In the two Sage Days I've been to, the schedule was something like this: 
Every morning, we would all congregate at the conference room, and there 
would be a talk. After the talk, on the first day, we each mentioned some 
topic we were going to work on, and this would be written on the 
whiteboard. As we continued around the room, people would join various 
groups that were forming on the whiteboard (often multiple groups). After 
everyone had found some topic to work on, we would usually go find people 
with the same topic and discuss some things to do. Then it was mid- to late 
morning, and from then until night were the coding sprints - the different 
groups would just sit together and work on whatever their topic was. People 
would drift from one group to another if they were doing multiple things. 
Many people also just worked solo on a trac ticket or something. People 
would come in and out of the conference room for example to go for meals, 
etc. On the following days, it was basically the same, except instead of 
assigning groups in the morning after the talk, we would go around the room 
and each say what we did the previous day, and what results were obtained.

Usually we had a general list of topics and particular trac tickets that we 
were working on, on the Sage wiki. For example, see 
http://wiki.sagemath.org/days29 (one I attended).

-Keshav

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