I recently read Model construction as a learning activity: a design space and review by Kurt VanLehn - http://www.tandfonline.com/doi/abs/10.1080/10494820.2013.803125?journalCode=nile20#.Ue6Nc74eqSo
A nice survey paper about the role building models can have in learning. Mostly about learning in schools (not much about university level). This paper mentions many others – two I found interesting were:
CTSiM: A Computational Thinking Environment for Learning Science through Simulation and Modeling
A visual language for students to conceptualise, construct visually, and run agent-based models. (The last step relies upon NetLogo.) Seems that a good deal of work is needed to prepare the system for any particular model but that it provides lots of scaffolding to students. Unclear how general this is. Paper also lists some nice design principles that the Behaviour Composer also follows.
An object-based learning tool for science enquiry
I couldn’t find this paper except for most of the pages in Google Books (Modeling and Simulation in Science and Mathematics Education, Volume 1).
Even those this was published in 1999 it seems like a very interesting system. Students could construction equations for an aggregate model and they can be simulated. BUT the system could also automatically transform the aggregate model to an ABM in StarLogo. I doubt that many ABMs can be constructed this way but those that can are great for giving students two ways of understanding the same phenomena and the relationship between aggregate and agent-based modelling.