1. STEM is running very slowly or runs out of memory on the larger data files. What is causing this? The reason is most likely STEM was started by double clicking on the .jar file instead of using the cmd file. If STEM was started from a command line it was likely the option to increase the amount of memory available to STEM (e.g. -mx512M) was omitted. For most uses of STEM, STEM needs more than the default maximum amount of memory given to Java programs. When starting STEM by double clicking on the .jar file, STEM gets the default maximum, but when started through the cmd file STEM has more memory available. 2. How do I save images of screens generated by STEM? As of version 1.3.8 the main interface can be saved to svg format by giving a .svg extension after clicking the disk icon on the main interface screen. Also any window can be saved using an operating system's screen capture feature. In windows that means pressing Alt+Print Screen while over the window you want to capture and then pasting it into the desired application. 3. Why am I get a message saying "All Genes Filtered"? You may have extra columns at the end of your file that appear as white space, but STEM is treating as time points with missing data. Make sure there are no extra columns when you press the 'View Data File' button.