Metadata-Version: 2.1
Name: loopdetect
Version: 0.1.0
Summary: A Python package for feedback loop detection in ODE models
Home-page: https://gitlab.com/kabaum/loopdetect
Author: Katharina Baum
Author-email: katharina.baum@hpi.de
License: BSD
Project-URL: Documentation, https://kabaum.gitlab.io/loopdetect
Description: # LoopDetect - comprehensive detection of feedback loops in ODE models
        
        ## Scope
        This Python package provides a handy framework to determine feedback loops (cycles, circuits) 
        in ordinary differential equation (ODE) models. 
        Feedback loops are paths from one node (variable) to itself without 
        visiting any other node twice, and they have important regulatory functions. 
        Together with the loop length it is also reported whether the loop is a positive 
        or a negative feedback loop. An upper limit of the number of feedback loops can 
        be entered to limit the runtime (which scales with feedback loop count). Model 
        parametrizations and values of the modelled variables are accounted for. Input 
        can be the Jacobian matrix of the ODE model or the function definition. 
        Graph-based algorithms from networkx are employed for path detection, numdifftools is used for 
        computing the Jacobian and pandas dataframes are used as output format.
        
        
        ## Installation
        
        Install the package with pip; within a terminal window, type
        ```bash
        pip install loopdetect
        ```
        Depending on your pip installation, you may be required to use pip3 as command instead.
        
        In order to use functions from LoopDetect within Python, call
        ```python
        # core functions
        import loopdetect.core 
        # examples
        import loopdetect.examples
        ```
        LoopDetect is tested for Python 3, especially with Python version 3.8, but could also run with older Python versions.
        
        In addition, LoopDetect can be found on [GitLab](https://gitlab.com/kabaum/loopdetect).
        
        
        
        ## Workflow and documentation
        
        Function documentation is available on the LoopDetect pages, https://kabaum.gitlab.io/loopdetect/. There, you can also find a detailed [workflow description](https://kabaum.gitlab.io/loopdetect/workflow.html).
        
        
        ## Licensing
        All code is licensed under the 3-clause BSD license, LoopDetect, Copyright (C) 2020  Katharina Baum.
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
