SysBiolWorkbench.readme

There were some incompatibilities with PyFRAP when Python was upgraded to version 3. We therefore provide a virtual box from which you can execute PyFRAP. This includes:
- PyFRAP tested/migrated to Python 3 (Ubuntu 20.04, Windows 10, macOS 10.15)
- A portable Linux/Ubuntu-based virtual machine, which is sufficiently isolated from forced (breaking) Python updates  
- Pre-installed accessory programs like Gmsh; helpful for developing new geometries
- A complete user and developer environment for this new version of PyFRAP

Installation instructions:

Please ask your IT support for help, as high administrative access to your computer is required to set up a VirtualBox. Please also consult the official documentation at https://www.virtualbox.org

1) Prepare your computer BIOS settings for VirtualBox
In general, each computer vendor has a different flavor of BIOS configuration, but here is a good overview: https://www.youtube.com/watch?v=MOuTxfzCvMY
How to enable Virtualization (VT-x) in Bios Windows 10:
- Press Windows key + R, type "cmd", hit enter
- Type in the following and hit enter: "systeminfo.exe"
- Go down to Hyper V requirements, to the right it says "Virtualization enabled firmware"
- There will be one of two options displayed: yes or no. If yes, continue to the next step
- If no, virtualization must be enabled as follows
- Close the cmd and navigate to the Windows start menu (click Windows key)
- Navigate to: Settings -- Update and security -- recovery (left); displayed: advanced startup -- restart now
- Select Trouble Shoot (use navigation keys, select with enter) -- advanced options -- UEFI Firmware Settings – Restart
- The startup menu will pop up, press F10 (Bios setup)
- Navigate with navigation keys to System Configuration, navigate to highlight Virtualization technology, hit enter
- Navigate down, to enable, hit enter
- Press F10, Exit saving changes? hit enter for yes
- Hyper V requirements should be enabled now

2) Download and install VirtualBox
https://www.virtualbox.org
- Click on Download Virtualbox 6.1, navigate to VirtualBox 6.1.34 platform packages, select Windows hosts
- Click on all supported platforms, under VirtualBox 6.1.34 Oracle VM VirtualBox extension packages, to install the extension packages

3) Download, install and run our Ubuntu-based VirtualBox-Image .ova file        
https://cloud.uni-konstanz.de/index.php/s/XYTHLDyHfGFzXmW
- Extract the file ubuntu.20.04-sysdevbiol-workbench-V03-minusvbiotext.ova to your Desktop
- Click on „import“ in the menu bar of the VB, and import the ubuntu20.04 ova-file from your Desktop
- After importing has been done successfully, start the ova – file
- Log into the Virtual Machine with the password FML-!“§ , open terminal (right click) and direct to the PyFRAP folder, via: “cd ~/PyFRAP-python3-alexblaessle/PyFRAP/pyfrp”
- Type in “python PyFRAP.py” or “sh run.sh”
- PyFRAP should be opened now

Please also have a look at this video to see how to run PyFRAP:
https://cloud.uni-konstanz.de/index.php/s/2XmkW3M4jo42mKT

In this new PyFRAP Python 3 version, there is a minor glitch in the final plot tab display. Please see the demo video at minute 15:23. The first plot fit is initially blank. Please carefully watch the video at the step where another plot is added which becomes visible; the first plot/tab can be ignored.

This new environment for PyFRAP in Python 3 is still quite new. In case you experience a bug: Please attach a copy the output of the terminal, so that we can understand the problem.