DE-Sim
DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python - Published in JOSS (2020)
Science Score: 93.0%
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Found 6 DOI reference(s) in README and JOSS metadata -
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Published in Journal of Open Source Software
Keywords
Repository
Python-based object-oriented discrete-event simulation tool for complex, data-driven modeling
Basic Info
Statistics
- Stars: 34
- Watchers: 8
- Forks: 5
- Open Issues: 16
- Releases: 17
Topics
Metadata Files
README.md
DE-Sim: a Python-based object-oriented discrete-event simulator for modeling complex systems
DE-Sim is an open-source, Python-based object-oriented discrete-event simulation (DES) tool that makes it easy to use large, heterogeneous datasets and high-level data science tools such as NumPy, Scipy, pandas, and SQLAlchemy to build and simulate complex computational models. Similar to Simula, DE-Sim models are implemented by defining logical process objects which read the values of a set of variables and schedule events to modify their values at discrete instants in time.
To help users build and simulate complex, data-driven models, DE-Sim provides the following features:
- High-level, object-oriented modeling: DE-Sim makes it easy for users to use object-oriented Python programming to build models. This makes it easy to use large, heterogeneous datasets and high-level data science packages such as NumPy, pandas, SciPy, and SQLAlchemy to build complex models.
- Stop conditions: DE-Sim makes it easy to terminate simulations when specific criteria are reached. Researchers can specify stop conditions as functions that return true when a simulation should conclude.
- Results checkpointing: DE-Sim makes it easy to record the results of simulations by using a configurable checkpointing module.
- Reproducible simulations: To help researchers debug simulations, repeated executions of the same simulation with the same configuration and same random number generator seed produce the same results.
- Space-time visualizations: DE-Sim generates space-time visualizations of simulation trajectories. These diagrams can help researchers understand and debug simulations.
Projects that use DE-Sim
DE-Sim has been used to develop WC-Sim, a multi-algorithmic simulator for whole-cell models.
Examples
- Minimal simulation: a minimal example of a simulation
- Random walk: a random one-dimensional walk which increments or decrements a variable with equal probability at each event
- Parallel hold (PHOLD): model developed by Richard Fujimoto for benchmarking parallel DES simulators
- Epidemic: an SIR model of an epidemic of an infectious disease
Tutorial
Please see sandbox.karrlab.org for interactive tutorials on creating and executing models with DE-Sim.
Template for models and simulations
de_sim/examples/minimal_simulation.py contains a template for implementing and simulating a model with DE-Sim.
Installation
- Install dependencies
* Python >= 3.7
* pip >= 19
- Install this package using one of these methods
* Install the latest release from PyPI
```
pip install de_sim
```
* Install a Docker image with the latest release from DockerHub
```
docker pull karrlab/de_sim
```
* Install the latest version from GitHub
```
pip install git+https://github.com/KarrLab/de_sim.git#egg=de_sim
```
API documentation
Please see the API documentation.
Performance
Please see the DE-Sim article for information about the performance of DE-Sim.
Strengths and weaknesses compared to other DES tools
Please see the DE-Sim article for a comparison of DE-Sim with other DES tools.
License
The package is released under the MIT license.
Citing DE-Sim
Please use the following reference to cite DE-Sim:
Arthur P. Goldberg & Jonathan Karr. (2020). DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python. Journal of Open Source Software, 5(55), 2685.
Contributing to DE-Sim
We enthusiastically welcome contributions to DE-Sim! Please see the guide to contributing and the developer's code of conduct.
Development team
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA by the following individuals:
Acknowledgements
This work was supported by National Science Foundation award 1649014, National Institutes of Health award R35GM119771, and the Icahn Institute for Data Science and Genomic Technology.
Questions and comments
Please submit questions and issues to GitHub or contact the Karr Lab.
Owner
- Name: Karr whole-cell modeling lab
- Login: KarrLab
- Kind: organization
- Email: info@karrlab.org
- Location: 1255 5th Avenue, New York NY 10029
- Website: https://www.karrlab.org
- Repositories: 64
- Profile: https://github.com/KarrLab
Developing whole-cell computational models to predict and engineer biology.
JOSS Publication
DE-Sim: an object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems in Python
Authors
Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Icahn Institute for Data Science and Genomic Technology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
Editor
Daniel S. Katz
Tags
dynamical modeling simulation discrete-event simulation object-oriented simulation parallel discrete-event simulation biochemical modeling whole-cell modelingGitHub Events
Total
- Watch event: 2
Last Year
- Watch event: 2
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Arthur Goldberg | a****g@g****m | 357 |
| Jonathan Karr | j****r@g****m | 93 |
| Karr whole-cell modeling lab daemon | 3****n | 1 |
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 66
- Total pull requests: 1
- Average time to close issues: 3 months
- Average time to close pull requests: N/A
- Total issue authors: 5
- Total pull request authors: 1
- Average comments per issue: 1.14
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- artgoldberg (53)
- jonrkarr (6)
- gonsie (3)
- yadudoc (3)
- tgianghanbin217 (1)
Pull Request Authors
- artgoldberg (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 36 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 18
- Total maintainers: 2
pypi.org: de-sim
object-oriented, discrete-event simulation tool for data-intensive modeling of complex systems
- Homepage: https://github.com/KarrLab/de_sim
- Documentation: https://de-sim.readthedocs.io/
- License: MIT
-
Latest release: 1.0.5
published about 5 years ago
Rankings
Dependencies
- wc_utils *
- sphinx >=1.8
- sphinx_fontawesome *
- sphinx_rtd_theme >=0.4.2
- sphinxcontrib_addmetahtml >=0.1.1
- sphinxcontrib_bibtex *
- sphinxcontrib_spelling *
- sphinxprettysearchresults *
- sphinx >=1.8
- sphinx_fontawesome *
- sphinx_rtd_theme >=0.4.2
- sphinxcontrib_addmetahtml >=0.1.1
- sphinxcontrib_bibtex *
- sphinxcontrib_googleanalytics >=0.1.1
- sphinxcontrib_spelling *
- sphinxprettysearchresults *
- configobj *
- logging2 *
- matplotlib *
- numpy *
- progressbar2 >=3.39
- pympler *
- setuptools *
- wc_utils >=0.0.16
- capturer * test
- ipykernel * test
- nbconvert * test
- nbformat * test