249 citations · 458 across the 11 of their papers we have counts for
12 papers
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu +68
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, becau…
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…
Spatial Stochastic Modeling with MCell and CellBlender
Sanjana Gupta, Jacob Czech, Robert Kuczewski +4
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical s…
Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology
Sanjana Gupta, Liam Hainsworth, Justin S. Hogg +2
Models of biological systems often have many unknown parameters that must be determined in order for model behavior to match experimental observations. Commonly-used methods for pa…
An Introduction to Rule-based Modeling of Immune Receptor Signaling
John A. P. Sekar, James R. Faeder
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can ha…
Formal Modeling and Analysis of Pancreatic Cancer Microenvironment
Qinsi Wang, Natasa Miskov-Zivanov, Bing Liu +3
The focus of pancreatic cancer research has been shifted from pancreatic cancer cells towards their microenvironment, involving pancreatic stellate cells that interact with cancer…