The Smoldyn User Community

Smoldyn is an open research tool that anyone may use. Because Smoldyn can be downloaded without registering, we do not know how many people use it. However, we do have some sense, based on e-mails that users have sent us and web site statistics (available here). Two scientists used Smoldyn 6 years ago, probably about 30 people used it a year ago, and we estimate that about 50 people use it currently. To the best of our knowledge, most current users are computational and experimental biologists, although several biophysicists use Smoldyn as well.

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

Steve Andrews wrote the core of the Smoldyn program and continues to maintain the program and coordinate further development. Smoldyn is sufficiently mature that there are plenty of roles for other contributors. These include: creating example configuration files, developing independent Smoldyn utility programs (such as wrl2smol and SmolCrowd), adding run-time commands to the program for simulation modification or observations, improving the user-interface, or adding to the simulation capabilities. At least two groups are currently developing parallel GPU implementations for Smoldyn. Please contact Steve if you are interested in joining the development team.

Developers

Steve Andrews (Fred Hutchinson Cancer Research Center) - P.I.
Nathan Addy (Lawrence Berkeley National Laboratory) - Wrote libmoleculizer module for rule-based reaction network expansion.

Collaborators

Upi Bhalla (National Centre for Biological Sciences, India) - Added the Smoldyn simulation core into the MOOSE program.
Jim Schaff and his group (University of Connecticut Health Center) - Adding the Smoldyn simulation core into Virtual Cell.
Lorenzo Dematte and Davide Prandi (University of Trento, Italy) - Parallelizing Smoldyn algorithms for GPU clusters, and also redesigning the Smoldyn input code using the Flex and Bison parser generators.
Roshan D'Souza and his group (University of Wisconsin, Milwaukee) - Rewriting Smoldyn to run on GPU clusters.

Funding

Smoldyn development has been funded by several research grants from the NIH, DOE, MITRE, and the NSF, although none were specifically targeted for Smoldyn.

We applied in June 2011 for an NIH grant for several years of focused Smoldyn development. In brief, it says that we want to (1) add support for biological filaments, such as cytoskeletons and DNA, (2) add support for dynamic surfaces to enable simulation of cell division, cell motility, etc., and (3) accelerate Smoldyn by about 200x using graphics processing units. Several users and collaborators wrote letters of support for this proposal; thank you for them!!! E-mail us if you want a copy of the full proposal.

Regardless of this funding opportunity, we will be happy 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.