I run the Manchester Game Jam which has been going for 4 years now. I'll happily answer any questions about running a jam. Here's a couple of tips off the top of my head.
Venue Make sure it is comfortable, warm and well lit. If you're going to be burning the midnight oil then least you can do is make sure it is a comfortable place to be. Make sure everyone knows where the toilets and washrooms are.
Atmosphere It shouldn't really have to be said but make sure everyone feels welcome. I try to greet everyone as they arrive and make sure they know my name and can ask me questions. Once everyone has arrived I make the announcements and go over the ground rules. I find making a couple of jokes at my own expense puts people at ease. I also regularly wander around the room during the jam asking people how their games are progressing.
Food and Drink You don't have to provide them, but make sure everyone can get food and drink from somewhere. A lot of people will forget to bring their own. Our venue has tea(we are British after all) making facilities and I always order in a couple of pizzas. Some of our regulars now also bring food and drink for the group.
Theme Make sure the theme has a lot of scope. We usually have 5 themes which are mix of random words and game mechanics, and let jammers choose one, some or all of them to use. Don't be too strict. If someone is really inspired but it doesn't fit the theme let them run with it.
Ending It We don't have a winner, but we do dedicate the last hour to presenting our games to the group. Some jammers will have been working so hard they won't of seen the other games so having a point when everyone tools down and shows off their stuff is a great way to end. I always show first to put the room at ease. Don't force anyone to come up, and encourage questions as people present the game.
There's probably loads more advice I can give, but thats all I can think of at the mo'. Feel free to ask me anything.
Here's a little info about the Manchester Game Jam
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