JGuiB User's Guide
Contents
1. Start a New Project 3 click checking box at the left of MODEL TOOLBAR to change which models want to fit this subject s data if necessary 4 click button to remove any previous subject if necessary 5 repeat step 1 to step 3 if more than one subject are used 6 click Results Run BOOMER Tab to next session 2 Optional Functions Copyright 2003 2007 PharmDataTech Taiwan 2 413 1 click one of models appearing at MODEL TOOLBAR to return PK PD Modeling tab if it is necessary to check this model definition in PARAMETER TAB again 2 click Copy or Paste button to respectively copy or paste your data to DATA LINE TAB from other documentations 3 Notes 1 When click Results Run BOOMER Tab to next session JGuiB will automatically check if all your data are entered completely Otherwise debugged window will pop up to show where your errors are and guide you how to make up Therefore please be sure you have already entered all data information in Subjects Data Weighting Tab before clicking Results Run BOOMER Tab to next session enter at least 5 data points X value and Y value for each data line in Normal Fitting and Simulation enter at least one data point for each data line in Bayesian If you use PD or PK PD model x value means concentration not time and Y value means effect not concentration for the data line related with2. and select this subject 3 enter data points X value and Y value in each data line using spreadsheet of DATA LINE TAB to edit data 4 click Add Row or Remove Row button to separately add or remove your data points 5 select an appropriate weighting scheme for this data line by clicking pull down menu of WEIGHTING SCHEME in Copyright 2003 2007 PharmDataTech Taiwan 12 Normal Fitting or Bayesian and then enter values for this weighting scheme if necessary such as a and b for Weight by 1 a Cp b 6 select an appropriate error type for this data line by clicking pull down menu of ERROR TYPE in Simulation and then enter ERROR FACTOR for this error type if necessary 7 click data line tab on the top of spreadsheet of DATA LINE TAB and select different data lines to edit data and then select an suitable weighting scheme or error type for each data line if more than one data line are used 8 click checking box at the left of MODEL TOOLBAR to assign which model wants to fit this subject s data 9 repeat step 1 to step 7 if more than one subject are used 10 click Results Run BOOMER Tab to next session B Edit a Previously Saved Project 1 select one subject by clicking pull down menu of SUBJECT and bring up this subject s data 2 edit or modify this subject s data including WEIGHTING SCHEME or ERROR TYPE if necessary same as A
3. OS X or Linux or a MS DOS in Windows and then execute the command java version to test if JRE has already been installed in their systems For example JRE v6 0 Update 1 in Windows XP for PC C java version Enter java version 1 6 0 01 Java TM SE Runtime Environment build 1 6 0 01 b06 Java HotSpot TM Client VM build 1 6 0 01 b06 mixed mode sharing If similar above messages show on screen this means that JRE has been successfully installed The only difference of messages may be the number of JRE version More information about JRE Copyright 2003 2007 PharmDataTech Taiwan installation can be referred to JDK 6 0 Documentation on Java technology website http java sun com javase 6 docs 1 2 BOOMER Installation JGuiB is just a GUI and will require working with BOOMER Therefore firstly users must go to BOOMER website http www boomer org to download the appropriate version for their systems The latest version of BOOMER is v3 3 3 January 30 2007 After unzipping BOOMER exe from the compressed file downloaded from BOOMER website users must make sure if the Permission Profile of the BOOMER execution for Mac OS X or Linux Fedora Core2 3 is setup well lf users ignore the procedure JGuiB will always show an error message for users to configure BOOMER path for JGuiB even users have done it before 1 3 JGuiB Installation 1 Mac OS X for Mac JGuiB provides users of Mac OS
