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Journal Articles
- 2022
[j12]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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022)- 2021
- [j11]Richard M. Jiang, Bruno Jacob, Matthew Geiger, Sean Matthew, Bryan Rumsey, Prashant Singh, Fredrik Wrede, Tau-Mu Yi, Brian Drawert, Andreas Hellander, Linda R. Petzold:
Epidemiological modeling in StochSS Live! Bioinform. 37(17): 2787-2788 (2021) - [j10]Samhita P. Banavar, Michael Trogdon, Brian Drawert, Tau-Mu Yi, Linda R. Petzold, Otger Campàs:
Coordinating cell polarization and morphogenesis through mechanical feedback. PLoS Comput. Biol. 17(1) (2021) - 2019
- [j9]Brian Drawert, Bruno Jacob, Zhen Li, Tau-Mu Yi, Linda R. Petzold:
A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. J. Comput. Phys. 378: 1-17 (2019) - 2018
- [j8]Michael Trogdon, Brian Drawert, Carlos Gomez, Samhita P. Banavar, Tau-Mu Yi, Otger Campàs, Linda R. Petzold:
The effect of cell geometry on polarization in budding yeast. PLoS Comput. Biol. 14(6) (2018) - 2016
- [j7]Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R. Petzold:
Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. PLoS Comput. Biol. 12(11) (2016) - [j6]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, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold:
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. PLoS Comput. Biol. 12(12) (2016) - [j5]Brian Drawert, Michael Trogdon, Salman Zubair Toor, Linda R. Petzold, Andreas Hellander:
MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. SIAM J. Sci. Comput. 38(3) (2016) - 2014
- [j4]Andreas Hellander, Michael J. Lawson, Brian Drawert, Linda R. Petzold:
Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting. J. Comput. Phys. 266: 89-100 (2014) - 2013
- [j3]Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda R. Petzold, Tau-Mu Yi:
Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLoS Comput. Biol. 9(7) (2013) - 2012
- [j2]Brian Drawert, Stefan Engblom, Andreas Hellander:
URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries. BMC Syst. Biol. 6: 76 (2012) - [j1]Chris Bunch, Brian Drawert, Navraj Chohan, Chandra Krintz, Linda R. Petzold, Khawaja S. Shams:
Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics. J. Grid Comput. 10(1): 23-46 (2012)
Conference and Workshop Papers
- 2014
- [c4]Geoffrey Douglas, Brian Drawert, Chandra Krintz, Rich Wolski:
CloudTracker: Using Execution Provenance to Optimize the Cost of Cloud Use. GECON 2014: 99-113 - [c3]Christopher B. Horuk, Geoffrey Douglas, Anand Gupta, Chandra Krintz, Benjamin B. Bales, Giovanni Bellesia, Brian Drawert, Rich Wolski, Linda R. Petzold, Andreas Hellander:
Automatic and portable cloud deployment for scientific simulations. HPCS 2014: 374-381 - 2012
- [c2]Per-Olov Östberg, Andreas Hellander, Brian Drawert, Erik Elmroth, Sverker Holmgren, Linda R. Petzold:
Abstractions for Scaling eScience Applications to Distributed Computing Environments - A StratUm Integration Case Study in Molecular Systems Biology. BIOINFORMATICS 2012: 290-294 - [c1]Per-Olov Östberg, Andreas Hellander, Brian Drawert, Erik Elmroth, Sverker Holmgren, Linda R. Petzold:
Reducing Complexity in Management of eScience Computations. CCGRID 2012: 845-852
Informal and Other Publications
- 2022
- [i3]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, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2015
- [i2]Brian Drawert, Michael Trogdon, Salman Zubair Toor, Linda R. Petzold, Andreas Hellander:
MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME. CoRR abs/1508.03604 (2015) - 2013
- [i1]Andreas Hellander, Michael J. Lawson, Brian Drawert, Linda R. Petzold:
Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting. CoRR abs/1305.3639 (2013)
Coauthor Index
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