Like True Circuits (not that this is how they run it). I just happen to know that True Circuits maintains their own version of spice that they downloaded from Berkeley and uses magic for layout.
The key is to use open source tools. You can use Matlab, and, the kids working in matlab probably got there on the strength of projects they did as students. So, get a Matlab trial license, try it out, see what you like. Then, look for that in the open-source world. If it doesn't exist, motivate a smart student to create it - he gets to put it on his resume and you get to create your stuff without giving your cake to Mathworks.
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