Hybrid Stochastic Sim for Supercomputers / News: Recent posts

Hy3S (Hybrid Stochastic Simulation for Supercomputers) uses advanced numerical methods to quickly simulate the stochastic dynamics of large biological systems. These simulations help scientists and engineers both study and design natural or synthetic biological systems for use in industrial or medical applications.

Currently, only well-mixed systems of biochemical reactions are supported, but the ideas behind the numerical methods can be applied to heterogeneous systems and ill-structured state spaces.... read more

Over the past few weeks many changes were made to both the simulation code and GUI in the CVS repository. Now is as good a time as any to formally release those changes as 'stable'.

Those changes are:

Bug fixes in the GUI: The species window in the GUI now correctly refreshes when the 'quickchange' kinetic constant changer is used. (If you left-click on one or more reactions, it will allow you to change the first kinetic parameter.) The GUI no longer allows the creation of a ExpType 2 file (Combinatorial variation of kinetic parameters / initial conditions) without any variations. ... read more

Bugs fixed:
A floating point exception that occurred after the simulations were finished (experienced only on the Solaris make), an infrequent (but significant) error in the update of the reaction residuals, and a precision error that results in a seg fault when the SaveTime is too small.

Known bugs:
Experimental Type #3 does not work.
GUI: Species box does not refresh correctly when the quickchange window is used to alter a kinetic parameter.
GUI: A NetCDF file with an ExpType of 2 (varying kinetic parameters / initial conditions) can be saved with no variations. This will ruin the NetCDF file.

The project web page is up at http://hysss.sourceforge.net! So far, it's information heavy and picture light, but I figure it's better that than the other way around. ;)

If you're interested in where this project is going, then check out the 'For Developers' part of the web site, especially the list of unfinished tasks. Progress should be speedy with updates to the source code CVS repository about once a week. Sourceforge doesn't track the number of commits to the CVS repository (as well as miscalculating the activity of this project) so please browse the CVS. The age of the files is correct.... read more

What's under the hood? Take a look.

The CVS has multiple 'subprojects'. The one named 'homhyss' is the homogeneous hybrid stochastic simulator.

Another subproject is named 'GUI' for the Matlab GUI that was developed to make it easier to create the necessary NetCDF files. The GUI is optional, but useful: while you can use any programming language to create the necessary NetCDF (model) files, the GUI allows you to quickly type in a system of reactions, set initial conditions, kinetic constants, and a few other parameters (such as end time, etc). The GUI requires Matlab v7 and the NetCDF Toolbox for Matlab, freely available at http://woodshole.er.usgs.gov/staffpages/cdenham/public_html/MexCDF/nc4ml5.html or at their new SourceForge home at http://sourceforge.net/projects/mexcdf/. ... read more

"Small" physical, chemical, and biological systems are becoming more important as science begins to understand how things happen in the "nano" world. Traditional mathematical tools that use ordinary differential equations are unable to capture the inherent fluctuations that occur in "small" systems. Stochastic methods that more accurately describe these systems have been in developement for the past twenty years. This project aims to collect, integrate, and disseminate software that quickly simulates the stochastic dynamics of physical, chemical, or biological systems. Research into developing faster algorithms is important, but producing usable code for use by the scientific community is important as well. Hopefully, by using the Open Source environment, scientists and engineers can freely collaborate and contribute useful code.... read more