thats if it possible and preferably without breaking it ?
Pick a bottle with a larger opening? Otherwise, a diamond grit hole saw or, if you have time, bottles and patience, a glass cutter and a few minuets to look up the instructions on cutting a hole in glass on line.
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I used a carbide tip 'ceramic tile/glass' drill bit to make quick work of drilling glass. They're kind of eye-drop shaped, and cut ceramic/glass like butter.
The best way would be with a drill bit designed for glass, in a drill press, with plenty of lubricant to prevent the bit and glass from overheating.
In the UK, I'd get some here http://www.maplin.co.uk/searchtemplate.asp?criteria=UV%20GLASS%20GLUE
If you really have to, the diamond saw method is easier than an oxy-fuel torch - that's a real glass blowers skill. If I were trying to fill the bottle, and I couldn't redesign to get it into the neck, I'd cut the bottle in half using a red hot wire, and then glue it back together with a UV cure glass glue - the joint would be invisible.
You'd need some practice bottles though. ;-)
where do you find the glass cure???
You could cut a hole with an oxyfuel torch. The trick is to do it without shattering the glass. Try heating it in a really hot oven before cutting. Then after cutting, heat the whole bottle with a cool yellow flame for a while. Then put it back in the oven and turn the oven off and wait until it cools.
Really, the best way to waterproof electronics is potting in plastic. Get a silicone baking mold about the size of your throwie and then cover it with clear epoxy
Why the side? Why not redesign around a battery which will fit down the neck?
ummmmm how would you do that ????? i mean like a 600mil bottle???
and how would it be waterproof cuase im putting water in it