Abstractions for Scaling eScience Applications to Distributed Computing Environments - A StratUm Integration Case Study in Molecular Systems Biology. - Per-Olov Östberg; Andreas Hellander; Brian Drawert; Erik Elmroth; Sverker Holmgren; Linda R. Petzold (BIOINFORMATICS, 2012)

Reducing Complexity in Management of eScience Computations. - Per-Olov Östberg; Andreas Hellander; Brian Drawert; Erik Elmroth; Sverker Holmgren; Linda R. Petzold (CCGRID, 2012)

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. - Brian Drawert; Stefan Engblom; Andreas Hellander (BMC Syst. Biol., 2012)

Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics. - Chris Bunch; Brian Drawert; Navraj Chohan; Chandra Krintz; Linda R. Petzold; Khawaja S. Shams (J. Grid Comput., 2012)

Spatial Stochastic Dynamics Enable Robust Cell Polarization. - Michael J. Lawson; Brian Drawert; Mustafa Khammash; Linda R. Petzold; Tau-Mu Yi (PLoS Comput. Biol., 2013)

CloudTracker: Using Execution Provenance to Optimize the Cost of Cloud Use. - Geoffrey Douglas; Brian Drawert; Chandra Krintz; Rich Wolski (GECON, 2014)

Automatic and portable cloud deployment for scientific simulations. - Christopher B. Horuk; Geoffrey Douglas; Anand Gupta; Chandra Krintz; Benjamin B. Bales; Giovanni Bellesia; Brian Drawert; Rich Wolski; Linda R. Petzold; Andreas Hellander (HPCS, 2014)

Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting. - Andreas Hellander; Michael J. Lawson; Brian Drawert; Linda R. Petzold (J. Comput. Phys., 2014)

Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. - Brian Drawert; Andreas Hellander; Benjamin B. Bales; Debjani Banerjee; Giovanni Bellesia; Bernie J. Daigle Jr.; Geoffrey Douglas; Mengyuan Gu; Anand Gupta; Stefan Hellander; Christopher B. Horuk; Dibyendu Nath; et al. (PLoS Comput. Biol., 2016)

Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. - Mahdi Golkaram; Stefan Hellander; Brian Drawert; Linda R. Petzold (PLoS Comput. Biol., 2016)

MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. - Brian Drawert; Michael Trogdon; Salman Zubair Toor; Linda R. Petzold; Andreas Hellander (SIAM J. Sci. Comput., 2016)

The effect of cell geometry on polarization in budding yeast. - Michael Trogdon; Brian Drawert; Carlos Gomez; Samhita P. Banavar; Tau-Mu Yi; Otger Campàs; Linda R. Petzold (PLoS Comput. Biol., 2018)

A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. - Brian Drawert; Bruno Jacob; Zhen Li 003; Tau-Mu Yi; Linda R. Petzold (J. Comput. Phys., 2019)

Epidemiological modeling in StochSS Live! - Richard M. Jiang 002; Bruno Jacob; Matthew Geiger; Sean Matthew; Bryan Rumsey; Prashant Singh; Fredrik Wrede; Tau-Mu Yi; Brian Drawert; Andreas Hellander; Linda R. Petzold (Bioinform., 2021)

Modified specifications grading in computer science: preliminary assessment and experience across five undergraduate courses. - Kevin R. Sanft; Brian Drawert; Adam Whitley 002 (J. Comput. Sci. Coll., 2021)

Coordinating cell polarization and morphogenesis through mechanical feedback. - Samhita P. Banavar; Michael Trogdon; Brian Drawert; Tau-Mu Yi; Linda R. Petzold; Otger Campàs (PLoS Comput. Biol., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)