Help getting started

Hi, i'm brand new to Biogears and was wondering if I could get some help on how to get started.


Best Answer

  • abrayabray Entry Level
    Answer ✓
    Can you tell if it is 64 bit or 32 bit?
    If it does not say 64 bit, it will say it.
    If it's 32 bit, it won't refer to a bit


  • abrayabray Entry Level
    Hi Kyle,
    What do you trying to do with BioGears?
  • Trying to get the engine to run with a scenario, but whenever I try to start it, it says "missing CommonDataModel.dll.

    Thanks for the swift response,
  • abrayabray Entry Level
    Are you using the SDK project to run a scenario? Or are you running the toolkit applications?
    What OS are you using? What Compiler if you are running code?
  • I'm using the scenario driver in the toolkit, I'm running on Windows 8.1.

  • abrayabray Entry Level
    Are you running the latest 5.0 BioGearsGUI.bat?
  • It says BioGears 5.0 Beta, so I assume yes.
  • abrayabray Entry Level
    So you crank up the GUI, and it pops up
    You Select a Scenario file via the File->Open menu
    Hit Execute and it pops up a dialog that it cannot find a dll

    Is that about right?
  • No, right when I try and boot up the engine, it loads and then gives me an error message right before it finished with the dll message.

  • abrayabray Entry Level
    Can you make sure you have java installed?
    Open a command prompt and type : java -version
    You should then see something like this

    C:\Users\abray>java -version
    java version "1.8.0_45"
    Java(TM) SE Runtime Environment (build 1.8.0_45-b14)
    Java HotSpot(TM) Client VM (build 25.45-b02, mixed mode)
  • Ok I checked and it said I was on version 1.8.0_45
  • Well my computer is 64 bit, however it does not say anything about it being 32 or 64 bits in the prompt
  • abrayabray Entry Level
    Can you try opening up the BIoGearsGUI.bat file up in an editor and removing the following lines:

    java -version 2>&1 | findstr "64-Bit" > nul 2>&1
    if %errorlevel% == 0 (
    set PATHFOLDER=x64
    set JLIBPATH=.\;.\x64

    try it, if that does not work, try changing these lines

    set PATHFOLDER=x86
    set JLIBPATH=.\;.\x86

    to this:

    set PATHFOLDER=x64
    set JLIBPATH=.\;.\x64

  • Unfortunately they didn't work, I did both.
    Here is what the .bat file currently looks likes

    @echo off
    set cp=
    set cp=%cp%.\BioGears.jar;

    set JAVA_OPTS=-Xmx1024m
    set JAVA_OPTS=%JAVA_OPTS% -classpath %cp%
    echo Using JAVA OPTS: %JAVA_OPTS%

    set PATHFOLDER=x64
    set JLIBPATH=.\;.\x64

    java -version 2>&1 | findstr "64-Bit" > nul 2>&1
    if %errorlevel% == 0 (
    set PATHFOLDER=x64
    set JLIBPATH=.\;.\x64


    start javaw.exe %JAVA_OPTS% -Djava.library.path=%JLIBPATH% mil.tatrc.physiology.biogears.gui.BioGearsGUI
  • Hi,
    I have similar problem with starting .

    system: Ubuntu 14.04 LTS x64
    command: java -version
    java version "1.8.0_77"
    Java(TM) SE Runtime Environment (build 1.8.0_77-b03)
    Java HotSpot(TM) 64-Bit Server VM (build 25.77-b03, mixed mode)

    System has all version of JRE (alternative )
    1 /usr/lib/jvm/java-6-oracle/jre/bin/java 1073
    2 /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java 1071
    3 /usr/lib/jvm/java-7-openjdk-i386/jre/bin/java 1070
    4 /usr/lib/jvm/java-7-oracle/jre/bin/java 1074
    * 5 /usr/lib/jvm/java-8-oracle/jre/bin/java 1072

    Still not working (((
    command: sh /home/malakhov/toolkit/
    Error: Could not find or load main class mil.tatrc.physiology.biogears.gui.BioGearsGUI

  • Hi Dima, try navigating in a terminal to the /home/malakhov/toolkit/ directory and then running the script from there. I have a suspicion that your error has to do with the working directory Java is searching in.
  • Thank you, dbyrd! It working, but only on Ubuntu 15.10 x64 =)

    On Ubuntu 14.04 LTS x64 GUI started, but loading of scenarios is "freezing"
    (a. on line -> INFO SESubstanceManager::165::Processing file Furosemide.xml)
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