The Smoldyn User Community

Smoldyn is an open research tool that anyone may use. Because Smoldyn can be downloaded without registering, I do not know how many people use it. However, in the research literature, Smoldyn tends to be cited at least as often as comparable simulators and it is widely used for research projects. The publications web page lists some of these uses.

Smoldyn users generally fall into 3 classes: (1) computational and experimental biologists who study cell systems, (2) researchers who study the biophysics of relatively simple phenomena, such as macromolecular crowding or multisite receptor phosphorylation, and (3) simulation method developers, who work on particle-based or other simulation methods.

Feedback from users is absolutely essential for continued Smoldyn development, so please do not hesitate to e-mail us (support@smoldyn.org). A large fraction of the features that Smoldyn offers were added in response to requests from users, and we will continue to add requested features, as possible. Also, we like to know who our users are, so that we can target development to meet their needs, so we can tell them about releases, and because information about them can help us raise money for continued development.

The Smoldyn Development Team

Principal investigator

Prior developers

Collaborators

Funding

Smoldyn development has been funded by a Simons Foundation grant awarded to Steve Andrews and by research grants from the NIH, DOE, MITRE, and the NSF that were not specifically targeted for Smoldyn. A colleague and I are applying for an NIH R01 which will hopefully fund some work on dynamic surfaces and GPU parallelization.

Upcoming development, depending on funding, includes: (1) add support for biological filaments, such as cytoskeletal filaments and DNA, (2) add support for dynamic surfaces to enable simulation of cell division, cell motility, etc., and (3) accelerate all of Smoldyn by about 200x using graphics processing units.

We will be delighted to add features to Smoldyn if users come up with the funding for their development. Other funding offers, collaborations, or suggestions are very welcome, of course.