Metadata-Version: 2.1
Name: pta
Version: 0.1.0
Summary: Probabilistic Thermodynamic Analysis of metabolic networks.
Home-page: https://gitlab.com/csb.ethz/pta
Author: Mattia G. Gollub
Author-email: mattia.gollub@bsse.ethz.ch
License: GPLv3 License
Download-URL: https://pypi.org/project/pta
Project-URL: Source Code, https://gitlab.com/csb.ethz/pta
Project-URL: Documentation, https://probabilistic-thermodynamic-analysis.readthedocs.io/en/latest/
Project-URL: Bug Tracker, https://gitlab.com/csb.ethz/pta/issues
Description: # Proabilistic Thermodynamic Analysis of metabolic networks.
        
        Probabilistic Thermodynamic Analysis (PTA) is a framework for the exploration of
        the thermodynamic properties of a metabolic network. In PTA, we consider the 
        *steady-state thermodynamic space* of a network, that is, the space of standard reaction 
        energies and metabolite concentrations that are compatible with steady state
        flux constraints. The uncertainty of the variables in the thermodynamic space is 
        modeled with a probability distribution, allowing analysis with optimization and
        sampling approaches:
        - **Probabilistic Metabolic Optimization (PMO)** aims at finding the most probable 
        values of reaction energies and metabolite concentrations that are compatible 
        with the steady state constrain. This method is particularly useful to indentify
        features of the network that are thermodynamically unrealistic. For example, PMO
        can identify substrate channeling, incorrect cofactors or inaccurate 
        directionalities.
        - **Thermodynamic and Flux Sampling (TFS)** allows to jointly sample the 
        thermodynamic and flux spaces of a network. The method provides estimates of 
        metabolite concentrations, reactions directions, and flux distributions.
        
        ## Installation
        
        `pip install pta`
        
        ## Usage
        
        Please see the online [documentation](https://probabilistic-thermodynamic-analysis.readthedocs.io/en/latest/).
        
        ## Cite us
        
        If you use PTA in a scientific publication, please cite our paper:
        
        Gollub, M.G., Kaltenbach, H.M., Stelling, J., 2020. "Probabilistic Thermodynamic 
        Analysis of Metabolic Networks". *biorXiv*. - 
        [pdf](https://www.biorxiv.org/content/10.1101/2020.08.14.250845v1.full.pdf)
        
Keywords: Gibbs energy,eQuilibrator,thermodynamics,metabolic network,reaction network,sampling
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.8
Description-Content-Type: text/markdown
