FAQs

Is my machine up to the required specs?
Please visit the Requirements section section of the BioLayout Express3D web site.
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 Express3D web 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 web site for more information.
What file types are supported?
Please visit the Tech Description 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 releavant published paper(s). For more details see micans.org/mcl.