tag:joss.theoj.org,2005:/papers/tagged/stochastic%20simulationJournal of Open Source Software2023-03-09T10:43:20ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/40212023-03-09T10:43:20Z2023-03-10T00:04:42ZFast and flexible simulation and parameter estimation for synthetic biology using bioscrapeacceptedv1.22022-11-23 08:27:41 UTC832023-03-09 10:43:20 UTC820235057AyushPandeyControl and Dynamical Systems, California Institute of Technology, Pasadena, CA, USA0000-0003-3590-4459WilliamPooleAltos Labs, San Francisco, CA, USA0000-0002-2958-6776AnandhSwaminathanGhost Locomotion, Mountain View, CA, USA0000-0001-9935-6530VictoriaHsiaoAmyris, Emeryville, CA, USA0000-0001-9297-1522RichardM.MurrayControl and Dynamical Systems and Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA0000-0002-5785-748110.21105/joss.05057https://doi.org/10.5281/zenodo.7677726Python, Cython, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.05057.pdfsynthetic biology, systems biology, deterministic and stochastic simulations, parameter inferencetag:joss.theoj.org,2005:Paper/34062022-05-26T04:16:44Z2022-05-27T00:00:59ZVTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU dataaccepted0.1.32022-03-01 13:44:50 UTC732022-05-26 04:16:44 UTC720224300MaximilianBittensFederal Institute for Geosciences and Natural Resources (BGR)0000-0001-9954-294X10.21105/joss.04300https://doi.org/10.5281/zenodo.6576155Juliahttps://joss.theoj.org/papers/10.21105/joss.04300.pdfVTK unstructered grid, Stochastic/parametric post-processing of simulation resultstag:joss.theoj.org,2005:Paper/14532021-11-19T11:24:18Z2023-04-25T09:38:16ZPyEscape: A narrow escape problem simulator package for Pythonaccepted1.02020-01-27 10:36:40 UTC472021-11-19 11:24:18 UTC520202072AoifeHughesJohn Innes Centre, Norwich, UK0000-0002-4572-5828RichardJ.MorrisJohn Innes Centre, Norwich, UKMelissaTomkinsJohn Innes Centre, Norwich, UK10.21105/joss.02072https://doi.org/10.5281/zenodo.3725946Python, Jupyter Notebookhttps://joss.theoj.org/papers/10.21105/joss.02072.pdfmathematics, simulations, stochastictag:joss.theoj.org,2005:Paper/27662021-10-07T16:04:09Z2022-01-18T12:08:50Zindividual: An R package for individual-based epidemiological modelsacceptedv0.1.12021-06-16 08:16:52 UTC662021-10-07 16:04:09 UTC620213539GiovanniD.CharlesMRC Centre for Global Infectious Disease Analysis, Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), Imperial College London, London, UK.SeanL.WuDivision of Epidemiology and Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA0000-0002-5781-949310.21105/joss.03539https://doi.org/10.5281/zenodo.5529932R, C++, Chttps://joss.theoj.org/papers/10.21105/joss.03539.pdfepidemiology, individual based, agent based, infectious disease, simulation, stochastictag:joss.theoj.org,2005:Paper/24392021-04-05T12:48:27Z2021-04-06T00:01:43Zepipack: An infectious disease modeling package for Pythonacceptedv0.1.12021-03-04 15:23:47 UTC602021-04-05 12:48:27 UTC620213097BenjaminF.MaierInstitute for Theoretical Biology, Humboldt-University of Berlin, Philippstr. 