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Open-Systems-Pharmacology / Pregnancy-Models

Physiologically Based Pharmacokinetic Models for Pregnant Women
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Issue with Pregnancy model in MoBi #26

Open mmalsmadi opened 1 year ago

mmalsmadi commented 1 year ago

Hello

I am trying to build a pregnancy model that I started in PK-Sim, sent to MoBi Then in MoBi I did the following all the steps advised in "Applied Concepts in PBPK Modeling: How to Extend an Open Systems Pharmacology Model to the Special Population of Pregnant Women"

Finally, when I tried to put the simulation together in MoBi, I got the following error message image

When tracked the path down I found the following set of parameters image

I went back to check the PkSim file for the related nonpregnant model, and these were the values image

Can you please help me sort out this issue?

Thanks Mo'tasem

Yuri05 commented 1 year ago

@AndreDlm

mmalsmadi commented 1 year ago

any thoughts?

mmalsmadi commented 1 year ago

attached are the files I am working on

1983 Justins Mother IM.zip

mmalsmadi commented 1 year ago

Can you please provide help!!!!!

I tried the new spatial structure and passive transport available here https://github.com/Open-Systems-Pharmacology/Pregnancy-Models/blame/master/BuildingBlocks/PassiveTransport_Pregnancy.pkml

and I got the following error message

Application: MoBi® 11.0.138

'>' is an unexpected token. The expected token is '='. Line 17, position 76.

Stack trace:

at System.Xml.XmlTextReaderImpl.Throw(Exception e)
   at System.Xml.XmlTextReaderImpl.ParseAttributes()
   at System.Xml.XmlTextReaderImpl.ParseElement()
   at System.Xml.XmlTextReaderImpl.ParseElementContent()
   at System.Xml.Linq.XContainer.ReadContentFrom(XmlReader r)
   at System.Xml.Linq.XContainer.ReadContentFrom(XmlReader r, LoadOptions o)
   at System.Xml.Linq.XElement.ReadElementFrom(XmlReader r, LoadOptions o)
   at System.Xml.Linq.XElement.Load(XmlReader reader, LoadOptions options)
   at System.Xml.Linq.XElement.Load(String uri, LoadOptions options)
   at MoBi.Presentation.Tasks.SerializationTask.LoadMany[T](String fileName, Boolean resetIds)
   at MoBi.Presentation.Tasks.Interaction.InteractionTask.LoadItems[T](String filename)
   at MoBi.Presentation.Tasks.Interaction.InteractionTasksForChildren`3.LoadItems(String filename)
   at MoBi.Presentation.Tasks.Interaction.InteractionTasksForChildren`3.adddItemsToProjectFromFile(String filename, TParent parent, IBuildingBlock buildingBlockWithFormulaCache)
   at MoBi.Presentation.Tasks.Interaction.InteractionTasksForChildren`3.AddExisting(TParent parent, IBuildingBlock buildingBlockWithFormulaCache)
   at MoBi.Presentation.UICommand.AddExistingCommandForBase`1.PerformExecute()
   at OSPSuite.Presentation.UICommands.ObjectUICommand`1.Execute()
   at OSPSuite.Presentation.UICommands.UICommandExtensions.ExecuteWithinExceptionHandler(IUICommand uiCommand, IEventPublisher eventPublisher, IChangePropagator changePropagator)
Yuri05 commented 1 year ago

Please make sure that you download the file PassiveTransport_Pregnancy.pkml and NOT the html page.

mmalsmadi commented 1 year ago

I already used the .pkml files not the html files

Regards, PassiveTransport&SpacialStructure_PregnantWoman.zip

Mo'tasem Alsmadi, PhD

Associate Professor Department of Pharmaceutical Technology Faculty of Pharmacy Jordan University of Science & Technology P.O.Box 3030 - Irbid 22110, Jordan Phone: +96227201000 Ext. 23522

From: Juri Solodenko @.> Sent: Tuesday, December 13, 2022 12:16 PM To: Open-Systems-Pharmacology/Pregnancy-Models @.> Cc: Mo'tasem Alsmadi @.>; Author @.> Subject: Re: [Open-Systems-Pharmacology/Pregnancy-Models] Issue with Pregnancy model in MoBi (Issue #26)

Please make sure that you download the file PassiveTransport_Pregnancy.pkmlhttps://raw.githubusercontent.com/Open-Systems-Pharmacology/Pregnancy-Models/master/BuildingBlocks/PassiveTransport_Pregnancy.pkml and NOT the html page.

— Reply to this email directly, view it on GitHubhttps://github.com/Open-Systems-Pharmacology/Pregnancy-Models/issues/26#issuecomment-1348131060, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AI6MN6XDXFKGAMBEPAWH4DLWNBEH7ANCNFSM6AAAAAASSXL2R4. You are receiving this because you authored the thread.Message ID: @.***>

Yuri05 commented 1 year ago

I just checked it: all pkml files can be loaded in MoBi. The error above comes if you try to load a html file.

To properly load a file from GitHub:

mmalsmadi commented 1 year ago

Thanks, now I was able to load the spatial structure and passive transport files, But, when I tried to set the new simulation based on the original simulation merged with pregnancy files after excluding the metabolic enzymes and undefined liver molecules from the molecule start values for the nine pregnancy-specific compartments in addition to the bone, I got the following error message

image

Did I miss anything?