249 citations · 250 across the 2 of their papers we have counts for
3 papers
MCell-R: A particle-resolution network-free spatial modeling framework
Jose-Juan Tapia, Ali Sinan Saglam, Jacob Czech +4
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed…
Visualizing Regulation in Rule-based Models
John A. P. Sekar, Jose-Juan Tapia, James R. Faeder
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites w…
BioNetGen 2.2: Advances in Rule-Based Modeling
Leonard A. Harris, Justin S. Hogg, Jose-Juan Tapia +7
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model spe…