4. Steps When firstly starting JGuiB the pop up message to configure BOOMER path will direct you to specify the location of BOOMER Without configuration of BOOMER path well JGuiB will automatically close until the configuration of BOOMER path is specified corrctly 2 Notes This step is absolutely required before BOOMER runs BAT file generated by JGuiB JGuiB will always prompt this message for users until the location of BOOMER is specified correctly 2 1 About Tab After correctly specifying BOOMER path About tab is the first tab showed in JGuiB Here are provided full information about JGuiB such as version number authors and contacting E mail address JGuiB has been released as freeware since June 10 2007 The provided version is fully functional only after a free registration Clicking Get free registration code icon to link to JGuiB registration center http jquib okpd org tw register php you will get a free registration code in your provided E mail after completely registration Copyright 2003 2007 PharmDataTech Taiwan Notes click About gt Registration to open registration windows and enter your name and registration code in your E mail The full functional JGuiB and all its examples will be supported 2 2 PK PD Modeling Tab 1 Required Steps step by step A Start a New Project 1 click File gt New to create a new project file 2 select one of BOOMER function
5. X to download the zip file JGuiB mac zip After downloaded into Mac the zip file will be automatically unzipped to JGuiB mac folder on Desktop Users can 1 open the JGuiB mac folder and then click JGuiB jar to run JGuiB or 2 open a terminal to type the command java jar Copyright 2003 2007 PharmDataTech Taiwan JGuiB jar in current directory to run JGuiB 2 Windows Win 9 x ME XP for PC Windows users have two methods to install JGuiB The zip file JGuiB windows zip same as Mac OS X can be provided and the steps of installing and running JGuiB are similar with those in Mac OS X systems The setup file JGuiB install exe is another file to install JGuiB for Windows users Users only need to run the setup file to install JGuiB easily and then just click JGuiB shortcut on Desktop to start JGuiB 8 Linux Fedora Core2 3 for PC For Linux users we provide the bin setup file JGuiBv3 O install bin with JRE v1 4 2 b01 to simultaneously install JGuiB and JRE Users only run the command JGuiB_install bin in terminal mode to finish JGuiB and JRE installation without complicated commands in Linux Clicking JGuiB icon in JGuiB program folder can run JGuiB in X Window but JGuiB must be run by typing java jar JGuiB jar in Terminal for some Linux systems such as Red Hat Mandrake and Debian Copyright 2003 2007 PharmDataTech Taiwan 2 JGuiB Tutorials 2 1 Configuration of BOOMER Path 1 Required
6. to next session JGuiB will automatically check if all parameters in PARAMETER TAB are defined well Otherwise debugged window will pop up to show where your errors are and then guide you how to correct them Therefore please be sure to have completely entered all required information in PK PD Model Tab before clicking Subject s Data Weighting Tab to next session 2 The more detailed information about Parameter Type Lists Parameter Properties Lists and Error Type Lists can be acquired from BOOMER online manual http www boomer org bmanual Copyright 2003 2007 PharmDataTech Taiwan 11 3 Users can employ JGuiB parameter types from Type 100 to Type110 to simply and effectively define uniform multiple dosing modeling including I V bolus I V infusion and extravascular route 4 If non uniform multiple dosing is necessary in model definition users must follow the rules of multiple dosage regimens to assign the name of dose as m Dose and the name of zero ordered constant as m RO You can define as many as 30 multiple doses Type 1 or zero order constants Type 3 4 JGuiB will automatically offer initial values for adjustable parameters when you do not assign in Bayesian estimation 2 4 Subjects Data Weighting Tab 1 Required Steps step by step A Start a New Project 1 click button to add a new subject and then give subject s name 2 click pull down menu of SUBJECT
7. Effect The more detailed information about WEIGHTING SCHEME and ERROR TYPE can be acquired from BOOMER online manual http www boomer org omanual 2 5 Results Run BOOMER Tab 1 Required Steps step by step Copyright 2003 2007 PharmDataTech Taiwan A Start a New Project 1 select the appropriate numerical integration method and fitting algorithm for your project by clicking pull down menu of NUMERICAL INTEGRATION and FITTING ALGORITHM and then enter all values for these two methods or do nothing to use the default settings from BOOMER 2 select which subject wants to edit by clicking pull down menu of SUBJECT 3 click one of models appearing at MODEL TOOLBAR and then click Name Output File to assign filename of this output file that this model fits with this subject s data 4 repeat step 2 to step 3 if more than one subject are used 5 click run JGuiB button to run this project 6 after completely you will see a message window to show Execute completely 7 click pull down menu of SUBJECT again and select which subject s output files you want to view and then click one of models appearing at MODEL TOOLBAR to bring up the View Output File button 8 click the View Output File button to pop up a full viewing window to show contents of this output file 9 repeat step 7 to step 8 if more than one output file are viewed B Edit a Previously Saved P
