https://github.com/libsbmlsim/sbml-sim
Simulator for SBML Models
https://github.com/libsbmlsim/sbml-sim
rust rust-crate sbml simulator systems-biology systems-biology-simulation
Last synced: 3 days ago
JSON representation
Simulator for SBML Models
- Host: GitHub
- URL: https://github.com/libsbmlsim/sbml-sim
- Owner: libsbmlsim
- License: apache-2.0
- Created: 2021-02-06T11:36:48.000Z (about 5 years ago)
- Default Branch: main
- Last Pushed: 2022-03-26T16:16:18.000Z (almost 4 years ago)
- Last Synced: 2025-10-25T03:25:32.784Z (5 months ago)
- Topics: rust, rust-crate, sbml, simulator, systems-biology, systems-biology-simulation
- Language: Rust
- Homepage: https://crates.io/crates/sbml-sim
- Size: 3.84 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE-APACHE.md
Awesome Lists containing this project
README
A simulator for SBML models.
Currently only parses a model using [sbml-rs](https://crates.io/crates/sbml-rs) and [mathml-rs](https://crates.io/crates/mathml-rs) with limited support.
To try out, run the following:
```
git clone https://github.com/ballaneypranav/sbml-sim
git clone https://github.com/ballaneypranav/sbml-rs
git clone https://github.com/ballaneypranav/mathml-rs
cd sbml-sim
cargo run [path to model]
```
As of now, only Euler, RK45 and RKF methods have been implemented.
To try it out, run
```
cargo run -- -i {path to model} -t 10 -s 100 -o out.csv -a
```
This runs the RKF45 integrator for 10 seconds over 100 integration steps.
To test, run:
```
cargo test --test core-semantic -- --test-threads=8 --logfile tests/tests.log > tests/tests.full.log
awk '{ print $2" "$1 }' tests/tests.log | sort -u > tests/tests.log.awked; mv tests/tests.log.awked tests/tests.log
source tests/venv/bin/activate
python3 tests/analyze.py tests/tests.log
```