I would just cut the silicone out with a razor scraper. Any place that sells paint will also sell razor scrapers for scraping paint off glass. A razor scraper will remove silicone from glass equally well.
You'll also need to remove the silicone from the wood, and you can do that with a razor too, but dull the razor beforehand, or use a duller tool to avoid cutting into the wood. Once you cut through the silicone and get the glass out, you should be able to remove most of the rest of the silicone from the wood with a paint scraper (without harming the wood).
Now, even though you'll probably think you've gotten all the silicone caulk off the glass and wood, you almost certainly won't have. Typically, there will be a thin film of silicone caulk that remains behind on the glass or wood that prevents any new silicone from sticking to those same surfaces. In order to get new silicone caulk to stick to those same places you need to remove the old silicone caulk completely. To learn how to do that, simply scroll down in this forum to the thread entitled "bathtub caulk" and read my long post on the first page of it.