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License: MIT License
Open access PBPK modelling platform
License: MIT License
When configuring LHS the parameter distributions default to uniform. The default lower and upper ranges appear reasonable for most parameters except Qliv, liver blood flow rate. This defaults to 0.1 - 1. This gives values as high as 0.99 or 99% cardiac output. This causes faulty simulations for any given output.
Fix: move to temp and delete dir on worker thread.
Return mean or median and display bounds of simulations with +/- 1-3 * standard deviation
Fix: plot subset of data; provide chart control to adjust.
At present RVis can create a design prior to executing a batch run (Monte Carlo and Latin Hypercube options) but it does not have an option of reading in an externally created design and batch running. This would be pretty useful for post processing of MCMC output and would link in with our other software tools (PopGen).
Test on Installed: .NET Framework 4.8, or 4.7.2
Symptom:
When running a simulation, a blank white screen appears (No graph displayed).
Fix?
The possible call to 'file:///C:' May be escalating security on this path due to it's potential to be a hyperlink. Is it possible to call C:\ directly without the File:///?
I don't understand the .NET sandbox security fully, but i believe the least priv approach is safest. This may be a better key to the fix:
https://docs.microsoft.com/en-us/previous-versions/dotnet/netframework-4.0/bb763046(v=vs.100)?redirectedfrom=MSDN
Workaround:
Edit RVisUI.exe.config
Below <runtime>
Paste: <loadFromRemoteSources enabled="true"/>
Logfile Error:
10:58:31 Failed to load module in C:\Apps\RVis_v0.8.11068.1\module\sensitivity System.IO.FileLoadException: Could not load file or assembly 'file:///C:\Apps\RVis_v0.8.11068.1\module\sensitivity\Sensitivity.dll' or one of its dependencies. Operation is not supported. (Exception from HRESULT: 0x80131515) File name: 'file:///C:\Apps\RVis_v0.8.11068.1\module\sensitivity\Sensitivity.dll' ---> System.NotSupportedException: An attempt was made to load an assembly from a network location which would have caused the assembly to be sandboxed in previous versions of the .NET Framework. This release of the .NET Framework does not enable CAS policy by default, so this load may be dangerous. If this load is not intended to sandbox the assembly, please enable the loadFromRemoteSources switch. See http://go.microsoft.com/fwlink/?LinkId=155569 for more information.
at System.Reflection.RuntimeAssembly._nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.nLoad(AssemblyName fileName, String codeBase, Evidence assemblySecurity, RuntimeAssembly locationHint, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadAssemblyName(AssemblyName assemblyRef, Evidence assemblySecurity, RuntimeAssembly reqAssembly, StackCrawlMark& stackMark, IntPtr pPrivHostBinder, Boolean throwOnFileNotFound, Boolean forIntrospection, Boolean suppressSecurityChecks)
at System.Reflection.RuntimeAssembly.InternalLoadFrom(String assemblyFile, Evidence securityEvidence, Byte[] hashValue, AssemblyHashAlgorithm hashAlgorithm, Boolean forIntrospection, Boolean suppressSecurityChecks, StackCrawlMark& stackMark)
at System.Reflection.Assembly.LoadFrom(String assemblyFile)
at Ninject.Modules.AssemblyNameRetriever.AssemblyChecker.GetAssemblyNames(IEnumerable1 filenames, Predicate
1 filter)
at Ninject.Modules.AssemblyNameRetriever.AssemblyChecker.GetAssemblyNames(IEnumerable1 filenames, Predicate
1 filter)
at Ninject.Modules.AssemblyNameRetriever.GetAssemblyNames(IEnumerable1 filenames, Predicate
1 filter)
at Ninject.Extensions.Conventions.BindingBuilder.AssemblyFinder.FindAssemblies(IEnumerable1 assemblies, Predicate
1 filter)
at Ninject.Extensions.Conventions.BindingBuilder.ConventionSyntax.FromAssembliesInPath(String path)
at RVisUI.Ioc.AppState.<>c__DisplayClass68_0.b__0(IFromSyntax x)
at Ninject.Extensions.Conventions.ExtensionsForIKernel.Bind(IBindingRoot kernel, Action1 configure) at RVisUI.Ioc.AppState.DoDirectoryBind(String directory)
Provide a zero lower bound limit for sliders to prevent biologically implausible values
Provide row numbers in the Samples field to match simulation line number in chart in Outputs. This should aid user to quickly identify suspect parameter(s).
In eFAST, the ranking of parameters fails if the range starts at 0 min. The parameters are assigned NAN. Setting the lower range to a >0 avoids this fault.
Add an option through configuration file to specify the location of the R installation directory for R.NET.
Useful for security settings that limit program access to registry files or for non-standard R installations.
Define/select a range of acceptable simulations from the LHS output from which the upper and lower limits of parameter distributions can be set.
Line 5 of .in file produces an error that Expected ,model-variable> before 'BDW"
line 16: Bad definition of experiment 1.
butadiene.template.in.txt
mcsim.butadiene.model.R.txt
Please note that the attachments are for the .in and .exe Butadiene files
Reinstating access by clicking question mark (help) on Import page to the information about executive functions and templates available here:
https://r-vis.github.io/doc/home/simulation-code/#executive-function
Calculation for ranking parameters in Morris test is not correct.
No response from program, will not load when the following Windows 10 STIG is applied.
https://www.stigviewer.com/stig/windows_10/2019-01-04/finding/V-63811
Solution:
The software should support FIPS compliant algos. Unless it's something stronger, then the workaround should be sufficient for now.
Workaround:
Powershell
Set-ItemProperty -Path "HKLM:\SYSTEM\CurrentControlSet\Control\Lsa\FipsAlgorithmPolicy" -Name "Enabled" -Value "0" -Force
And/Or Disable the GPO:
Configure the policy value for Computer Configuration >> Windows Settings >> Security Settings
>> Local Policies >> Security Options >> "System cryptography: Use FIPS compliant algorithms for encryption, hashing, and signing" to "Disabled".
User should be able to click on a spurious simulation in the LHS chart and identify the suspect line of parameters in the design. These parameter values can then be tested as inputs in the plotter module to test whether the fault can be reproduced and the spurious parameter(s) values identified.
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