BMSS 2.0.14

A package for dyanmic model analysis.

BMSS2

This package supports routine building and analysis of kinetic models for biological systems. This includes simulation, sensitivity analysis, model selection and identifiability analysis. The whole package is database-driven which allows one to interactively retrieve, store and update model information and implementation from/into SQL databases to ensure reproducibility and reusability, particularly for ease of model selection.

Note: An extensible web app database listing some of the pre-established models can be found at https://sbr.syncti.org/bmss2

Documentation

The documentation can be found at https://bmss2.readthedocs.io/en/latest/BMSS.html

Features

• Database-driven model manipulation and storage
• Model simulation
• Sensitivity analysis
• Parameter estimation using Bayesian Inference
• Model selection
• Trace analysis for a posteriori identifiability analysis
• Strike-GOLDD algorithm in Python for a priori identifiability analysis
• Support read/export of models in SBML format and model export in COMBINE archive

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 synbiopython

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 [e-mail] 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