ArticlePLoS computational biology2016
Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed.
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- Modelling COVID-19 mutant dynamics: understanding the interplay between viral evolution and disease transmission dynamics.Royal Society open science · 2024Article
- Modeling spillover dynamics: understanding emerging pathogens of public health concern.Scientific reports · 2024Article
- Catalyst: Fast and flexible modeling of reaction networks.PLoS computational biology · 2023Article
- Fostering discoveries in the era of exascale computing: How the next generation of supercomputers empowers computational and experimental biophysics alike.Biophysical journal · 2023Review
- GillesPy2: A Biochemical Modeling Framework for Simulation Driven Biological Discovery.Letters in biomathematics · 2023Article
- Systematic comparison of modeling fidelity levels and parameter inference settings applied to negative feedback gene regulation.PLoS computational biology · 2022Article
- Saving the Devils Is in the Details: Tasmanian Devil Facial Tumor Disease Can Be Eliminated with Interventions.Letters in biomathematics · 2022Article
- Universally valid reduction of multiscale stochastic biochemical systems using simple non-elementary propensities.PLoS computational biology · 2021Article
- FiCoS: A fine-grained and coarse-grained GPU-powered deterministic simulator for biochemical networks.PLoS computational biology · 2021Article
- Programmatic modeling for biological systems.Current opinion in systems biology · 2021Article
- RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats.Nucleic acids research · 2021Article
- Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators.BMC bioinformatics · 2021Article
- A multiscale compartment-based model of stochastic gene regulatory networks using hitting-time analysis.The Journal of chemical physics · 2021Article
- Scalable machine learning-assisted model exploration and inference using Sciope.Bioinformatics (Oxford, England) · 2021Article
- Quantifying the roles of space and stochasticity in computer simulations for cell biology and cellular biochemistry.Molecular biology of the cell · 2021Article
- Beyond Deterministic Models in Drug Discovery and Development.Trends in pharmacological sciences · 2020Review
- Best Practices for Making Reproducible Biochemical Models.Cell systems · 2020Review
- Mechanistic Modeling of Biochemical Systems without A Priori Parameter Values Using the Design Space Toolbox v.3.0.iScience · 2020Article
- Hierarchical algorithm for the reaction-diffusion master equation.The Journal of chemical physics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
17 authors.
Funding
Abstract
We present StochSS: Stochastic Simulation as a Service, an integrated development environment for modeling and simulation of both deterministic and discrete stochastic biochemical systems in up to three dimensions. An easy to use graphical user interface enables researchers to quickly develop and simulate a biological model on a desktop or laptop, which can then be expanded to incorporate increasing levels of complexity. StochSS features state-of-the-art simulation engines. As the demand for computational power increases, StochSS can seamlessly scale computing resources in the cloud. In addition, StochSS can be deployed as a multi-user software environment where collaborators share computational resources and exchange models via a public model repository. We demonstrate the capabilities and ease of use of StochSS with an example of model development and simulation at increasing levels of complexity.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.