19 Software on IQdesktop

19.1 Modeling Software

19.1.1 NONMEM

  • At least one version of NONMEM is always available on IQdesktop see here.
  • Since IQdesktop 1.4.0 we aim for two versions of NONMEM, allowing some user flexibility. It generally is assumed though that the default version is the earlier version.
  • NONMEM can be executed from command line, via IQR Tools, or via PsN.
    • The command line commands are in the style of
      • nmfe743 control output for single core runs
      • nmfe743par ncores control output for single multicore runs
    • where 743 here indicates the version of NONMEM.
  • IQR Tools allows to specify the version to use (see the setup_IQRtools() function in IQR Tools).

19.1.2 MONOLIX

  • At least one version of MONOLIX is always available on IQdesktop see here.
  • Since IQdesktop 1.4.0 we aim for two versions of MONOLIX, allowing some user flexibility. It generally is assumed though that the default version is the earlier version.
  • MONOLIX can be started from the Menu Bar by clicking on the MONOLIX icon. If there is more than one MONOLIX icon then the newer version is first and the latest version is last. If you hover with the mouse over the icon you also get a tooltip, indicating the version.
  • MONOLIX can also be started from within IQR Tools.
  • IQR Tools allows to specify the version to use (see the setup_IQRtools() function in IQR Tools).

19.1.3 MATLAB

  • One version of MATLAB is installed on IQdesktop since version 1.4.0.
  • We aim to always provide the most current version of MATLAB when we build a new IQdesktop version.
  • MATLAB can be started by clicking on the icon in the Menu Bar. Or alternatively by typing matlab on the command line.
  • Help for different command line options when starting MATLAB can be obtained through executing matlab -help.
  • MATLAB without the GUI can be started by matlab -nodesktop.
  • When no license file information for MATLAB is provided in the IQdesktop config file, MATLAB will ask to login when started. If you have a valid license => login and use MATLAB. You only need to log in once as long as your IQdesktop container is running.

19.1.3.1 MATLAB Toolboxes

  • A selection of MATLAB toolboxes is installed by default. As of IQdesktop 2.0.0:
    • Curve Fitting Toolbox
    • Global Optimization Toolbox
    • Optimization Toolbox
    • Parallel Computing Toolbox
    • SimBiology
    • Statistics and Machine Learning Toolbox
  • You can only use the toolboxes for which your license is valid.
  • If additional toolboxes are of interested => contact and we will likely consider these in the next IQdesktop release.

19.1.4 R, Rscript & Rstudio

  • Since IQdesktop 2.0.0 we aim for providing two versions of R. The underlying reason is that the transition from R3 to R4 is still ongoing for many M&S packages and not yet fully completed.
  • Currently installed R versions (2.0.0): 3.6.3 and 4.0.3.
  • The older version is considered to be the default version. IQR Tools is only installed on the older version.
  • R can conveniently started by clicking on the Rstudio icon in the Menu Bar. This will always use the default (older R) version.
  • Starting R or using Rscript is also possible from command line by calling R or Rscript. This will start the default (older) version.
  • A specific version of R can be started from command line by R-3.6.3 or Rscript-3.6.3 where 3.6.3 indicates the desired (and available) version.
  • Rstudio can also be started with a defined version of R by calling from command line rstudio-4.0.3, where again 4.0.3 refers to the desired R version to run in Rstudio.

19.1.5 IQR Tools & IQnca

19.1.6 CellDesigner

  • Software for graphical drawing of pathway diagrams (and more)
  • Can export pathway diagrams as SBML files
  • IQR Tools can easily import those SBML files
  • For more information on CellDesigner see here: http://celldesigner.org/
  • Can be started from command line by celldesigner or just cell
Possible use of CellDesigner on IQdesktop

19.1.7 PsN

19.2 Reporting Software

19.2.1 IQReport

19.2.2 VSCODE

  • Used as general text editor in IQdesktop - in addition to gedit. Both are readily available to start from the Menu Bar.
  • VSCODE is the editor of choice in IQdesktop to edit IQReport documents. Syntax highlighting is provided, the flow of the document is mapped and the following shortcuts are provided for the compilation (etc.) of an IQReport RMD document to MS Word:
    • SHIFT+CTRL+B: builds an IQReport RMD document to MS Word
    • SHIFT+CTRL+V: view a compiled MS Word document (in LibreOffice … does not always look nice. Better open it in Word

19.2.3 IQSlides

19.3 Where is MS Office?

IQdesktop is a Linux based system. As such there is no Word, Powerpoint, or Excel available on it right out of the box. Sure, Libreoffice is installed and doing a reasonable job. Even better with respect to look and feel and rendering of Microsoft Office documents is OnlyOffice, which is available on IQdesktop since version 2.0.1.

Sometimes though, the use of Word, Powerpoint, or Excel has a strong advantage. Or you might want to read your emails quickly on IQdesktop.

Here are very simple solutions on how you can easily use MS Office software on files in IQdesktop:

  • Type office on the command line. Firefox will open the MS Office 365 webpage that will allow you to use MS Office software in the cloud (if you have an account and your organization allows it).
  • Map IQdesktop as a network drive on your MacOS or Windows PC and access MS Office files stored on IQdesktop directly from your local PC. This mapping is explained here.
Example of PowerPoint used on IQdesktop via Office 365.

19.4 Stay connected

Home office was coming during 2020 and likely staying for a while. Staying connected with coworkers is thus important also when working from within IQdesktop. Especially when working in full screen mode it can be good to have quick access to email or chat from within IQdesktop. For this some useful command line commands are provided:

  • gmail: Starts firefox on the gmail webpage. Log in and stay easily connected for the duration of the IQdesktop container session.
  • hangouts: Starts firefox on the hangouts webpage. Log in and stay easily connected for the duration of the IQdesktop container session.
  • office: Starts firefox on the Office 365 webpage. Log in and stay easily connected for the duration of the IQdesktop container session. With access to Outlook and Skype.

Note that virtual meetings are not something supported by IQdesktop as this requires connection to some microphone, speaker, and ideally also a webcam.