Dealing with several packages of software, most of them currently available under public licences is an art, and most definately an underestimated knowledge. As most software runs on JAVA, which is not a bad thing, the VM very often needs some modifications to be fully up to speed. With my 1Gb of RAM I’m currently experiencing quite a lot ‘out of memory heap’ errors with the JAVA-enabled programs. It can often be fixed by setting the maxHeapSize to a little more agressive behaviour or simply to a lager maximum, but this requires some knowledge and creative thinking.
Being an information technology student this is ok, but for the average user, fiddling about with the java.exe commandline switches might be a barrier which is too steep. Anyway, that was my rant on programs such as ProtegÃ© and currently Owl2Prefuse, a beta-release created by one of my fellow students.
Not being able to do what I want is pretty frustrating, especially if you know it has to work, and it might work if the programmer hasn’t been sloppy in actually programming it. This way I had to focus more on getting my stuff right, instead of focussing on the task at hand; converting an XBLR taxonomy into an OWL ontology.