SpringSaLaD version 2 released

2017-12-07T18:45:57+00:00 December 7th, 2017|News, NRCAM publication|

11-30-2017. Version 2 of the SpringSaLaD software was released today. The primary new feature is the ability to directly build models from atomic coordinates in pdb files, using an interactive 3D viewer to compare the course-grained linked spheres representation in SpringSaLaD with the PDB structure.

New publication of novel free-boundary model of a moving cell

2017-12-07T18:43:17+00:00 December 7th, 2017|News, NRCAM publication|

11-14-2017. A new publication, Nickaeen et al. 2017, from the VCell team describes a novel free-boundary model of actin -myosin contractility that couples force-balance and myosin transport equations. A previously developed mass-conservation algorithm originally developed for VCell to solve parabolic equations in moving domains with know kinematics was augmented by coupling with the FronTier front-tracking software and a segregated solver.

New publication describes hybrid deterministic – stochastic spatial solver

2016-12-28T16:02:07+00:00 December 28th, 2016|News, NRCAM publication|

A new publication in PLoS Computational Biology from Boris Slepchenko and coworkers describes the new hybrid deterministic stochastic spatial solver used in VCell.  Schaff, J.C., F. Gao, Y. Li, I.L. Novak, and B.M. Slepchenko. 2016. Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput Biol. 12:e1005236. PMID 27959915

 

2016-12-06T21:26:17+00:00 September 15th, 2016|News, NRCAM publication|

2016-09-15 A new publication in Bioinformatics by Jim Schaff and Michael Blinov describes the new Rule-based modeling features in VCell 6.0. See Schaff et al., 2016. Rule-based modeling with Virtual Cell. BioInformatrics 23:2880-2882, PMID 27497444

2016-12-06T21:27:29+00:00 February 2nd, 2016|News, NRCAM publication|

2016-02-02 Paul Michalski and Les Loew describe their new Spring SaLaD sofware for spatial, stochastic, particle-based modeling of biochemical systems at the mesoscale. See the publication Michalski and Loew, 2016. SpringSaLaD: A Spatial, Particle-Based Biochemical Simulation Platform with Excluded Volume. Biophysical Journal 110:523-529. PMID 26840718