Matches in SemOpenAlex for { <https://semopenalex.org/work/W4319915909> ?p ?o ?g. }
Showing items 1 to 48 of
48
with 100 items per page.
- W4319915909 endingPage "414a" @default.
- W4319915909 startingPage "414a" @default.
- W4319915909 abstract "Virtual Cell (VCell, http://vcell.org) is free open-source software for modeling cell biological systems. Biology-based interface is designed for researchers with no programming/scripting experience: they enter reactions and reaction rules in an intuitive graphical way, and VCell automatically creates the math for you. Models and simulations can be accessed from anywhere using the VCell database; models can be shared among collaborators or made publicly available. Simulations can be run locally (on a user's computer) or using our server - a job can be sent to a server and results can be retrieved any time later. VCell provides a variety of simulation frameworks. The same reaction network can be simulated using deterministic (compartmental ODE) and/or stochastic reactions (SSA solvers) simulators. By adding a geometry for compartments and diffusion for species, the same reaction network can be simulated as a reaction-diffusion-advection PDE with support for 2D kinematics and/or using spatial stochastic (reaction-diffusion with Smoldyn, http://smoldyn.org). Geometries from 2D or 3D microscope images or from idealized analytical expressions can be used, and membrane flux, lateral membrane diffusion and electrophysiology could be incorporated. If elements of the model are defined by reaction rules (using a novel graphical user interface for defining, visualizing, and verifying rule-based models), the model can be simulated using BioNetGen (http://bionetgen.org) engine and/or network-free agent-based simulations. The VCell models can be exchanged with other tools using standard formats such as SBML and BNGL, as well as exported as MatLab, SED-ML, and COMBINE archive. The latest developments include better support of SBML features, the possibility to fully annotate the models, view models online, interact with ImageJ, and send simulations to runBiosimulations (https://run.biosimulations.org) service for online simulations and visualization with modified parameters. (Supported by NIGMS grant R24 GM137787)" @default.
- W4319915909 created "2023-02-11" @default.
- W4319915909 creator A5027644564 @default.
- W4319915909 creator A5027838944 @default.
- W4319915909 creator A5066544731 @default.
- W4319915909 creator A5072236973 @default.
- W4319915909 date "2023-02-01" @default.
- W4319915909 modified "2023-09-25" @default.
- W4319915909 title "Virtual cell modeling and simulation software" @default.
- W4319915909 doi "https://doi.org/10.1016/j.bpj.2022.11.2249" @default.
- W4319915909 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36784114" @default.
- W4319915909 hasPublicationYear "2023" @default.
- W4319915909 type Work @default.
- W4319915909 citedByCount "0" @default.
- W4319915909 crossrefType "journal-article" @default.
- W4319915909 hasAuthorship W4319915909A5027644564 @default.
- W4319915909 hasAuthorship W4319915909A5027838944 @default.
- W4319915909 hasAuthorship W4319915909A5066544731 @default.
- W4319915909 hasAuthorship W4319915909A5072236973 @default.
- W4319915909 hasConcept C111919701 @default.
- W4319915909 hasConcept C115903868 @default.
- W4319915909 hasConcept C2777904410 @default.
- W4319915909 hasConcept C41008148 @default.
- W4319915909 hasConceptScore W4319915909C111919701 @default.
- W4319915909 hasConceptScore W4319915909C115903868 @default.
- W4319915909 hasConceptScore W4319915909C2777904410 @default.
- W4319915909 hasConceptScore W4319915909C41008148 @default.
- W4319915909 hasIssue "3" @default.
- W4319915909 hasLocation W43199159091 @default.
- W4319915909 hasLocation W43199159092 @default.
- W4319915909 hasOpenAccess W4319915909 @default.
- W4319915909 hasPrimaryLocation W43199159091 @default.
- W4319915909 hasRelatedWork W2066151176 @default.
- W4319915909 hasRelatedWork W2093432410 @default.
- W4319915909 hasRelatedWork W2104185553 @default.
- W4319915909 hasRelatedWork W2271843438 @default.
- W4319915909 hasRelatedWork W2338700700 @default.
- W4319915909 hasRelatedWork W2368896908 @default.
- W4319915909 hasRelatedWork W2370368730 @default.
- W4319915909 hasRelatedWork W2465263532 @default.
- W4319915909 hasRelatedWork W3033257081 @default.
- W4319915909 hasRelatedWork W80997479 @default.
- W4319915909 hasVolume "122" @default.
- W4319915909 isParatext "false" @default.
- W4319915909 isRetracted "false" @default.
- W4319915909 workType "article" @default.