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

• Steve Andrews (Fred Hutchinson Cancer Research Center, Seattle University, and University of Washington) - Wrote the core of the Smoldyn program and continues to maintain the program and coordinate further development. See his webpage.

Other developers

• Dilawar Singh (Subconscious Compute Pvt. Ltd. Bangalore, India and National Centre for Biological Sciences, India) - Primary developer for Python bindings.

Prior developers

• Nathan Addy - Wrote libmoleculizer module for rule-based reaction network expansion, AutoTools build system, and pthreads parallel computation code.
• Martin Robinson - Wrote the NSV module for hybrid simulation.

Collaborators

• Jim Schaff and his group (University of Connecticut Health Center) - Adding the Smoldyn simulation core into Virtual Cell.
• Upi Bhalla (National Centre for Biological Sciences, India) - Added the Smoldyn simulation core into the MOOSE program.
• Radek Erban and Martin Robinson (University of Oxford) - Adding lattice-based simulation capabilities to Smoldyn to enable multiscale simulation.
• Carlos Lopez and Shawn Garbett (Vanderbilt University) - Adding Smoldyn to the PySB family of tools.
• Roshan D'Souza and his group (University of Wisconsin, Milwaukee) - Rewriting Smoldyn to run on GPU clusters.
• Lorenzo Dematte (University of Trento, Italy) - Parallelized Smoldyn algorithms for GPU clusters.

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.