Just finished the new version of the GillespieSSA package. The tar ball of the new version is posted on its web page (here). I also submitted it to CRAN so in (due time) it should appear on the official R package list.
What’s new in this release? Lots of bug fixes. The Binomial tau-leap method has been completely rewritten (resulting in a more stable and faster SSA method), I have implemented a novel nu-tiling algorithm for the state change matrix which substantially simplifies the definition of certain types of systems having a large number of states and/or reaction channels. The nu-tiling is a new and still experimental algorithm and is still awaiting proper documentation (i.e. being described in a manuscript) down the road. If any one wishes to take advantage of it and gets stuck feel free to contact me. I also improved the ssa.plot() function making it more efficient and flexible when displaying very large time series (i.e. large number of states and/or many time points).
What is not new? Well, I am still only providing a unix tar ball. Packaging it for Windows seems to be a time consuming and painful process so am postponing the inevitable until I have a large block of free time available (like that is ever going to happen). Otherwise volunteers taking on this task are more than welcome to pitch in.