8. JGuiB User s Guide a GUI based pharmacokinetic and pharmacodynamic modeling assistant tool for BOOMER Version 3 0 2007 06 28 JGuiB Development Team Tech Support jquib taiwan gmail com Copyright 2003 2007 PharmDataTech Taiwan Table of Contents PCTACE ress EE 3 Le ICI orerny i e c 4 1 1 Java Runtime Environment JRE Installation 3 1 2 BOOMER Installation TS JOB Ins tallatlOFi serren a a deseas 2 JOUIB TUtottalsc axi eae teo asi ex e 2 1 Configuration of BOOMER Path eeeeeeesesssesseesee 2 2 est Mit iopcm a A EE iets 2 3 PK PD Modeling Tab 2 4 Subjects Data Weighting Tab sssesssrsrrrrnrrrnrrrnrrrnrrrnrrnnne 2 5 Results Run BOOMER Tab 31 iere ee bebe nidacconm 3 Examples JO JODIB sodio host aa eeraa A PEDF UNGUON Serana a a E aia 4 1 Help on the Interface of JGuiB Z2 OLS Meliore eh EHE PUN EE rv Eu PESE des Copyright 2003 2007 PharmDataTech Taiwan Preface Welcome to JGuiB Java GUI for BOOMER JGuiB is a graphic front end GUI written in Java SE used to be called J2SE compiled with JDK v5 0 update 04 designed and implemented to work with BOOMER which is an excellent PK PD modeling program One does not eventually need JGuiB at all to run BOOMER if a user is familiar with BOOMER under MS DOS or terminal mode MacOS X JGuiB turns interactive menu driven mode of BOOMER into a G
9. Type 3 3 click 0 Fix 1 Adjust 2 SD 3 DD in the panel of PARAMETER TAB to pop up Parameter Properties Lists 4 click Error Type in the panel of PARAMETER TAB to pop up Error Type Lists in Simulation 5 click graphical window to zoom the model picture in a new window in Built in Model or write a note to describe your own defined model at right of low text field in User s Defined Model 6 When select a built in model and then click Save as button of Built in Model to save this built in model as your own model to further modify 7 In User s Defined Model you can click Enter in last row of Copyright 2003 2007 PharmDataTech Taiwan 10 PARAMETER TAB to add a row in PARAMETER TAB one by one if more than one row are increased Click Remove Parameter to remove the last row in PARAMETER TAB if necessary 8 You can use Citrl C and Ctrl V to copy and paste your data in PARAMETER TAB 9 click button to select an auxiliary video avi file demo i e Normal Fitting Simulation Bayesian or Multiple Dosage Regimen automatically downloaded from JGuiB website http jguib pkpd org tw 10 click Help gt BOOMER website or JGuiB website to directly link respective websites also can click BOOMER website or JGuiB website button in menu toolbar 3 Notes 1 When click Subject s Data Weighting Tab
10. UI based window application using command line mode of BOOMER JGuiB includes three most commonly used functions of BOOMER in PK PD modeling normal fitting simulation and Bayesian estimation JGuiB can process more than one PK PD model max 4 models in one project file with various weighting schemes simultaneously using one data set Meanwhile Bayesian estimation can also be applied to the field of clinical pharmacokinetic services with only one single data point Cp at steady state Currently JGuiB supports both PC Win 9 x ME NT XP Linux Fedora Core 2 or 3 for PC Intel x86 or above and Macintosh MacOS X computers Acknowledgement Thanks to Dr Bourne the maker of BOOMER for his sincere assistance through the whole project Copyright 2003 2007 PharmDataTech Taiwan 1 JGuiB Software http jquib pkpd org tw 1 1 Java Runtime Environment JRE Installation Regardless of running any Java application including JGuiB users must download and install JRE in their respective systems in advance and confirm the PATH of java exe to be accessible in their systems JRE v6 0 Update 1 is suggested for users of Windows and JRE v1 4 2 Ox is suitable for users of Linux Fedora Core2 3 JGuiB had something wrong with JRE v5 0 in Linux Fedora Core 2 3 but was fine with JRE v1 4 2 Ox Because Apple has optimized built in JRE on Mac OS X such as iMac users need not install JRE in Apple systems Users can open a terminal Mac
11. enytoin Gentamicin Vancomycin and Cyclosporin A in Bayesian estimation Since version 3 0 JGuiB adds two new examples specially to estimate bioavailability using Bayesian estimation and they can be applied in BA BE data analysis Copyright 2003 2007 PharmDataTech Taiwan 4 Help Functions 4 1 Help on the Interface of JGuiB JGuiB provides 5 auxiliary functions in PK PD Modeling tab including Parameter Type Lists Rules of Multiple Dosage Regimens Parameter Properties Lists Error Type Lists and visualized modeling graphs in built in library Moreover JGuiB also provide user s guide that can be used to click Help gt JGuiB User s Guide or click JGuiB User s Guide icon in menu toolbar 4 2 On Line Help When visiting BOOMER or JGuiB website for getting more information users only need to click Help gt BOOMER website or JGuiB website on the interface of JGuiB to directly link to these two websites with default web browser Users also can click BOOMER website or JGuiB website button in menu toolbar to approach same effect in menu In addition to linking BOOMER or JGuiB website users can click button in every tab to download a video demo i e Normal Fitting Simulation Bayesian or Multiple Dosage Regimen from JGuiB website and then acquire more information how to use JGuiB Copyright 2003 2007 PharmDataTech Taiwa
