A package for dyanmic model analysis.
Project description
BMSS2
This package supports routine analysis of kinetic models for biological systems. This includes simulation, sensitivity analysis, model selection and identifiability analysis. A web app database of our models can be found at https://engbio.syncti.org/BMSS2/index.html
Documentation
The documentation can be found at https://bmss2.readthedocs.io/en/latest/BMSS.html
Features
- Database-driven model storage
- Simulation and sensitivity analysis and result plotting
- Model fitting and selection
- Trace analysis for a posteriori identifiability analysis
- Strike-GOLDD algorithm in Python for a priori identifiability analysis
- Export of models in SBML format
For more information, refer to the BMSS2 documentation. If you wish to know more about our work, visit the NUS Engineering Biology Lab website.
Recommended IDE
Spyder IDE from Anaconda Distribution Anaconda Installation
Recommended: Python 3.7, Other Python versions will be tested soon.
Dependencies:
Install the dependent packages using pip as shown below.
pip install numpy matplotlib seaborn pandas numba scipy SALib dnaplotlib pyyaml
Optional
If you wish to put your code in notebook format, install Jupyter using pip as shown below.
pip install jupyter
or if you are using Anaconda:
conda install jupyter
Getting started
The examples folder contains
- Step-by-step explanations of BMSS2's functionalities labeled as tutorials
- Case studies for the characterization of common genetic constructs labeled as examples.
License
Copyright 2020 EngBioNUS
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
Contact Us
Please feel free to contact us at EngBioBMSS.help@gmail.com if you have any questions or to report any bugs.
Contributing to the Project
Anyone and everyone is welcome to contribute. Please review the guidelines for contributing
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