.java
19.0 kB
BiosimulationsHdf5Writer.java
7.7 kB
HDF5ExecutionResults.java
1.3 kB
Hdf5DataContainer.java
1.1 kB
Hdf5DataExtractor.java
4.8 kB
Hdf5DataPreparer.java
8.5 kB
Hdf5DataSourceSpatialVarDataItem.java
5.6 kB
Hdf5SedmlMetadata.java
948 Bytes
Hdf5SedmlResultData.java
205 Bytes
Hdf5SedmlResults.java
245 Bytes
Hdf5SedmlResultsNonspatial.java
496 Bytes
Hdf5SedmlResultsSpatial.java
369 Bytes
MissingDataException.java
227 Bytes
NonspatialDataMapping.java
1.9 kB
NonspatialResultsConverter.java
15.2 kB
SimpleDataGenCalculator.java
3.1 kB
SpatialDataMapping.java
2.0 kB
SpatialResultsConverter.java
13.2 kB
sbml
MemoryLogger.java
1.2 kB
ModelCommand.java
3.4 kB
trace
Span.java
1.7 kB
TraceEvent.java
606 Bytes
Tracer.java
3.0 kB
vcml
ExportOmexBatchCommand.java
3.5 kB
ExportOmexCommand.java
2.7 kB
ImportOmexBatchCommand.java
2.4 kB
ImportOmexCommand.java
2.4 kB
ValidateBatchCommand.java
3.3 kB
VcmlOmexConverter.java
8.7 kB
VcmlValidator.java
6.6 kB
resources
log4j2.xml
905 Bytes
test
java
org
vcell
cli
run
BSTSBasedOmexExecTest.java
9.3 kB
BSTSBasedTestSuiteFiles.java
8.0 kB
BiosimulationsExecTest.java
8.4 kB
BiosimulationsFiles.java
2.1 kB
ExecuteImplTest.java
2.1 kB
SpatialArchiveFiles.java
1.9 kB
SpatialExecTest.java
8.6 kB
hdf5
BiosimulationsHdf5WriterTest.java
7.8 kB
trace
TracerTest.java
2.2 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
vcell-cli-utils
.gitignore
1.4 kB
CHANGELOG.md
528 Bytes
License
1.1 kB
README.md
1.8 kB
mypy.ini
193 Bytes
poetry.lock
189.1 kB
pyproject.toml
1.3 kB
setup.cfg
117 Bytes
tests
cli_test.py
1.2 kB
fixtures
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
vcell_cli_utils
__init__.py
0 Bytes
cli.py
16.5 kB
status.py
14.1 kB
wrapper.py
3.0 kB