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13. rmDataTech Taiwan clicking run JGuiB button to run BOOMER The output filename should be less than 8 characters without adding extension such as OUT Only give like test_001 and use legal characters for filename of output files When macro constant exponential functions parameter type 8 10 or Hill equation parameter type 11 13 are only used for model definition NUMERICAL INTEGRATION will be disabled for any integrated equation JGuiB will automatically deal with this problem when generating BAT files for your project FITTING ALGORITHM will be ignored in Simulation and JGuiB will take care of this problem when generating BAT files for your project The more detailed information about NUMERICAL INTEGRATION and FITTING ALGORITHM can be accessed from BOOMER online manual http www boomer org bmanual Copyright 2003 2007 PharmDataTech Taiwan 3 Examples of JGuiB JGuiB v3 0 package provides 19 examples of normal fitting 6 s simulation 5 s and Bayesian estimation 8 s Six examples in BOOMER online manual http www boomer org Zbmanual were completely converted into JGuiB and related model and data in some examples of JGuiB were acquired from other PK PD software such as ADAPT II WinNonlin WinBUGS and JavaPK Generally speaking JGuiB supports complicated examples of PBPK model and also contains four examples for TDM Therapeutic Drug Monitoring drugs i e Ph
14. roject 1 change NUMERICAL INTEGRATION and FITTING ALGORITHM or edit the values for the two methods if Copyright 2003 2007 PharmDataTech Taiwan necessary 2 rename the output file same as A Start a New Project step 2 to step 4 if necessary 3 click run JGuiB button to run this project After JGuiB completely runs you will see a message window to show Execute completely 4 view output file same as A Start a New Project step 7 to step 9 2 Optional Functions 1 click the checking box in the left hand side of model toolbar to select which output files you want to print on your printer select All or Selective and click Print Output File button to print all or selected output files 2 If only one model fits this subject s data you can ignore to click model toolbar in the steps of Name Output File and View Output File 3 click the checking box of Generate Batch File to generate BAT files for these output files if necessary 3 Notes 1 When click run JGuiB button to run your project JGuiB will automatically check if NUMERICAL INTEGRATION FITTING ALGORITHM and Name Output File are properly prepared Otherwise debugged window will pop up to show where your errors are and guide you how to do Therefore please be sure you have already assigned the filename of your necessary output files in Results Run BOOMER Tab before Copyright 2003 2007 Pha
15. s from METHOD OF ANALYSIS i e Normal Fitting Simulation or Bayesian 3 select Built in Model or User s Defined Model 4 select a built in model by clicking pull down menu of CHOOSE THE BUILT IN PK PD MODEL or click NEW button to assign the name of your own model 5 edit parameters in PARAMETER TAB or define your own model 6 click Add Model button to add this model to appear at MODEL TOOLBAR and then add other models one by one if more than one model are used 7 click Subject s Data Weighting Tab to next session B Edit a Previously Saved Project 1 click File gt Open to open a previously saved project file 2 click one of models appearing at MODEL TOOLBAR to bring Copyright 2003 2007 PharmDataTech Taiwan up its PARAMETER TAB 3 edit or modify parameters in PARAMETER TAB one by one if more than one model are used and if necessary 4 click Remove Model button to remove any previous defined model if necessary 5 click Subject s Data Weighting Tab to next session 2 Optional Functions 1 click Type in the panel of PARAMETER TAB to pop up Parameter Type Lists to show BOOMER s parameter types that JGuiB supports 2 click Parameter Name in the panel of PARAMETER TAB to pop up Rules of Multiple Dosage Regimens to express how to define multiple dosing model with m Dose Dose Type 1 and m RO Zero Order Constant
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