The paper specifies the development of a toolkit to run synthetic science laboratories. The aim was to facilitate collaborative experimenting for problem-based learning in a virtual lab. The goal was to demonstrate virtual experimenting by use of interactive 3D visualization and simulation. Technology was developed over six years and in part designed in explicit accordance to didactic models. For tests, we built a virtual lab that comprised media tools and complex computer simulations, and we evaluated it with promising results. Students used data from meteorology and experimented together. Generally, they enjoyed using the system and collaborated in a motivated way. We identified which tools they preferred. The paper indicates ways to improve the design of virtual labs by use of our toolkit.