https://github.com/matthiaskoenig/sbscl-simulator-comparison
Comparing SBSCL simulation results with other simulators
https://github.com/matthiaskoenig/sbscl-simulator-comparison
Last synced: 4 months ago
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Comparing SBSCL simulation results with other simulators
- Host: GitHub
- URL: https://github.com/matthiaskoenig/sbscl-simulator-comparison
- Owner: matthiaskoenig
- Created: 2018-05-16T15:30:28.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2022-06-21T21:25:17.000Z (almost 3 years ago)
- Last Synced: 2025-01-04T20:25:30.269Z (5 months ago)
- Language: Python
- Homepage:
- Size: 141 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# Comparing SBSCL simulator
Comparison of SBSCL (https://github.com/draeger-lab/SBSCL) against other simulators
for correctness and performance.
Comparisons are performed for FBA simulations and ODE simulations.
## FBA
The BiGG model collections are compared against results from `cobrapy` (https://github.com/opencobra/cobrapy)
and `cameo` (https://cameo.bio/index.html).
The bigg database is available from
https://github.com/SBRG/bigg_models
A dump of all models is available from
https://www.dropbox.com/sh/ye05djxrpxy37da/AAD6GrSRTt4MRfuIpprlnLYba?dl=0
The models for comparison are included in this repository in
```
models/bigg-v1.6
```
The results of the FBA simulations are available in
```
results/fba
```
Objective values are compared between different simulators.
Model loading and optimization are benchmarked via repeated execution.
### ODE
ODE models are compared between different simulators:
- `roadrunner`
- `copasi`
- `AMICI`
## Installation
```
pip install -r requirements.txt
```
© 2017-2021 Matthias König