13, D-10115 Berlin, Robert Koch Institute, Nordufer 20, D-13353 Berlin0000-0001-7414-882310.21105/joss.03097https://doi.org/10.5281/zenodo.4655616Pythonhttps://joss.theoj.org/papers/10.21105/joss.03097.pdfinfectious disease modeling, stochastic simulations, computer algebra systems, networks, visualizationtag:joss.theoj.org,2005:Paper/16812020-09-23T23:14:18Z2021-02-15T11:30:40ZCancerSim: A Cancer Simulation Package for Python 3acceptedv1.0.02020-05-25 12:26:03 UTC532020-09-23 23:14:18 UTC520202436LukaOpasicMax-Planck-Institute for Evolutionary Biology, Plön, Germany0000-0001-7595-1722JacobG.ScottCleveland Clinic, Cleveland, OH, US0000-0003-2971-7673ArneTraulsenMax-Planck-Institute for Evolutionary Biology, Plön, Germany0000-0002-0669-5267CarstenFortmann-GroteMax-Planck-Institute for Evolutionary Biology, Plön, Germany0000-0002-2579-554610.21105/joss.02436https://doi.org/10.5281/zenodo.4034071Python, OpenEdge ABLhttps://joss.theoj.org/papers/10.21105/joss.02436.pdfstochastic simulation, tumour growth, tumour sampling, cancer biologytag:joss.theoj.org,2005:Paper/16692020-09-07T23:50:55Z2021-02-15T11:30:43ZFlint: a simulator for biological and physiological models in ordinary and stochastic differential equationsacceptedv2.3.02020-05-22 02:28:34 UTC532020-09-07 23:50:55 UTC520202331TakeshiAbeGraduate School of Medicine, Yamaguchi University0000-0002-7074-4561YoshiyukiAsaiGraduate School of Medicine, Yamaguchi University0000-0001-5519-430610.21105/joss.02331https://doi.org/10.5281/zenodo.4017040M4, C++, Chttps://joss.theoj.org/papers/10.21105/joss.02331.pdfbiology, physiology, numerical analysis, simulation, ODE, SDEtag:joss.theoj.org,2005:Paper/17552020-08-17T04:46:00Z2021-02-15T11:30:27ZChips-n-Salsa: A Java Library of Customizable, Hybridizable, Iterative, Parallel, Stochastic, and Self-Adaptive Local Search Algorithmsacceptedv1.02020-06-19 14:49:21 UTC522020-08-17 04:46:00 UTC520202448VincentA.CicirelloComputer Science, School of Business, Stockton University, Galloway, NJ 082050000-0003-1072-855910.21105/joss.02448https://doi.org/10.5281/zenodo.3974614Javahttps://joss.theoj.org/papers/10.21105/joss.02448.pdfstochastic local search, parallel metaheuristics, self-adaptive, simulated annealing, discrete optimization, combinatorial optimizationtag:joss.theoj.org,2005:Paper/16082020-06-19T20:03:13Z2021-02-15T11:30:48ZStoSpa2: A C++ software package for stochastic simulations of spatially extended systemsacceptedv2.0.272020-05-20 14:09:00 UTC502020-06-19 20:03:13 UTC520202293BartoszJ.BartmanskiMathematical Institute, University of Oxford, Woodstock Road, Oxford, OX2 6GG, UK0000-0002-0495-9150RuthE.BakerMathematical Institute, University of Oxford, Woodstock Road, Oxford, OX2 6GG, UK10.21105/joss.02293https://doi.org/10.5281/zenodo.3901670C++, Pythonhttps://joss.theoj.org/papers/10.21105/joss.02293.pdfStochastic simulations, Chemical master equation, Reaction-diffusion master equationtag:joss.theoj.org,2005:Paper/11742019-12-20T14:37:33Z2021-02-15T11:31:44ZEoN (Epidemics on Networks): a fast, flexible Python package for simulation, analytic approximation, and analysis of epidemics on networksacceptedv1.0.82019-08-20 05:10:27 UTC442019-12-20 14:37:33 UTC420191731JoelC.MillerLa Trobe University, Melbourne, Australia, Institute for Disease Modeling, Seattle, Washington, USA0000-0003-4426-0405TonyTingInstitute for Disease Modeling, Seattle, Washington, USA10.21105/joss.01731https://doi.org/10.5281/zenodo.3572756Pythonhttps://joss.theoj.org/papers/10.21105/joss.01731.pdfSIR, SIS, Epidemic, Network, Stochastic simulation