Frequently Asked Questions

Is my machine up to the required specifications?
Please visit the Requirements section of the BioLayout Express3D web site.
Why am I unable to install BioLayout Express3D on a Mac?
You may see the error message BioLayout Express3D is damaged and can’t be opened. You should eject the disk image. This is due to OS X blocking applications that are not from the Apple App Store or have not been digitally signed by Apple. 
Before you can install unsigned software, you need to change your security settings in System Preferences. Go to Apple Menu > System Preferences > Security & Privacy.
In the General section, check the setting of Allow application downloaded from:
You can choose from 3 options:

  • Mac App Store
  • Mac App Store and identified developers
  • Anywhere

This option needs to be set to Anywhere. Then open the .dmg file and drag the BioLayout Express3D application to your Applications directory.

Why will the program not open?
Try running the webstart version (Launch button on Home page) and opening some of the example graphs available under the datasets page of the website. Start with small graphs and build up from there in order to test your hardware/software configuration and its ability to render large graphs. If this fails contact support@biolayout.org.
The program runs fine with the example datasets but crashes when I try to open my file, why?
Chances are the format of your file is wrong. Check the recommended file formats.
Why does the program open but some features do not work?
Try updating your drivers (see Requirements for links).
I tried to load a large map and BioLayout Express3D crashed/did not work/is not responding!
Large maps are very memory consuming. You maybe don’t have enough main RAM installed on your machine. Please try a smaller map or a machine with more installed main RAM. Please visit the Requirements section of the BioLayout Express3Dweb site.
I experience rendering/image quality problems when using BioLayout Express3D!
Please try to install the latest OpenGL drivers for your machine configuration.
Why do I need a high-end graphics card for large maps?
Please see the question/answer above and visit the Requirements section of the BioLayout Express3D web site.
What is OpenGL?
Please visit the official OpenGL website for more information.
What file types are supported?
Please visit the Technology section of the BioLayout Express3D web site for more details on supported file types.
What is MCL clustering and how does it work?
The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs based on simulation of (stochastic) flow in graphs. The algorithm was invented/discovered by Stijn van Dongen at the Centre for Mathematics and Computer Science (also known as CWI) in the Netherlands. The MCL algorithm is very fast, very scalable, and has a number of attractive properties causing it to deliver high-quality clusterings.
Please visit the Publications section of the BioLayout Express3D web site for relevant published paper(s). For more details see micans.org/mcl.