There are multiple ways of doing it. I'm just using constant acceleration examples since those are the easiest. But I just want to note that there are more ways of accelerating e.g. jerk-limited.
1 Trapezoidal Velocity Profile Trajectory - Block
To use this Block the the Robotics System Toolbox is needed. I find it quite unintuitive to use (e.g. I do not understand the Waypoints quite fully), but it does the job with a bit of fiddeling around. It gives the position, velocity and acceleration at a given time
2 Manual acceleration with integration and Step - Block
For this you only need to know how the acceleration time gets calculated: 
As Initial value you choose the acceleration. But be aware that the integraion process is not very reliable if your simulation step time is high. So if you use this check the results and keep you maximum simulation step size low. Also this just accelerates and does not decelerate. 3 Own MATLAB function
You can write your own function using a MATLAB-Function-Block. This should also have the time as one input. Then you can either a) calculate the acceleration time (see above) and output the acceleration similar to the Step-Block above. Then you can integrate again to get the velocity/position. [also as above: Integration problem on long step times]
b) or calculate the position by hand and output it directly. Here you implement the functionality of the above mentioned "Trapezoidal Velocity Profile Trajectory - Block" yourself. But probably with less features. I'll post some function code as a comment on this Answer
With both you can also easily decelerate by providing a negative acceleration/decelerating position.
4 ???
There are probably other ways of doing it aswell, But I don't know them yet
